{
"cells": [
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Thu Aug 31 13:07:47 PDT 2017\n"
]
}
],
"source": [
"%%bash\n",
"date"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"friedman-Studio-XPS-7100\n"
]
}
],
"source": [
"%%bash\n",
"hostname"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Architecture: x86_64\n",
"CPU op-mode(s): 32-bit, 64-bit\n",
"Byte Order: Little Endian\n",
"CPU(s): 4\n",
"On-line CPU(s) list: 0-3\n",
"Thread(s) per core: 1\n",
"Core(s) per socket: 4\n",
"Socket(s): 1\n",
"NUMA node(s): 1\n",
"Vendor ID: AuthenticAMD\n",
"CPU family: 16\n",
"Model: 5\n",
"Model name: AMD Athlon(tm) II X4 630 Processor\n",
"Stepping: 2\n",
"CPU MHz: 2800.000\n",
"CPU max MHz: 2800.0000\n",
"CPU min MHz: 800.0000\n",
"BogoMIPS: 5586.35\n",
"Virtualization: AMD-V\n",
"L1d cache: 64K\n",
"L1i cache: 64K\n",
"L2 cache: 512K\n",
"NUMA node0 CPU(s): 0-3\n",
"Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc rep_good nopl nonstop_tsc extd_apicid pni monitor cx16 popcnt lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt hw_pstate vmmcall npt lbrv svm_lock nrip_save\n"
]
}
],
"source": [
"%%bash\n",
"lscpu"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Format Ava's Master Sheet"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"##### Look at beginning of file"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"accession_number\tID #\tcage_number\tsite\tTW(g)\tSW(g)\tSL(mm)\tcomments\tweight(mg)\tconcentration(ng/uL)\textraction_date\textraction_initials\textraction_method\telution_volume(uL)\tquant_method\tquant_date\tquant_initials\tstorage_box_name\tbox_slot\r\n",
"15:08\t1\t11\t\t13.15\t3.81\t48.2\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08\t2\t11\t\t10.65\t3.43\t46.1\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08\t3\t11\t\t17.35\t4.77\t52.8\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08\t4\t11\t\t11.17\t3.57\t45.3\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08\t5\t11\t\t13.26\t3.86\t48.3\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08\t6\t11\t\t12.01\t3.76\t48\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08\t7\t10\t\t10.04\t3.18\t43.5\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08\t8\t10\t\t8.25\t2.67\t41.6\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08\t9\t10\t\t14.09\t3.76\t46.6\t\t\t\t\t\t\t\t\t\t\t\t\r\n"
]
}
],
"source": [
"%%bash\n",
"head ava_master_ab_list.tsv"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Want to create new header line that does not contain ```ID #``` column."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Use awk to extract the first record of the file (i.e. the existing header row; ```NR==```) and exclude the second column. \n",
"\n",
"Also, tell awk that input file is tab-delimited (```-F \"\\t\"```) and that output should also be tab-delimited (```BEGIN { OFS = \"\\t\" }```)."
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"accession_number\tcage_number\tsite\tTW(g)\tSW(g)\tSL(mm)\n"
]
}
],
"source": [
"%%bash\n",
"awk -F \"\\t\" 'BEGIN { OFS = \"\\t\" } \\\n",
"NR==1 \\\n",
"{print $1, $3, $4, $5, $6, $7}' ava_master_ab_list.tsv"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Looks good, but how many columns are there?\n",
"\n",
"Use awk to print the number of fields (i.e. columns; ```{print NF}```) in the first record (```NR==1```)"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"19\n"
]
}
],
"source": [
"%%bash\n",
"awk -F \"\\t\" 'BEGIN { OFS = \"\\t\" } \\\n",
"NR==1 \\\n",
"{print NF}' ava_master_ab_list.tsv"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Use ```cut``` to print all column names, except column two."
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"bash: line 1: unexpected EOF while looking for matching `''\n",
"bash: line 5: syntax error: unexpected end of file\n"
]
}
],
"source": [
"%%bash\n",
"awk -F \"\\t\" 'BEGIN { OFS = \"\\t\" } \\\n",
"NR==1 \\\n",
"ava_master_ab_list.tsv | \\\n",
"cut -f1,3-"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"accession_number\tcage_number\tsite\tTW(g)\tSW(g)\tSL(mm)\tcomments\tweight(mg)\tconcentration(ng/uL)\textraction_date\textraction_initials\textraction_method\telution_volume(uL)\tquant_method\tquant_date\tquant_initials\tstorage_box_name\tbox_slot\r\n"
]
}
],
"source": [
"%%bash\n",
"awk -F \"\\t\" 'BEGIN { OFS = \"\\t\" } \\\n",
"NR==1' \\\n",
"ava_master_ab_list.tsv | \\\n",
"cut -f1,3-"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Looks good.\n",
"\n",
"Write the output to a file."
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"%%bash\n",
"awk -F \"\\t\" 'BEGIN { OFS = \"\\t\" } \\\n",
"NR==1' \\\n",
"ava_master_ab_list.tsv | \\\n",
"cut -f1,3- > ava_master_ab_list_formatted.tsv"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"accession_number\tcage_number\tsite\tTW(g)\tSW(g)\tSL(mm)\tcomments\tweight(mg)\tconcentration(ng/uL)\textraction_date\textraction_initials\textraction_method\telution_volume(uL)\tquant_method\tquant_date\tquant_initials\tstorage_box_name\tbox_slot\r\n"
]
}
],
"source": [
"%%bash\n",
"head ava_master_ab_list_formatted.tsv"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"18\n"
]
}
],
"source": [
"%%bash\n",
"awk -F \"\\t\" 'BEGIN { OFS = \"\\t\" } \\\n",
"NR==1 \\\n",
"{print NF}' ava_master_ab_list_formatted.tsv"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Use awk to combine the accession number column and the ID# column data. Also format the ID# data into a three digit number."
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"%%bash\n",
"awk -F \"\\t\" '{ printf \"%s-%03d\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\n\", \\\n",
"$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18 ,$19 }' \\\n",
"ava_master_ab_list.tsv | \\\n",
"head | \\\n",
"tail -n +2 >> \\\n",
"ava_master_ab_list_formatted.tsv"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"15:08-001\t11\t\t13.15\t3.81\t48.2\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-002\t11\t\t10.65\t3.43\t46.1\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-003\t11\t\t17.35\t4.77\t52.8\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-004\t11\t\t11.17\t3.57\t45.3\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-005\t11\t\t13.26\t3.86\t48.3\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-006\t11\t\t12.01\t3.76\t48\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-007\t10\t\t10.04\t3.18\t43.5\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-008\t10\t\t8.25\t2.67\t41.6\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-009\t10\t\t14.09\t3.76\t46.6\t\t\t\t\t\t\t\t\t\t\t\t\r\n"
]
}
],
"source": [
"%%bash\n",
"awk -F \"\\t\" '{ printf \"%s-%03d\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\n\", \\\n",
"$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18 ,$19 }' \\\n",
"ava_master_ab_list.tsv | \\\n",
"head | \\\n",
"tail -n +2"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"%%bash\n",
"awk -F \"\\t\" 'BEGIN { OFS = \"\\t\" } \\\n",
"NR==1' \\\n",
"ava_master_ab_list.tsv | \\\n",
"cut -f1,3- > ava_master_ab_list_formatted.tsv"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"accession_number\tcage_number\tsite\tTW(g)\tSW(g)\tSL(mm)\tcomments\tweight(mg)\tconcentration(ng/uL)\textraction_date\textraction_initials\textraction_method\telution_volume(uL)\tquant_method\tquant_date\tquant_initials\tstorage_box_name\tbox_slot\r\n"
]
}
],
"source": [
"%%bash\n",
"head ava_master_ab_list_formatted.tsv"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"15:08-001\t11\t\t13.15\t3.81\t48.2\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-002\t11\t\t10.65\t3.43\t46.1\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-003\t11\t\t17.35\t4.77\t52.8\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-004\t11\t\t11.17\t3.57\t45.3\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-005\t11\t\t13.26\t3.86\t48.3\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-006\t11\t\t12.01\t3.76\t48\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-007\t10\t\t10.04\t3.18\t43.5\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-008\t10\t\t8.25\t2.67\t41.6\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-009\t10\t\t14.09\t3.76\t46.6\t\t\t\t\t\t\t\t\t\t\t\t\r\n"
]
}
],
"source": [
"%%bash\n",
"awk -F \"\\t\" '{ printf \"%s-%03d\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\n\", \\\n",
"$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18 ,$19 }' \\\n",
"ava_master_ab_list.tsv | \\\n",
"head | \\\n",
"tail -n +2 | awk 'NF'"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"6\n",
"6\n",
"6\n",
"6\n",
"6\n",
"6\n",
"6\n",
"6\n",
"6\n"
]
}
],
"source": [
"%%bash\n",
"awk -F \"\\t\" '{ printf \"%s-%03d\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\n\", \\\n",
"$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18 ,$19 }' \\\n",
"ava_master_ab_list.tsv | \\\n",
"head | \\\n",
"tail -n +2 | awk '{print NF}'"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"18\n"
]
}
],
"source": [
"%%bash\n",
"awk -F \"\\t\" '{ printf \"%s-%03d\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\n\", \\\n",
"$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18 ,$19 }' \\\n",
"ava_master_ab_list.tsv | \\\n",
"head | \\\n",
"tail -n +2 | \\\n",
"head -1 | \\\n",
"awk -F \"\\t\" '{print NF}'"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Whoops! Finally noticed I left the ```head``` command in there! That's why the above steps were producing the wrong result."
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"%%bash\n",
"awk -F \"\\t\" '{ printf \"%s-%03d\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\n\", \\\n",
"$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18 ,$19 }' \\\n",
"ava_master_ab_list.tsv | \\\n",
"tail -n +2 >> \\\n",
"ava_master_ab_list_formatted.tsv"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"accession_number\tcage_number\tsite\tTW(g)\tSW(g)\tSL(mm)\tcomments\tweight(mg)\tconcentration(ng/uL)\textraction_date\textraction_initials\textraction_method\telution_volume(uL)\tquant_method\tquant_date\tquant_initials\tstorage_box_name\tbox_slot\r\n",
"15:08-001\t11\t\t13.15\t3.81\t48.2\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-002\t11\t\t10.65\t3.43\t46.1\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-003\t11\t\t17.35\t4.77\t52.8\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-004\t11\t\t11.17\t3.57\t45.3\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-005\t11\t\t13.26\t3.86\t48.3\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-006\t11\t\t12.01\t3.76\t48\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-007\t10\t\t10.04\t3.18\t43.5\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-008\t10\t\t8.25\t2.67\t41.6\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-009\t10\t\t14.09\t3.76\t46.6\t\t\t\t\t\t\t\t\t\t\t\t\r\n"
]
}
],
"source": [
"%%bash\n",
"head ava_master_ab_list_formatted.tsv"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"---"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Format Extraction List from 20170502"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Perform same actions to this file as I did to Ava's Master List above."
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"accession_number\tTissue #\tCage Number\tSite\tTW(g)\tSW(g)\tSL(mm)\tcomments\tweight(mg)\tconcentration(ng/uL)\textraction_date\textraction_initials\textraction_method\telution_volume(uL)\tquant_method\tquant_date\tquant_initials\tstorage_box_name\tbox_slot\r\n",
"15:08\t2\t11\tCorona\t\t\t\t\t0.047\t5.82\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08\t3\t11\tCorona\t\t\t\t\t0.114\t44.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08\t4\t11\tCorona\t\t\t\t\t0.046\t2.46\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08\t5\t11\tCorona\t\t\t\t\t0.156\t74\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08\t6\t11\tCorona\t\t\t\t\t0.204\t78.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08\t27\t13\tCorona\t\t\t\t\t0.107\t27.2\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08\t28\t13\tCorona\t\t\t\t\t0.176\t78.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08\t29\t13\tCorona\t\t\t\t\t0.144\t44.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08\t31\t13\tCorona\t\t\t\t\t0.071\t8.24\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n"
]
}
],
"source": [
"%%bash\n",
"head 20170502_Ava_Ab_List.tsv"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"19\n"
]
}
],
"source": [
"%%bash\n",
"awk -F \"\\t\" 'BEGIN { OFS = \"\\t\" } \\\n",
"NR==1 \\\n",
"{print NF}' 20170502_Ava_Ab_List.tsv"
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"%%bash\n",
"awk -F \"\\t\" 'BEGIN { OFS = \"\\t\" } \\\n",
"NR==1' \\\n",
"ava_master_ab_list.tsv | \\\n",
"cut -f1,3- > 20170502_Ava_Ab_List_formatted.tsv"
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"accession_number\tcage_number\tsite\tTW(g)\tSW(g)\tSL(mm)\tcomments\tweight(mg)\tconcentration(ng/uL)\textraction_date\textraction_initials\textraction_method\telution_volume(uL)\tquant_method\tquant_date\tquant_initials\tstorage_box_name\tbox_slot\r\n"
]
}
],
"source": [
"%%bash\n",
"head 20170502_Ava_Ab_List_formatted.tsv"
]
},
{
"cell_type": "code",
"execution_count": 29,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"18\n"
]
}
],
"source": [
"%%bash\n",
"awk -F \"\\t\" 'BEGIN { OFS = \"\\t\" } \\\n",
"{print NF}' 20170502_Ava_Ab_List_formatted.tsv"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"15:08-002\t11\tCorona\t\t\t\t\t0.047\t5.82\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-003\t11\tCorona\t\t\t\t\t0.114\t44.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-004\t11\tCorona\t\t\t\t\t0.046\t2.46\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-005\t11\tCorona\t\t\t\t\t0.156\t74\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-006\t11\tCorona\t\t\t\t\t0.204\t78.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-027\t13\tCorona\t\t\t\t\t0.107\t27.2\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-028\t13\tCorona\t\t\t\t\t0.176\t78.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-029\t13\tCorona\t\t\t\t\t0.144\t44.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-031\t13\tCorona\t\t\t\t\t0.071\t8.24\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n"
]
}
],
"source": [
"%%bash\n",
"awk -F \"\\t\" '{ printf \"%s-%03d\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\n\", \\\n",
"$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18 ,$19 }' \\\n",
"20170502_Ava_Ab_List.tsv | \\\n",
"head | \\\n",
"tail -n +2"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"18\n",
"18\n",
"18\n",
"18\n",
"18\n",
"18\n",
"18\n",
"18\n",
"18\n"
]
}
],
"source": [
"%%bash\n",
"awk -F \"\\t\" '{ printf \"%s-%03d\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\n\", \\\n",
"$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18 ,$19 }' \\\n",
"20170502_Ava_Ab_List.tsv | \\\n",
"head | \\\n",
"tail -n +2 | \\\n",
"awk -F \"\\t\" '{print NF}'"
]
},
{
"cell_type": "code",
"execution_count": 32,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"%%bash\n",
"awk -F \"\\t\" '{ printf \"%s-%03d\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\n\", \\\n",
"$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18 ,$19 }' \\\n",
"20170502_Ava_Ab_List.tsv | \\\n",
"tail -n +2 >> \\\n",
"20170502_Ava_Ab_List_formatted.tsv"
]
},
{
"cell_type": "code",
"execution_count": 33,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"accession_number\tcage_number\tsite\tTW(g)\tSW(g)\tSL(mm)\tcomments\tweight(mg)\tconcentration(ng/uL)\textraction_date\textraction_initials\textraction_method\telution_volume(uL)\tquant_method\tquant_date\tquant_initials\tstorage_box_name\tbox_slot\r\n",
"15:08-002\t11\tCorona\t\t\t\t\t0.047\t5.82\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-003\t11\tCorona\t\t\t\t\t0.114\t44.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-004\t11\tCorona\t\t\t\t\t0.046\t2.46\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-005\t11\tCorona\t\t\t\t\t0.156\t74\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-006\t11\tCorona\t\t\t\t\t0.204\t78.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-027\t13\tCorona\t\t\t\t\t0.107\t27.2\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-028\t13\tCorona\t\t\t\t\t0.176\t78.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-029\t13\tCorona\t\t\t\t\t0.144\t44.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-031\t13\tCorona\t\t\t\t\t0.071\t8.24\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n"
]
}
],
"source": [
"%%bash\n",
"head 20170502_Ava_Ab_List_formatted.tsv"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"---"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Format My Other Extraction File"
]
},
{
"cell_type": "code",
"execution_count": 34,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"accession_number\tcage_number\tsite\tTW(g)\tSW(g)\tSL(mm)\tcomments\tweight(mg)\tconcentration(ng/uL)\textraction_date\textraction_initials\textraction_method\telution_volume(uL)\tquant_method\tquant_date\tquant_initials\tstorage_box_name\tbox_slot\r\n",
"15:11-89\t21\t\t\t\t\t\t147\t168\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA1\r\n",
"15:11-90\t21\t\t\t\t\t\t112\t69.2\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA2\r\n",
"15:11-91\t21\t\t\t\t\t\t101\t70.4\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA3\r\n",
"15:11-92\t21\t\t\t\t\t\t45\t58.8\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA4\r\n",
"15:11-93\t21\t\t\t\t\t\t128\t61.6\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA5\r\n",
"15:11-84\t17\t\t\t\t\t\t57\t48\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA6\r\n",
"15:11-85\t17\t\t\t\t\t\t40\t80\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA7\r\n",
"15:11-86\t17\t\t\t\t\t\t85\t138\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA8\r\n",
"15:11-87\t17\t\t\t\t\t\t74\t68\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA9\r\n"
]
}
],
"source": [
"%%bash\n",
"head Ava_WS_Transmission_DNA_Extractions.tsv"
]
},
{
"cell_type": "code",
"execution_count": 35,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"18\n"
]
}
],
"source": [
"%%bash\n",
"awk -F \"\\t\" 'NR==1 {print NF}' Ava_WS_Transmission_DNA_Extractions.tsv"
]
},
{
"cell_type": "code",
"execution_count": 36,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"accession_number\tcage_number\tsite\tTW(g)\tSW(g)\tSL(mm)\tcomments\tweight(mg)\tconcentration(ng/uL)\textraction_date\textraction_initials\textraction_method\telution_volume(uL)\tquant_method\tquant_date\tquant_initials\tstorage_box_name\tbox_slot\r\n"
]
}
],
"source": [
"%%bash\n",
"awk -F \"\\t\" 'NR==1' Ava_WS_Transmission_DNA_Extractions.tsv"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Header looks good; write the header to a new file."
]
},
{
"cell_type": "code",
"execution_count": 37,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"%%bash\n",
"awk -F \"\\t\" 'NR==1' Ava_WS_Transmission_DNA_Extractions.tsv > Ava_WS_Transmission_DNA_Extractions_formatted.tsv"
]
},
{
"cell_type": "code",
"execution_count": 38,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"accession_number\tcage_number\tsite\tTW(g)\tSW(g)\tSL(mm)\tcomments\tweight(mg)\tconcentration(ng/uL)\textraction_date\textraction_initials\textraction_method\telution_volume(uL)\tquant_method\tquant_date\tquant_initials\tstorage_box_name\tbox_slot\r\n"
]
}
],
"source": [
"%%bash\n",
"head Ava_WS_Transmission_DNA_Extractions_formatted.tsv"
]
},
{
"cell_type": "code",
"execution_count": 39,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"15:9-144\t23\t\t\t\t\t\t50\t60\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tB2\r\n"
]
}
],
"source": [
"%%bash\n",
"awk -F'[-:]' 'NR==12' Ava_WS_Transmission_DNA_Extractions.tsv"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Use regular expression in field separator to select hyphen, colon, or tab (```-F'[-:\\t]'```) and count the number of fields. Original number fields, just using tab delimiter, was 18."
]
},
{
"cell_type": "code",
"execution_count": 40,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"20\n"
]
}
],
"source": [
"%%bash\n",
"awk -F'[-:\\t]' 'NR==12 {print NF}' Ava_WS_Transmission_DNA_Extractions.tsv"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Combine first three fields to read like this: nn:nn:nnn\n",
"\n",
"Print out each remaining field in a tab-delimited fashion, followed by a newline."
]
},
{
"cell_type": "code",
"execution_count": 41,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"15:11-089\t21\t\t\t\t\t\t147\t168\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA1\r\n",
"15:11-090\t21\t\t\t\t\t\t112\t69.2\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA2\r\n",
"15:11-091\t21\t\t\t\t\t\t101\t70.4\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA3\r\n",
"15:11-092\t21\t\t\t\t\t\t45\t58.8\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA4\r\n",
"15:11-093\t21\t\t\t\t\t\t128\t61.6\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA5\r\n",
"15:11-084\t17\t\t\t\t\t\t57\t48\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA6\r\n",
"15:11-085\t17\t\t\t\t\t\t40\t80\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA7\r\n",
"15:11-086\t17\t\t\t\t\t\t85\t138\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA8\r\n",
"15:11-087\t17\t\t\t\t\t\t74\t68\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA9\r\n",
"15:11-088\t17\t\t\t\t\t\t125\t18.2\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tB1\r\n",
"15:09-144\t23\t\t\t\t\t\t50\t60\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tB2\r\n"
]
}
],
"source": [
"%%bash\n",
"awk -F'[-:\\t]' '{ printf \"%s:%02d-%03d\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\n\", \\\n",
"$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18, $19, $20}' \\\n",
"Ava_WS_Transmission_DNA_Extractions.tsv | \\\n",
"head -12 | tail -n +2"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Append the result to the previously made file that contains the header."
]
},
{
"cell_type": "code",
"execution_count": 42,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"%%bash\n",
"awk -F'[-:\\t]' '{ printf \"%s:%02d-%03d\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\t%s\\n\", \\\n",
"$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18, $19, $20}' \\\n",
"Ava_WS_Transmission_DNA_Extractions.tsv | \\\n",
"tail -n +2 >> Ava_WS_Transmission_DNA_Extractions_formatted.tsv"
]
},
{
"cell_type": "code",
"execution_count": 43,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"accession_number\tcage_number\tsite\tTW(g)\tSW(g)\tSL(mm)\tcomments\tweight(mg)\tconcentration(ng/uL)\textraction_date\textraction_initials\textraction_method\telution_volume(uL)\tquant_method\tquant_date\tquant_initials\tstorage_box_name\tbox_slot\r\n",
"15:11-089\t21\t\t\t\t\t\t147\t168\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA1\r\n",
"15:11-090\t21\t\t\t\t\t\t112\t69.2\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA2\r\n",
"15:11-091\t21\t\t\t\t\t\t101\t70.4\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA3\r\n",
"15:11-092\t21\t\t\t\t\t\t45\t58.8\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA4\r\n",
"15:11-093\t21\t\t\t\t\t\t128\t61.6\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA5\r\n",
"15:11-084\t17\t\t\t\t\t\t57\t48\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA6\r\n",
"15:11-085\t17\t\t\t\t\t\t40\t80\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA7\r\n",
"15:11-086\t17\t\t\t\t\t\t85\t138\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA8\r\n",
"15:11-087\t17\t\t\t\t\t\t74\t68\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA9\r\n"
]
}
],
"source": [
"%%bash\n",
"head Ava_WS_Transmission_DNA_Extractions_formatted.tsv"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"---"
]
},
{
"cell_type": "code",
"execution_count": 44,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"cp: missing destination file operand after 'Ava_WS_Transmission_DNA_Extractions_formatted.tsv'\n",
"Try 'cp --help' for more information.\n"
]
}
],
"source": [
"%%bash\n",
"cp Ava_WS_Transmission_DNA_Extractions_formatted.tsv > Ava_WS_Transmission_DNA_Extractions_all.tsv"
]
},
{
"cell_type": "code",
"execution_count": 45,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"%%bash\n",
"cp Ava_WS_Transmission_DNA_Extractions_formatted.tsv Ava_WS_Transmission_DNA_Extractions_all.tsv"
]
},
{
"cell_type": "code",
"execution_count": 46,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"accession_number\tcage_number\tsite\tTW(g)\tSW(g)\tSL(mm)\tcomments\tweight(mg)\tconcentration(ng/uL)\textraction_date\textraction_initials\textraction_method\telution_volume(uL)\tquant_method\tquant_date\tquant_initials\tstorage_box_name\tbox_slot\r\n",
"15:11-089\t21\t\t\t\t\t\t147\t168\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA1\r\n",
"15:11-090\t21\t\t\t\t\t\t112\t69.2\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA2\r\n",
"15:11-091\t21\t\t\t\t\t\t101\t70.4\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA3\r\n",
"15:11-092\t21\t\t\t\t\t\t45\t58.8\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA4\r\n",
"15:11-093\t21\t\t\t\t\t\t128\t61.6\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA5\r\n",
"15:11-084\t17\t\t\t\t\t\t57\t48\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA6\r\n",
"15:11-085\t17\t\t\t\t\t\t40\t80\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA7\r\n",
"15:11-086\t17\t\t\t\t\t\t85\t138\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA8\r\n",
"15:11-087\t17\t\t\t\t\t\t74\t68\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA9\r\n"
]
}
],
"source": [
"%%bash\n",
"head Ava_WS_Transmission_DNA_Extractions_all.tsv"
]
},
{
"cell_type": "code",
"execution_count": 47,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"195 Ava_WS_Transmission_DNA_Extractions_all.tsv\n",
"123 20170502_Ava_Ab_List_formatted.tsv\n"
]
}
],
"source": [
"%%bash\n",
"wc -l Ava_WS_Transmission_DNA_Extractions_all.tsv\n",
"wc -l 20170502_Ava_Ab_List_formatted.tsv"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Append the contents, sans header (i.e. all rows after the first row; ```'NR>1'```), of the one file to the other."
]
},
{
"cell_type": "code",
"execution_count": 48,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"%%bash\n",
"awk 'NR>1' 20170502_Ava_Ab_List_formatted.tsv >> Ava_WS_Transmission_DNA_Extractions_all.tsv"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Quick line count to verify that the two files have been combined into one."
]
},
{
"cell_type": "code",
"execution_count": 49,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"317 Ava_WS_Transmission_DNA_Extractions_all.tsv\n"
]
}
],
"source": [
"%%bash\n",
"wc -l Ava_WS_Transmission_DNA_Extractions_all.tsv"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"---"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Join the master list with the extraction list to identify samples that still need to be processed."
]
},
{
"cell_type": "code",
"execution_count": 50,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"15:08-002 11 10.65 3.43 46.1 \r",
" 11 Corona 0.047 5.82 20170504 SJW 20170509 SJW \r\n",
"15:08-003 11 17.35 4.77 52.8 \r",
" 11 Corona 0.114 44.4 20170504 SJW 20170509 SJW \r\n",
"15:08-004 11 11.17 3.57 45.3 \r",
" 11 Corona 0.046 2.46 20170504 SJW 20170509 SJW \r\n",
"15:08-005 11 13.26 3.86 48.3 \r",
" 11 Corona 0.156 74 20170504 SJW 20170509 SJW \r\n",
"15:08-006 11 12.01 3.76 48 \r",
" 11 Corona 0.204 78.4 20170504 SJW 20170509 SJW \r\n",
"15:08-022 13 15.74 4.41 48.9 \r",
" 13 190 26.2 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 C8\r\n",
"15:08-023 13 11.68 3.34 45.2 \r",
" 13 124 98.8 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 C9\r\n",
"15:08-024 13 14.21 3.99 47.9 \r",
" 13 70 93.4 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 D1\r\n",
"15:08-025 13 9.16 2.74 41.6 \r",
" 13 50 26.6 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 D2\r\n",
"15:08-026 13 10.1 3.17 44.3 \r",
" 13 50 45.2 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 D3\r\n"
]
}
],
"source": [
"%%bash\n",
"join <(sort ava_master_ab_list_formatted.tsv) <(sort Ava_WS_Transmission_DNA_Extractions_all.tsv) | head"
]
},
{
"cell_type": "code",
"execution_count": 51,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"15:08-001\t11\t\t13.15\t3.81\t48.2\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-002\t11\t\t10.65\t3.43\t46.1\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-003\t11\t\t17.35\t4.77\t52.8\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-004\t11\t\t11.17\t3.57\t45.3\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-005\t11\t\t13.26\t3.86\t48.3\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-006\t11\t\t12.01\t3.76\t48\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-007\t10\t\t10.04\t3.18\t43.5\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-008\t10\t\t8.25\t2.67\t41.6\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-009\t10\t\t14.09\t3.76\t46.6\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-010\t10\t\t10.9\t3.36\t45\t\t\t\t\t\t\t\t\t\t\t\t\r\n"
]
}
],
"source": [
"%%bash\n",
"sort ava_master_ab_list_formatted.tsv | head"
]
},
{
"cell_type": "code",
"execution_count": 52,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"15:08-002\t11\tCorona\t\t\t\t\t0.047\t5.82\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-003\t11\tCorona\t\t\t\t\t0.114\t44.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-004\t11\tCorona\t\t\t\t\t0.046\t2.46\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-005\t11\tCorona\t\t\t\t\t0.156\t74\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-006\t11\tCorona\t\t\t\t\t0.204\t78.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-022\t13\t\t\t\t\t\t190\t26.2\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tC8\r\n",
"15:08-023\t13\t\t\t\t\t\t124\t98.8\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tC9\r\n",
"15:08-024\t13\t\t\t\t\t\t70\t93.4\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tD1\r\n",
"15:08-025\t13\t\t\t\t\t\t50\t26.6\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tD2\r\n",
"15:08-026\t13\t\t\t\t\t\t50\t45.2\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tD3\r\n",
"15:08-027\t13\tCorona\t\t\t\t\t0.107\t27.2\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-028\t13\tCorona\t\t\t\t\t0.176\t78.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-029\t13\tCorona\t\t\t\t\t0.144\t44.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-031\t13\tCorona\t\t\t\t\t0.071\t8.24\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-032\t13\tCorona\t\t\t\t\t0.134\t31.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-040\t6\t\t\t\t\t\t96\t170\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tB7\r\n",
"15:08-041\t6\t\t\t\t\t\t88\t128\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tB8\r\n",
"15:08-042\t6\t\t\t\t\t\t78\t76.4\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tB9\r\n",
"15:08-043\t6\t\t\t\t\t\t213\t67.4\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tC1\r\n",
"15:08-044\t6\t\t\t\t\t\t255\t71.2\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tC2\r\n",
"15:08-045\t6\tCorona\t\t\t\t\t0.13\t2.44\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-046\t12\t\t\t\t\t\t61\t31.8\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tC3\r\n",
"15:08-047\t12\t\t\t\t\t\t34\t7.28\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tC4\r\n",
"15:08-048\t12\t\t\t\t\t\t68\t132\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tC5\r\n",
"15:08-049\t12\t\t\t\t\t\t114\t87.6\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tC6\r\n",
"15:08-050\t12\t\t\t\t\t\t106\t55.2\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tC7\r\n",
"15:08-051\t12\tCorona\t\t\t\t\t0.117\t36.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-052\t12\tCorona\t\t\t\t\t0.041\t2.64\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-053\t12\tCorona\t\t\t\t\t0.044\t2.18\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-054\t12\tCorona\t\t\t\t\t0.173\t98.2\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-055\t2\tCorona\t\t\t\t\t0.117\t7.44\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-086\t6\tCorona\t\t\t\t\t0.052\t16.1\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-087\t6\tCorona\t\t\t\t\t0.165\t105\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-088\t6\tCorona\t\t\t\t\t0.064\t8.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-089\t6\tCorona\t\t\t\t\t0.122\t33.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-094\t11\tCorona\t\t\t\t\t0.042\t4.98\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-095\t11\t\t\t\t\t\t5.88\t73\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tD4\r\n",
"15:08-096\t11\t\t\t\t\t\t21.4\t74\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tD5\r\n",
"15:08-097\t11\t\t\t\t\t\t9.32\t73\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tD6\r\n",
"15:08-098\t11\t\t\t\t\t\t62\t130\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tD7\r\n",
"15:08-099\t11\t\t\t\t\t\t6\t42\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tD8\r\n",
"15:08-100\t1\t\t\t\t\t\t24\t106\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tD9\r\n",
"15:08-101\t1\t\t\t\t\t\t5.4\t96\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tE1\r\n",
"15:08-102\t1\t\t\t\t\t\t15\t91\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tE2\r\n",
"15:08-103\t1\t\t\t\t\t\t15.5\t79\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tE3\r\n",
"15:08-104\t1\t\t\t\t\t\t7.34\t48\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tE4\r\n",
"15:08-105\t1\t\t\t\t\t\t39.4\t197\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tE5\r\n",
"15:08-118\t12\tCorona\t\t\t\t\t0.125\t36\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-001\tControl\t\t\t\t\t\t116\t117\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tF7\r\n",
"15:09-002\tControl\t\t\t\t\t\t68\t132\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tF8\r\n",
"15:09-003\tControl\t\t\t\t\t\t138\t65.2\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tF9\r\n",
"15:09-004\t\t\t\t\t\t\t108\t\t\t\t\t\t\t\t\t\t\r\n",
"15:09-005\t\t\t\t\t\t\t148\t\t\t\t\t\t\t\t\t\t\r\n",
"15:09-006\t\t\t\t\t\t\t172\t\t\t\t\t\t\t\t\t\t\r\n",
"15:09-007\t\t\t\t\t\t\t112\t\t\t\t\t\t\t\t\t\t\r\n",
"15:09-008\t\t\t\t\t\t\t180\t\t\t\t\t\t\t\t\t\t\r\n",
"15:09-010\tControl\t\t\t\t\t\t135\t116\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tG1\r\n",
"15:09-011\tControl\t\t\t\t\t\t96\t80.2\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tG2\r\n",
"15:09-012\t\t\t\t\t\t\t92\t\t\t\t\t\t\t\t\t\t\r\n",
"15:09-013\t\t\t\t\t\t\t100\t\t\t\t\t\t\t\t\t\t\r\n",
"15:09-014\t\t\t\t\t\t\t69\t\t\t\t\t\t\t\t\t\t\r\n",
"15:09-015\t\t\t\t\t\t\t237\t\t\t\t\t\t\t\t\t\t\r\n",
"15:09-016\t\t\t\t\t\t\t170\t\t\t\t\t\t\t\t\t\t\r\n",
"15:09-022\tControl\t\t\t\t\t\t100\t220\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tG3\r\n",
"15:09-023\tControl\t\t\t\t\t\t117\t198\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tG4\r\n",
"15:09-032\tControl\t\t\t\t\t\t51\t75\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tG5\r\n",
"15:09-033\tControl\t\t\t\t\t\t115\t124\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tG6\r\n",
"15:09-034\tControl\t\t\t\t\t\t190\t234\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tG7\r\n",
"15:09-035\t\t\t\t\t\t\t148\t\t\t\t\t\t\t\t\t\t\r\n",
"15:09-036\t\t\t\t\t\t\t155\t\t\t\t\t\t\t\t\t\t\r\n",
"15:09-037\t\t\t\t\t\t\t161\t\t\t\t\t\t\t\t\t\t\r\n",
"15:09-038\t\t\t\t\t\t\t214\t\t\t\t\t\t\t\t\t\t\r\n",
"15:09-039\t\t\t\t\t\t\t67\t\t\t\t\t\t\t\t\t\t\r\n",
"15:09-060\t26\tGoleta\t\t\t\t\t0.138\t33.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-061\t26\tGoleta\t\t\t\t\t0.052\t3.26\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-062\t26\tGoleta\t\t\t\t\t0.111\t24\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-119\t16\t\t\t\t\t\t30\t63.8\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tD9\r\n",
"15:09-120\t16\t\t\t\t\t\t24\t9.78\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tE1\r\n",
"15:09-121\t16\t\t\t\t\t\t53\t98.2\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tE2\r\n",
"15:09-122\t16\t\t\t\t\t\t155\t166\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tE3\r\n",
"15:09-123\t16\t\t\t\t\t\t152\t140\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tE4\r\n",
"15:09-140\t23\tGoleta\t\t\t\t\t0.049\t7.82\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-141\t23\tGoleta\t\t\t\t\t0.057\t3.74\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-142\t23\tGoleta\t\t\t\t\t0.023\tOut of range\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-143\t23\tGoleta\t\t\t\t\t0.036\t2.16\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-144\t23\t\t\t\t\t\t50\t60\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tB2\r\n",
"15:09-145\t23\t\t\t\t\t\t51\t72\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tB3\r\n",
"15:09-146\t23\t\t\t\t\t\t43\t121\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tB4\r\n",
"15:09-147\t23\t\t\t\t\t\t84\t159\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tB5\r\n",
"15:09-148\t23\t\t\t\t\t\t66\t41.8\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tB6\r\n",
"15:09-149\t23\tGoleta\t\t\t\t\t0.094\t15.7\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-150\t23\tGoleta\t\t\t\t\t0.184\t6.48\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-173\t22\tGoleta\t\t\t\t\t0.116\t92.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-174\t22\tGoleta\t\t\t\t\t0.102\t28.2\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-228\t18\t\t\t\t\t\t120\t117\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tE5\r\n",
"15:09-229\t18\t\t\t\t\t\t37\t83.4\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tE6\r\n",
"15:09-230\t18\t\t\t\t\t\t113\t43\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tE7\r\n",
"15:09-231\t18\t\t\t\t\t\t144\t93.8\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tE8\r\n",
"15:09-232\t18\t\t\t\t\t\t173\t43.6\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tE9\r\n",
"15:09-233\t18\tGoleta\t\t\t\t\t0.119\t8.3\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-234\t18\tGoleta\t\t\t\t\t0.136\t58.6\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-235\t18\tGoleta\t\t\t\t\t0.156\t64.2\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-236\t18\tGoleta\t\t\t\t\t0.176\t78.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-237\t18\tGoleta\t\t\t\t\t0.169\t44.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-245\t19\t\t\t\t\t\t157\t60.4\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tF1\r\n",
"15:09-246\t19\t\t\t\t\t\t128\t101\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tF2\r\n",
"15:09-247\t19\t\t\t\t\t\t111\t114\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tF3\r\n",
"15:09-248\t19\t\t\t\t\t\t116\t84.8\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tF4\r\n",
"15:09-249\t19\t\t\t\t\t\t171\t91.2\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tF5\r\n",
"15:09-250\t19\tGoleta\t\t\t\t\t0.168\t37.2\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-251\t19\tGoleta\t\t\t\t\t0.12\t23.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-252\t19\tGoleta\t\t\t\t\t0.146\t38.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-253\t19\tGoleta\t\t\t\t\t0.106\t35\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-254\t19\tGoleta\t\t\t\t\t0.147\t58.6\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-269\t20\tGoleta\t\t\t\t\t0.137\t39.2\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-270\t20\tGoleta\t\t\t\t\t0.114\t33.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-271\t20\tGoleta\t\t\t\t\t0.092\t12.2\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-272\t20\tGoleta\t\t\t\t\t0.093\t3.56\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:09-273\t20\tGoleta\t\t\t\t\t0.088\t3.36\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-001\t1\t\t\t\t\t\t10.4\t43\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tE6\r\n",
"15:10-002\t1\t\t\t\t\t\t69.4\t187\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tE7\r\n",
"15:10-003\t1\t\t\t\t\t\t19.3\t123\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tE8\r\n",
"15:10-004\t1\t\t\t\t\t\t14.4\t83\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tE9\r\n",
"15:10-005\t1\t\t\t\t\t\t28.2\t123\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tF1\r\n",
"15:10-006\t1\tCorona\t\t\t\t\t0.153\t41.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-007\t1\tCorona\t\t\t\t\t0.086\t10.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-008\t1\tCorona\t\t\t\t\t0.111\t6.22\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-009\t1\tCorona\t\t\t\t\t0.091\t27.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-010\t1\tCorona\t\t\t\t\t0.129\t9.14\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-019\t9\tCorona\t\t\t\t\t0.065\t18.9\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-020\t9\tCorona\t\t\t\t\t0.158\t105\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-021\t9\tCorona\t\t\t\t\t0.094\t29.6\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-022\t9\tCorona\t\t\t\t\t0.063\t5.9\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-023\t9\tCorona\t\t\t\t\t0.084\t13.6\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-024\t9\tCorona\t\t\t\t\t0.071\t21.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-025\t9\t\t\t\t\t\t63\t226\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tC3\r\n",
"15:10-026\t9\t\t\t\t\t\t65\t133\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tC4\r\n",
"15:10-027\t9\t\t\t\t\t\t37\t182\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tC5\r\n",
"15:10-028\t9\t\t\t\t\t\t166\t194\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tC6\r\n",
"15:10-029\t9\t\t\t\t\t\t27.2\t92\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tC7\r\n",
"15:10-030\tControl\t\t\t\t\t\t103\t163\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tG8\r\n",
"15:10-031\tControl\t\t\t\t\t\t83\t104\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tG9\r\n",
"15:10-032\tControl\t\t\t\t\t\t116\t174\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tH1\r\n",
"15:10-033\t\t\t\t\t\t\t64\t\t\t\t\t\t\t\t\t\t\r\n",
"15:10-034\t\t\t\t\t\t\t113\t\t\t\t\t\t\t\t\t\t\r\n",
"15:10-040\t2\t\t\t\t\t\t51.2\t114\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tC8\r\n",
"15:10-041\t2\t\t\t\t\t\t27.6\t102\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tC9\r\n",
"15:10-042\t2\t\t\t\t\t\t28\t96\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tD1\r\n",
"15:10-043\t2\t\t\t\t\t\t21.4\t101\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tD2\r\n",
"15:10-044\t2\t\t\t\t\t\t31.2\t128\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tD3\r\n",
"15:10-045\t2\tCorona\t\t\t\t\t0.079\t13.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-046\t2\tCorona\t\t\t\t\t0.086\t19.1\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-047\t2\tCorona\t\t\t\t\t0.079\t19.3\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-048\t2\tCorona\t\t\t\t\t0.067\t6.84\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-049\t2\tCorona\t\t\t\t\t0.072\t21\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-050\t10\t\t\t\t\t\t89\t102\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tB2\r\n",
"15:10-051\t10\t\t\t\t\t\t80\t133\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tB3\r\n",
"15:10-052\t10\t\t\t\t\t\t54\t45.8\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tB4\r\n",
"15:10-053\t10\t\t\t\t\t\t59\t56\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tB5\r\n",
"15:10-054\t10\t\t\t\t\t\t68\t65.6\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tB6\r\n",
"15:10-055\t10\tCorona\t\t\t\t\t0.062\t5.24\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-056\t10\tCorona\t\t\t\t\t0.098\t10.7\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-057\t10\tCorona\t\t\t\t\t0.113\t19.1\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-058\t10\tCorona\t\t\t\t\t0.079\t5.08\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-059\t10\tCorona\t\t\t\t\t0.085\t7.92\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:10-065\tControl\t\t\t\t\t\t190\t98\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tH2\r\n",
"15:10-066\tControl\t\t\t\t\t\t112\t182\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tH3\r\n",
"15:10-067\t\t\t\t\t\t\t108\t\t\t\t\t\t\t\t\t\t\r\n",
"15:11-001\t28\t\t\t\t\t\t103\t80.4\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tH9\r\n",
"15:11-002\t28\t\t\t\t\t\t69\t78.6\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tI1\r\n",
"15:11-003\t28\t\t\t\t\t\t105\t43.2\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tI2\r\n",
"15:11-004\t28\t\t\t\t\t\t60\t61\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tI3\r\n",
"15:11-005\t28\t\t\t\t\t\t111\t38.6\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tI4\r\n",
"15:11-006\t28\tGoleta\t\t\t\t\t0.126\t28.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-007\t28\tGoleta\t\t\t\t\t0.072\t7.5\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-008\t28\tGoleta\t\t\t\t\t0.117\t15.1\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-009\t28\tGoleta\t\t\t\t\t0.068\t11.9\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-013\t28\tGoleta\t\t\t\t\t0.119\t24.6\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-021\t26\t\t\t\t\t\t53\t42.8\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tF6\r\n",
"15:11-022\t26\t\t\t\t\t\t110\t56.4\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tF7\r\n",
"15:11-023\t26\t\t\t\t\t\t56\t77.2\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tF8\r\n",
"15:11-024\t26\t\t\t\t\t\t96\t107\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tF9\r\n",
"15:11-025\t26\t\t\t\t\t\t134\t90.4\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tG1\r\n",
"15:11-026\t26\tGoleta\t\t\t\t\t0.117\t25\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-027\t26\tGoleta\t\t\t\t\t0.113\t50\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-028\t26\tGoleta\t\t\t\t\t0.117\t41.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-029\t26\tGoleta\t\t\t\t\t0.075\t8.34\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-030\t27\t\t\t\t\t\t12.8\t82\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tF2\r\n",
"15:11-031\t27\t\t\t\t\t\t27.4\t121\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tF3\r\n",
"15:11-032\t27\t\t\t\t\t\t10.2\t83\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tF4\r\n",
"15:11-033\t27\t\t\t\t\t\t36\t113\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tF5\r\n",
"15:11-034\t27\t\t\t\t\t\t19.6\t66\t20160725\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160725\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tF6\r\n",
"15:11-035\t27\tGoleta\t\t\t\t\t0.064\t6.34\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-042\t27\tGoleta\t\t\t\t\t0.145\t25.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-043\t27\tGoleta\t\t\t\t\t0.098\t30.6\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-044\t27\tGoleta\t\t\t\t\t0.095\t14.2\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-045\t27\tGoleta\t\t\t\t\t0.045\t6.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-046\t27\tGoleta\t\t\t\t\t0.041\t4.08\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-049\t24\t\t\t\t\t\t103\t102\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tA1\r\n",
"15:11-050\t24\t\t\t\t\t\t86\t53\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tA2\r\n",
"15:11-051\t24\t\t\t\t\t\t54\t86.4\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tA3\r\n",
"15:11-052\t24\t\t\t\t\t\t65\t142\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tA4\r\n",
"15:11-053\t24\t\t\t\t\t\t130\t85.4\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tA5\r\n",
"15:11-054\t24\tGoleta\t\t\t\t\t0.13\t20.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-055\t24\tGoleta\t\t\t\t\t0.072\t10.9\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-056\t24\tGoleta\t\t\t\t\t0.066\t13\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-057\t24\tGoleta\t\t\t\t\t0.074\t11\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-058\t24\tGoleta\t\t\t\t\t0.055\t5.5\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-062\t22\t\t\t\t\t\t79\t83.2\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tA6\r\n",
"15:11-063\t22\t\t\t\t\t\t189\t87.2\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tA7\r\n",
"15:11-064\t22\t\t\t\t\t\t93\t98\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tA8\r\n",
"15:11-065\t22\t\t\t\t\t\t63\t109\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tA9\r\n",
"15:11-066\t22\t\t\t\t\t\t81\t111\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tB1\r\n",
"15:11-067\t22\tGoleta\t\t\t\t\t0.15\t78.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-068\t22\tGoleta\t\t\t\t\t0.128\t32.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-069\t22\tGoleta\t\t\t\t\t0.068\t7.96\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-076\t17\tGoleta\t\t\t\t\t0.112\t27.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-077\t17\tGoleta\t\t\t\t\t0.085\t16.1\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-078\t17\tGoleta\t\t\t\t\t0.148\t32.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-079\t17\tGoleta\t\t\t\t\t0.126\t17\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-080\t17\tGoleta\t\t\t\t\t0.111\t27.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-082\t17\tGoleta\t\t\t\t\t0.058\t4.12\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-083\t17\tGoleta\t\t\t\t\t0.089\t4.44\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-084\t17\t\t\t\t\t\t57\t48\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA6\r\n",
"15:11-085\t17\t\t\t\t\t\t40\t80\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA7\r\n",
"15:11-086\t17\t\t\t\t\t\t85\t138\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA8\r\n",
"15:11-087\t17\t\t\t\t\t\t74\t68\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA9\r\n",
"15:11-088\t17\t\t\t\t\t\t125\t18.2\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tB1\r\n",
"15:11-089\t21\t\t\t\t\t\t147\t168\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA1\r\n",
"15:11-090\t21\t\t\t\t\t\t112\t69.2\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA2\r\n",
"15:11-091\t21\t\t\t\t\t\t101\t70.4\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA3\r\n",
"15:11-092\t21\t\t\t\t\t\t45\t58.8\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA4\r\n",
"15:11-093\t21\t\t\t\t\t\t128\t61.6\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tA5\r\n",
"15:11-094\t21\tGoleta\t\t\t\t\t0.07\t18.9\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-095\t21\tGoleta\t\t\t\t\t0.052\t3.12\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-096\t21\tGoleta\t\t\t\t\t0.073\t5.64\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-097\t21\tGoleta\t\t\t\t\t0.133\t26.2\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-098\t21\tGoleta\t\t\t\t\t0.111\t42.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-099\t21\tGoleta\t\t\t\t\t0.072\t3.94\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-100\t20\t\t\t\t\t\t135\t29\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tB7\r\n",
"15:11-101\t20\t\t\t\t\t\t103\t133\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tB8\r\n",
"15:11-102\t20\t\t\t\t\t\t143\t116\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tB9\r\n",
"15:11-103\t20\t\t\t\t\t\t53\t163\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tC1\r\n",
"15:11-104\t20\t\t\t\t\t\t106\t162\t20160721\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160721\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tC2\r\n",
"15:11-105\t20\tGoleta\t\t\t\t\t0.095\t21\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-106\t20\tGoleta\t\t\t\t\t0.138\t107\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-107\t15\t\t\t\t\t\t131\t180\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tD4\r\n",
"15:11-108\t15\t\t\t\t\t\t96\t224\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tD5\r\n",
"15:11-109\t15\t\t\t\t\t\t111\t146\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tD6\r\n",
"15:11-110\t15\t\t\t\t\t\t127\t153\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tD7\r\n",
"15:11-111\t15\t\t\t\t\t\t120\t224\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tD8\r\n",
"15:11-112\t15\tGoleta\t\t\t\t\t0.103\t27.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-113\t15\tGoleta\t\t\t\t\t0.44\tOut of range\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-114\t15\tGoleta\t\t\t\t\t0.057\t2.78\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-115\t15\tGoleta\t\t\t\t\t0.076\t8.76\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-116\t15\tGoleta\t\t\t\t\t0.158\t26.8\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-123\t25\t\t\t\t\t\t30\t41.8\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tI5\r\n",
"15:11-124\t25\t\t\t\t\t\t63\t105\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tI6\r\n",
"15:11-125\t25\t\t\t\t\t\t67\t87\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tI7\r\n",
"15:11-126\t25\t\t\t\t\t\t70\t72.8\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tI8\r\n",
"15:11-127\t25\t\t\t\t\t\t185\t140\t20160810\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tI9\r\n",
"15:11-128\t25\tGoleta\t\t\t\t\t0.152\t52.2\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-129\t25\tGoleta\t\t\t\t\t0.07\t15.7\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-130\t25\tGoleta\t\t\t\t\t0.12\t49\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-131\t25\tGoleta\t\t\t\t\t0.069\t11.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-132\t25\tGoleta\t\t\t\t\t0.049\t4.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-142\tControl\t\t\t\t\t\t89\t99.6\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tH4\r\n",
"15:11-143\tControl\t\t\t\t\t\t94\t96\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tH5\r\n",
"15:11-144\tControl\t\t\t\t\t\t94\t181\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tH6\r\n",
"15:11-145\t\t\t\t\t\t\t0.045\t6.06\t20170509\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-146\t\t\t\t\t\t\t0.061\t8.96\t20170509\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-147\t\t\t\t\t\t\t0.056\tOut of range\t20170509\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-148\t\t\t\t\t\t\t0.102\t13.5\t20170509\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:11-149\t\t\t\t\t\t\t0.064\tOut of range\t20170509\tSJW\t\t\t\t20170509\tSJW\t\t\n",
"15:11-153\tControl\t\t\t\t\t\t206\t186\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tH7\r\n",
"15:11-154\tControl\t\t\t\t\t\t116\t171\t20160809\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160810\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 1\tH8\r\n",
"15:11-155\t\t\t\t\t\t\t211\t\t\t\t\t\t\t\t\t\t\n",
"accession_number\tcage_number\tsite\tTW(g)\tSW(g)\tSL(mm)\tcomments\tweight(mg)\tconcentration(ng/uL)\textraction_date\textraction_initials\textraction_method\telution_volume(uL)\tquant_method\tquant_date\tquant_initials\tstorage_box_name\tbox_slot\r\n",
"Corona 10 fecal 10/10/15:00-000\t\t\t\t\t96\t8.88\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tI7\r",
"\t\t\n",
"Corona 1 fecal 10/10/15:00-000\t\t\t\t\t104\t8.36\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 3\tA2\r",
"\t\t\n",
"Corona 2 fecal 10/10/15:00-000\t\t\t\t\t119\t8.08\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tI6\r",
"\t\t\n",
"Corona 9 fecal 10/10/15:00-000\t\t\t\t\t89\t16.8\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tH8\r",
"\t\t\n",
"Corona C10 fecal 9/29/15:00-000\t\t\t\t\t50\t7\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tH1\r",
"\t\t\n",
"Corona C1 fecal 9/29/15:00-000\t\t\t\t\t83\t9.84\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tG9\r",
"\t\t\n",
"Corona C2 fecal 9/29/15:00-000\t\t\t\t\t99\t5.56\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tH3\r",
"\t\t\n",
"Corona C4 fecal 9/29/15:00-000\t\t\t\t\t74\t14.8\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tH4\r",
"\t\t\n",
"Corona Control A fecal 8/11/2015:00-000\t\t\t\t\t173\t5.6\t20160825\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tG4\r",
"\t\t\n",
"Corona Control A fecal 9/29/2015:00-000\t\t\t\t\t69\t4.56\t20160825\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tG5\r",
"\t\t\n",
"Corona Control B fecal 8/11/2015:00-000\t\t\t\t\t137\t4.52\t20160825\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tG6\r",
"\t\t\n",
"Corona Control B fecal 9/29/2015:00-000\t\t\t\t\t161\t9.8\t20160825\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tG7\r",
"\t\t\n",
"Goleta 15 fecal 10/10/15:00-000\t\t\t\t\t109\t9.84\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tH7\r",
"\t\t\n",
"Goleta 17 fecal 10/10/15:00-000\t\t\t\t\t63\t12.8\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 3\tA3\r",
"\t\t\n",
"Goleta 20 fecal 10/10/15:00-000\t\t\t\t\t64\t5.84\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tI8\r",
"\t\t\n",
"Goleta 21 fecal 10/10/15:00-000\t\t\t\t\t57\t20.8\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tH5\r",
"\t\t\n",
"Goleta 22 fecal 10/10/15:00-000\t\t\t\t\t77\t4.68\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 3\tA5\r",
"\t\t\n",
"Goleta 24 fecal 10/10/15:00-000\t\t\t\t\t141\t8.72\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 3\tA1\r",
"\t\t\n",
"Goleta 25 fecal 10/10/15:00-000\t\t\t\t\t76\t8\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tI5\r",
"\t\t\n",
"Goleta 26 fecal 10/10/15:00-000\t\t\t\t\t80\t7.44\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tH6\r",
"\t\t\n",
"Goleta 27 fecal 10/10/15:00-000\t\t\t\t\t53\t9.12\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tI9\r",
"\t\t\n",
"Goleta 28 fecal 10/10/15:00-000\t\t\t\t\t186\t13.4\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 3\tA4\r",
"\t\t\n",
"Goleta C15 fecal 9/29/15:00-000\t\t\t\t\t59\t12.1\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 3\tB2\r",
"\t\t\n",
"Goleta C17 fecal 9/29/15:00-000\t\t\t\t\t66\t12.3\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tI3\r",
"\t\t\n",
"Goleta C18 fecal 9/29/15:00-000\t\t\t\t\t0\t2.6\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tI2\r",
"\t\t\n",
"Goleta C20 fecal 9/29/15:00-000\t\t\t\t\t94\t10.6\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 3\tA8\r",
"\t\t\n",
"Goleta C21 fecal 9/29/15:00-000\t\t\t\t\t81\t15\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tG8\r",
"\t\t\n",
"Goleta C22 fecal 9/29/15:00-000\t\t\t\t\t114\t10.7\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tI1\r",
"\t\t\n",
"Goleta C24 fecal 9/24/15:00-000\t\t\t\t\t53\t8.16\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tH2\r",
"\t\t\n",
"Goleta C25 fecal 9/29/15:00-000\t\t\t\t\t52\t7.12\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 3\tB1\r",
"\t\t\n",
"Goleta C26 fecal 9/28/15:00-000\t\t\t\t\t36\t5.36\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 3\tB3\r",
"\t\t\n",
"Goleta C27 fecal 9/29/15:00-000\t\t\t\t\t70\t10.6\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tI4\r",
"\t\t\n",
"Goleta C28 fecal 9/29/15:00-000\t\t\t\t\t39\t3.86\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 3\tB4\r",
"\t\t\n",
"Goleta Control A fecal 9/1/15:00-000\t\t\t\t\t115\t3.86\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 3\tA6\r",
"\t\t\n",
"Goleta Control A fecal 9/29/15:00-000\t\t\t\t\t92\t10.3\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 3\tA9\r",
"\t\t\n",
"Goleta Control B fecal 9/1/15:00-000\t\t\t\t\t98\t4.12\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 3\tA7\r",
"\t\t\n",
"Goleta Control B fecal 9/29/15:00-000\t\t\t\t\t84\t13\t20160831\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tH9\r",
"\t\t\n",
"incoming water A 9/22/15:00-000\t\t\t\t\t\t2.53\t20160818\tSJW\tDNeasy Blood & Tissue Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tG2\r",
"\t\t\n",
"incoming water B 9/22/15:00-000\t\t\t\t\t\t0.294\t20160818\tSJW\tDNeasy Blood & Tissue Kit\t100\tqubit\t20160901\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tG3\r",
"\t\t\n"
]
}
],
"source": [
"%%bash\n",
"sort Ava_WS_Transmission_DNA_Extractions_all.tsv"
]
},
{
"cell_type": "code",
"execution_count": 53,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"15:08-002\t11\t\t10.65\t3.43\t46.1\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.047\t5.82\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-003\t11\t\t17.35\t4.77\t52.8\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.114\t44.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-004\t11\t\t11.17\t3.57\t45.3\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.046\t2.46\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-005\t11\t\t13.26\t3.86\t48.3\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.156\t74\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-006\t11\t\t12.01\t3.76\t48\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.204\t78.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-022\t13\t\t15.74\t4.41\t48.9\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t13\t\t\t\t\t\t190\t26.2\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tC8\r\n",
"15:08-023\t13\t\t11.68\t3.34\t45.2\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t13\t\t\t\t\t\t124\t98.8\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tC9\r\n",
"15:08-024\t13\t\t14.21\t3.99\t47.9\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t13\t\t\t\t\t\t70\t93.4\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tD1\r\n",
"15:08-025\t13\t\t9.16\t2.74\t41.6\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t13\t\t\t\t\t\t50\t26.6\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tD2\r\n",
"15:08-026\t13\t\t10.1\t3.17\t44.3\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t13\t\t\t\t\t\t50\t45.2\t20160817\tSJW\tQIAmp Fast DNA Stool Mini Kit\t100\tqubit\t20160817\tSJW\tAva WS Transmission Study DNA Extractions by Sam Box 2\tD3\r\n"
]
}
],
"source": [
"%%bash\n",
"join -t $'\\t' <(sort ava_master_ab_list_formatted.tsv) <(sort Ava_WS_Transmission_DNA_Extractions_all.tsv) | head"
]
},
{
"cell_type": "code",
"execution_count": 54,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"15:08-001\t11\t\t13.15\t3.81\t48.2\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-002\t11\t\t10.65\t3.43\t46.1\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.047\t5.82\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-003\t11\t\t17.35\t4.77\t52.8\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.114\t44.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-004\t11\t\t11.17\t3.57\t45.3\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.046\t2.46\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-005\t11\t\t13.26\t3.86\t48.3\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.156\t74\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-006\t11\t\t12.01\t3.76\t48\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.204\t78.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-007\t10\t\t10.04\t3.18\t43.5\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-008\t10\t\t8.25\t2.67\t41.6\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-009\t10\t\t14.09\t3.76\t46.6\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-010\t10\t\t10.9\t3.36\t45\t\t\t\t\t\t\t\t\t\t\t\t\r\n"
]
}
],
"source": [
"%%bash\n",
"join -a1 -t $'\\t' <(sort ava_master_ab_list_formatted.tsv) <(sort Ava_WS_Transmission_DNA_Extractions_all.tsv) | head"
]
},
{
"cell_type": "code",
"execution_count": 55,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"15:08-001\t11\t\t13.15\t3.81\t48.2\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-002\t11\t\t10.65\t3.43\t46.1\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.047\t5.82\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-003\t11\t\t17.35\t4.77\t52.8\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.114\t44.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-004\t11\t\t11.17\t3.57\t45.3\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.046\t2.46\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-005\t11\t\t13.26\t3.86\t48.3\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.156\t74\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-006\t11\t\t12.01\t3.76\t48\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.204\t78.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-007\t10\t\t10.04\t3.18\t43.5\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-008\t10\t\t8.25\t2.67\t41.6\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-009\t10\t\t14.09\t3.76\t46.6\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-010\t10\t\t10.9\t3.36\t45\t\t\t\t\t\t\t\t\t\t\t\t\r\n"
]
}
],
"source": [
"%%bash\n",
"join -a1 -a2 -t $'\\t' <(sort ava_master_ab_list_formatted.tsv) <(sort Ava_WS_Transmission_DNA_Extractions_all.tsv) | head"
]
},
{
"cell_type": "code",
"execution_count": 56,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"15:08-001\t11\t\t13.15\t3.81\t48.2\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-002\t11\t\t10.65\t3.43\t46.1\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.047\t5.82\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-003\t11\t\t17.35\t4.77\t52.8\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.114\t44.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-004\t11\t\t11.17\t3.57\t45.3\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.046\t2.46\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-005\t11\t\t13.26\t3.86\t48.3\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.156\t74\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-006\t11\t\t12.01\t3.76\t48\t\t\t\t\t\t\t\t\t\t\t\t\r",
"\t11\tCorona\t\t\t\t\t0.204\t78.4\t20170504\tSJW\t\t\t\t20170509\tSJW\t\t\r\n",
"15:08-007\t10\t\t10.04\t3.18\t43.5\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-008\t10\t\t8.25\t2.67\t41.6\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-009\t10\t\t14.09\t3.76\t46.6\t\t\t\t\t\t\t\t\t\t\t\t\r\n",
"15:08-010\t10\t\t10.9\t3.36\t45\t\t\t\t\t\t\t\t\t\t\t\t\r\n"
]
}
],
"source": [
"%%bash\n",
"join -t $'\\t' -a1 -a2 -1 1 -2 1 <(sort ava_master_ab_list_formatted.tsv) <(sort Ava_WS_Transmission_DNA_Extractions_all.tsv) | head"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
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