%%bash
date
Thu Aug 31 13:07:47 PDT 2017
%%bash
hostname
friedman-Studio-XPS-7100
%%bash
lscpu
Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 4 On-line CPU(s) list: 0-3 Thread(s) per core: 1 Core(s) per socket: 4 Socket(s): 1 NUMA node(s): 1 Vendor ID: AuthenticAMD CPU family: 16 Model: 5 Model name: AMD Athlon(tm) II X4 630 Processor Stepping: 2 CPU MHz: 2800.000 CPU max MHz: 2800.0000 CPU min MHz: 800.0000 BogoMIPS: 5586.35 Virtualization: AMD-V L1d cache: 64K L1i cache: 64K L2 cache: 512K NUMA node0 CPU(s): 0-3 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
%%bash
head ava_master_ab_list.tsv
accession_number ID # cage_number site TW(g) SW(g) SL(mm) comments weight(mg) concentration(ng/uL) extraction_date extraction_initials extraction_method elution_volume(uL) quant_method quant_date quant_initials storage_box_name box_slot 15:08 1 11 13.15 3.81 48.2 15:08 2 11 10.65 3.43 46.1 15:08 3 11 17.35 4.77 52.8 15:08 4 11 11.17 3.57 45.3 15:08 5 11 13.26 3.86 48.3 15:08 6 11 12.01 3.76 48 15:08 7 10 10.04 3.18 43.5 15:08 8 10 8.25 2.67 41.6 15:08 9 10 14.09 3.76 46.6
ID #
column.¶Use awk to extract the first record of the file (i.e. the existing header row; NR==
) and exclude the second column.
Also, tell awk that input file is tab-delimited (-F "\t"
) and that output should also be tab-delimited (BEGIN { OFS = "\t" }
).
%%bash
awk -F "\t" 'BEGIN { OFS = "\t" } \
NR==1 \
{print $1, $3, $4, $5, $6, $7}' ava_master_ab_list.tsv
accession_number cage_number site TW(g) SW(g) SL(mm)
Looks good, but how many columns are there?
Use awk to print the number of fields (i.e. columns; {print NF}
) in the first record (NR==1
)
%%bash
awk -F "\t" 'BEGIN { OFS = "\t" } \
NR==1 \
{print NF}' ava_master_ab_list.tsv
19
Use cut
to print all column names, except column two.
%%bash
awk -F "\t" 'BEGIN { OFS = "\t" } \
NR==1 \
ava_master_ab_list.tsv | \
cut -f1,3-
bash: line 1: unexpected EOF while looking for matching `'' bash: line 5: syntax error: unexpected end of file
%%bash
awk -F "\t" 'BEGIN { OFS = "\t" } \
NR==1' \
ava_master_ab_list.tsv | \
cut -f1,3-
accession_number cage_number site TW(g) SW(g) SL(mm) comments weight(mg) concentration(ng/uL) extraction_date extraction_initials extraction_method elution_volume(uL) quant_method quant_date quant_initials storage_box_name box_slot
Looks good.
Write the output to a file.
%%bash
awk -F "\t" 'BEGIN { OFS = "\t" } \
NR==1' \
ava_master_ab_list.tsv | \
cut -f1,3- > ava_master_ab_list_formatted.tsv
%%bash
head ava_master_ab_list_formatted.tsv
accession_number cage_number site TW(g) SW(g) SL(mm) comments weight(mg) concentration(ng/uL) extraction_date extraction_initials extraction_method elution_volume(uL) quant_method quant_date quant_initials storage_box_name box_slot
%%bash
awk -F "\t" 'BEGIN { OFS = "\t" } \
NR==1 \
{print NF}' ava_master_ab_list_formatted.tsv
18
Use awk to combine the accession number column and the ID# column data. Also format the ID# data into a three digit number.
%%bash
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", \
$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18 ,$19 }' \
ava_master_ab_list.tsv | \
head | \
tail -n +2 >> \
ava_master_ab_list_formatted.tsv
%%bash
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", \
$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18 ,$19 }' \
ava_master_ab_list.tsv | \
head | \
tail -n +2
15:08-001 11 13.15 3.81 48.2 15:08-002 11 10.65 3.43 46.1 15:08-003 11 17.35 4.77 52.8 15:08-004 11 11.17 3.57 45.3 15:08-005 11 13.26 3.86 48.3 15:08-006 11 12.01 3.76 48 15:08-007 10 10.04 3.18 43.5 15:08-008 10 8.25 2.67 41.6 15:08-009 10 14.09 3.76 46.6
%%bash
awk -F "\t" 'BEGIN { OFS = "\t" } \
NR==1' \
ava_master_ab_list.tsv | \
cut -f1,3- > ava_master_ab_list_formatted.tsv
%%bash
head ava_master_ab_list_formatted.tsv
accession_number cage_number site TW(g) SW(g) SL(mm) comments weight(mg) concentration(ng/uL) extraction_date extraction_initials extraction_method elution_volume(uL) quant_method quant_date quant_initials storage_box_name box_slot
%%bash
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", \
$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18 ,$19 }' \
ava_master_ab_list.tsv | \
head | \
tail -n +2 | awk 'NF'
15:08-001 11 13.15 3.81 48.2 15:08-002 11 10.65 3.43 46.1 15:08-003 11 17.35 4.77 52.8 15:08-004 11 11.17 3.57 45.3 15:08-005 11 13.26 3.86 48.3 15:08-006 11 12.01 3.76 48 15:08-007 10 10.04 3.18 43.5 15:08-008 10 8.25 2.67 41.6 15:08-009 10 14.09 3.76 46.6
%%bash
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", \
$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18 ,$19 }' \
ava_master_ab_list.tsv | \
head | \
tail -n +2 | awk '{print NF}'
6 6 6 6 6 6 6 6 6
%%bash
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", \
$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18 ,$19 }' \
ava_master_ab_list.tsv | \
head | \
tail -n +2 | \
head -1 | \
awk -F "\t" '{print NF}'
18
Whoops! Finally noticed I left the head
command in there! That's why the above steps were producing the wrong result.
%%bash
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", \
$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18 ,$19 }' \
ava_master_ab_list.tsv | \
tail -n +2 >> \
ava_master_ab_list_formatted.tsv
%%bash
head ava_master_ab_list_formatted.tsv
accession_number cage_number site TW(g) SW(g) SL(mm) comments weight(mg) concentration(ng/uL) extraction_date extraction_initials extraction_method elution_volume(uL) quant_method quant_date quant_initials storage_box_name box_slot 15:08-001 11 13.15 3.81 48.2 15:08-002 11 10.65 3.43 46.1 15:08-003 11 17.35 4.77 52.8 15:08-004 11 11.17 3.57 45.3 15:08-005 11 13.26 3.86 48.3 15:08-006 11 12.01 3.76 48 15:08-007 10 10.04 3.18 43.5 15:08-008 10 8.25 2.67 41.6 15:08-009 10 14.09 3.76 46.6
Perform same actions to this file as I did to Ava's Master List above.
%%bash
head 20170502_Ava_Ab_List.tsv
accession_number Tissue # Cage Number Site TW(g) SW(g) SL(mm) comments weight(mg) concentration(ng/uL) extraction_date extraction_initials extraction_method elution_volume(uL) quant_method quant_date quant_initials storage_box_name box_slot 15:08 2 11 Corona 0.047 5.82 20170504 SJW 20170509 SJW 15:08 3 11 Corona 0.114 44.4 20170504 SJW 20170509 SJW 15:08 4 11 Corona 0.046 2.46 20170504 SJW 20170509 SJW 15:08 5 11 Corona 0.156 74 20170504 SJW 20170509 SJW 15:08 6 11 Corona 0.204 78.4 20170504 SJW 20170509 SJW 15:08 27 13 Corona 0.107 27.2 20170504 SJW 20170509 SJW 15:08 28 13 Corona 0.176 78.8 20170504 SJW 20170509 SJW 15:08 29 13 Corona 0.144 44.4 20170504 SJW 20170509 SJW 15:08 31 13 Corona 0.071 8.24 20170504 SJW 20170509 SJW
%%bash
awk -F "\t" 'BEGIN { OFS = "\t" } \
NR==1 \
{print NF}' 20170502_Ava_Ab_List.tsv
19
%%bash
awk -F "\t" 'BEGIN { OFS = "\t" } \
NR==1' \
ava_master_ab_list.tsv | \
cut -f1,3- > 20170502_Ava_Ab_List_formatted.tsv
%%bash
head 20170502_Ava_Ab_List_formatted.tsv
accession_number cage_number site TW(g) SW(g) SL(mm) comments weight(mg) concentration(ng/uL) extraction_date extraction_initials extraction_method elution_volume(uL) quant_method quant_date quant_initials storage_box_name box_slot
%%bash
awk -F "\t" 'BEGIN { OFS = "\t" } \
{print NF}' 20170502_Ava_Ab_List_formatted.tsv
18
%%bash
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", \
$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18 ,$19 }' \
20170502_Ava_Ab_List.tsv | \
head | \
tail -n +2
15:08-002 11 Corona 0.047 5.82 20170504 SJW 20170509 SJW 15:08-003 11 Corona 0.114 44.4 20170504 SJW 20170509 SJW 15:08-004 11 Corona 0.046 2.46 20170504 SJW 20170509 SJW 15:08-005 11 Corona 0.156 74 20170504 SJW 20170509 SJW 15:08-006 11 Corona 0.204 78.4 20170504 SJW 20170509 SJW 15:08-027 13 Corona 0.107 27.2 20170504 SJW 20170509 SJW 15:08-028 13 Corona 0.176 78.8 20170504 SJW 20170509 SJW 15:08-029 13 Corona 0.144 44.4 20170504 SJW 20170509 SJW 15:08-031 13 Corona 0.071 8.24 20170504 SJW 20170509 SJW
%%bash
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", \
$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18 ,$19 }' \
20170502_Ava_Ab_List.tsv | \
head | \
tail -n +2 | \
awk -F "\t" '{print NF}'
18 18 18 18 18 18 18 18 18
%%bash
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", \
$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18 ,$19 }' \
20170502_Ava_Ab_List.tsv | \
tail -n +2 >> \
20170502_Ava_Ab_List_formatted.tsv
%%bash
head 20170502_Ava_Ab_List_formatted.tsv
accession_number cage_number site TW(g) SW(g) SL(mm) comments weight(mg) concentration(ng/uL) extraction_date extraction_initials extraction_method elution_volume(uL) quant_method quant_date quant_initials storage_box_name box_slot 15:08-002 11 Corona 0.047 5.82 20170504 SJW 20170509 SJW 15:08-003 11 Corona 0.114 44.4 20170504 SJW 20170509 SJW 15:08-004 11 Corona 0.046 2.46 20170504 SJW 20170509 SJW 15:08-005 11 Corona 0.156 74 20170504 SJW 20170509 SJW 15:08-006 11 Corona 0.204 78.4 20170504 SJW 20170509 SJW 15:08-027 13 Corona 0.107 27.2 20170504 SJW 20170509 SJW 15:08-028 13 Corona 0.176 78.8 20170504 SJW 20170509 SJW 15:08-029 13 Corona 0.144 44.4 20170504 SJW 20170509 SJW 15:08-031 13 Corona 0.071 8.24 20170504 SJW 20170509 SJW
%%bash
head Ava_WS_Transmission_DNA_Extractions.tsv
accession_number cage_number site TW(g) SW(g) SL(mm) comments weight(mg) concentration(ng/uL) extraction_date extraction_initials extraction_method elution_volume(uL) quant_method quant_date quant_initials storage_box_name box_slot 15:11-89 21 147 168 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A1 15:11-90 21 112 69.2 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A2 15:11-91 21 101 70.4 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A3 15:11-92 21 45 58.8 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A4 15:11-93 21 128 61.6 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A5 15:11-84 17 57 48 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A6 15:11-85 17 40 80 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A7 15:11-86 17 85 138 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A8 15:11-87 17 74 68 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A9
%%bash
awk -F "\t" 'NR==1 {print NF}' Ava_WS_Transmission_DNA_Extractions.tsv
18
%%bash
awk -F "\t" 'NR==1' Ava_WS_Transmission_DNA_Extractions.tsv
accession_number cage_number site TW(g) SW(g) SL(mm) comments weight(mg) concentration(ng/uL) extraction_date extraction_initials extraction_method elution_volume(uL) quant_method quant_date quant_initials storage_box_name box_slot
Header looks good; write the header to a new file.
%%bash
awk -F "\t" 'NR==1' Ava_WS_Transmission_DNA_Extractions.tsv > Ava_WS_Transmission_DNA_Extractions_formatted.tsv
%%bash
head Ava_WS_Transmission_DNA_Extractions_formatted.tsv
accession_number cage_number site TW(g) SW(g) SL(mm) comments weight(mg) concentration(ng/uL) extraction_date extraction_initials extraction_method elution_volume(uL) quant_method quant_date quant_initials storage_box_name box_slot
%%bash
awk -F'[-:]' 'NR==12' Ava_WS_Transmission_DNA_Extractions.tsv
15:9-144 23 50 60 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 B2
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.
%%bash
awk -F'[-:\t]' 'NR==12 {print NF}' Ava_WS_Transmission_DNA_Extractions.tsv
20
Combine first three fields to read like this: nn:nn:nnn
Print out each remaining field in a tab-delimited fashion, followed by a newline.
%%bash
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", \
$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18, $19, $20}' \
Ava_WS_Transmission_DNA_Extractions.tsv | \
head -12 | tail -n +2
15:11-089 21 147 168 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A1 15:11-090 21 112 69.2 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A2 15:11-091 21 101 70.4 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A3 15:11-092 21 45 58.8 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A4 15:11-093 21 128 61.6 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A5 15:11-084 17 57 48 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A6 15:11-085 17 40 80 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A7 15:11-086 17 85 138 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A8 15:11-087 17 74 68 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A9 15:11-088 17 125 18.2 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 B1 15:09-144 23 50 60 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 B2
Append the result to the previously made file that contains the header.
%%bash
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", \
$1 ,$2 ,$3 ,$4 ,$5 ,$6 ,$7 ,$8 ,$9 ,$10 ,$11 ,$12 ,$13 ,$14 ,$15 ,$16 ,$17 ,$18, $19, $20}' \
Ava_WS_Transmission_DNA_Extractions.tsv | \
tail -n +2 >> Ava_WS_Transmission_DNA_Extractions_formatted.tsv
%%bash
head Ava_WS_Transmission_DNA_Extractions_formatted.tsv
accession_number cage_number site TW(g) SW(g) SL(mm) comments weight(mg) concentration(ng/uL) extraction_date extraction_initials extraction_method elution_volume(uL) quant_method quant_date quant_initials storage_box_name box_slot 15:11-089 21 147 168 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A1 15:11-090 21 112 69.2 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A2 15:11-091 21 101 70.4 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A3 15:11-092 21 45 58.8 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A4 15:11-093 21 128 61.6 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A5 15:11-084 17 57 48 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A6 15:11-085 17 40 80 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A7 15:11-086 17 85 138 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A8 15:11-087 17 74 68 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A9
%%bash
cp Ava_WS_Transmission_DNA_Extractions_formatted.tsv > Ava_WS_Transmission_DNA_Extractions_all.tsv
cp: missing destination file operand after 'Ava_WS_Transmission_DNA_Extractions_formatted.tsv' Try 'cp --help' for more information.
%%bash
cp Ava_WS_Transmission_DNA_Extractions_formatted.tsv Ava_WS_Transmission_DNA_Extractions_all.tsv
%%bash
head Ava_WS_Transmission_DNA_Extractions_all.tsv
accession_number cage_number site TW(g) SW(g) SL(mm) comments weight(mg) concentration(ng/uL) extraction_date extraction_initials extraction_method elution_volume(uL) quant_method quant_date quant_initials storage_box_name box_slot 15:11-089 21 147 168 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A1 15:11-090 21 112 69.2 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A2 15:11-091 21 101 70.4 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A3 15:11-092 21 45 58.8 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A4 15:11-093 21 128 61.6 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A5 15:11-084 17 57 48 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A6 15:11-085 17 40 80 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A7 15:11-086 17 85 138 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A8 15:11-087 17 74 68 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A9
%%bash
wc -l Ava_WS_Transmission_DNA_Extractions_all.tsv
wc -l 20170502_Ava_Ab_List_formatted.tsv
195 Ava_WS_Transmission_DNA_Extractions_all.tsv 123 20170502_Ava_Ab_List_formatted.tsv
Append the contents, sans header (i.e. all rows after the first row; 'NR>1'
), of the one file to the other.
%%bash
awk 'NR>1' 20170502_Ava_Ab_List_formatted.tsv >> Ava_WS_Transmission_DNA_Extractions_all.tsv
Quick line count to verify that the two files have been combined into one.
%%bash
wc -l Ava_WS_Transmission_DNA_Extractions_all.tsv
317 Ava_WS_Transmission_DNA_Extractions_all.tsv
%%bash
join <(sort ava_master_ab_list_formatted.tsv) <(sort Ava_WS_Transmission_DNA_Extractions_all.tsv) | head
11 Corona 0.047 5.82 20170504 SJW 20170509 SJW 11 Corona 0.114 44.4 20170504 SJW 20170509 SJW 11 Corona 0.046 2.46 20170504 SJW 20170509 SJW 11 Corona 0.156 74 20170504 SJW 20170509 SJW 11 Corona 0.204 78.4 20170504 SJW 20170509 SJW 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 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 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 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 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
%%bash
sort ava_master_ab_list_formatted.tsv | head
15:08-001 11 13.15 3.81 48.2 15:08-002 11 10.65 3.43 46.1 15:08-003 11 17.35 4.77 52.8 15:08-004 11 11.17 3.57 45.3 15:08-005 11 13.26 3.86 48.3 15:08-006 11 12.01 3.76 48 15:08-007 10 10.04 3.18 43.5 15:08-008 10 8.25 2.67 41.6 15:08-009 10 14.09 3.76 46.6 15:08-010 10 10.9 3.36 45
%%bash
sort Ava_WS_Transmission_DNA_Extractions_all.tsv
15:08-002 11 Corona 0.047 5.82 20170504 SJW 20170509 SJW 15:08-003 11 Corona 0.114 44.4 20170504 SJW 20170509 SJW 15:08-004 11 Corona 0.046 2.46 20170504 SJW 20170509 SJW 15:08-005 11 Corona 0.156 74 20170504 SJW 20170509 SJW 15:08-006 11 Corona 0.204 78.4 20170504 SJW 20170509 SJW 15:08-022 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 15:08-023 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 15:08-024 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 15:08-025 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 15:08-026 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 15:08-027 13 Corona 0.107 27.2 20170504 SJW 20170509 SJW 15:08-028 13 Corona 0.176 78.8 20170504 SJW 20170509 SJW 15:08-029 13 Corona 0.144 44.4 20170504 SJW 20170509 SJW 15:08-031 13 Corona 0.071 8.24 20170504 SJW 20170509 SJW 15:08-032 13 Corona 0.134 31.8 20170504 SJW 20170509 SJW 15:08-040 6 96 170 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 B7 15:08-041 6 88 128 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 B8 15:08-042 6 78 76.4 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 B9 15:08-043 6 213 67.4 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 C1 15:08-044 6 255 71.2 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 C2 15:08-045 6 Corona 0.13 2.44 20170504 SJW 20170509 SJW 15:08-046 12 61 31.8 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 C3 15:08-047 12 34 7.28 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 C4 15:08-048 12 68 132 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 C5 15:08-049 12 114 87.6 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 C6 15:08-050 12 106 55.2 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 C7 15:08-051 12 Corona 0.117 36.8 20170504 SJW 20170509 SJW 15:08-052 12 Corona 0.041 2.64 20170504 SJW 20170509 SJW 15:08-053 12 Corona 0.044 2.18 20170504 SJW 20170509 SJW 15:08-054 12 Corona 0.173 98.2 20170504 SJW 20170509 SJW 15:08-055 2 Corona 0.117 7.44 20170504 SJW 20170509 SJW 15:08-086 6 Corona 0.052 16.1 20170504 SJW 20170509 SJW 15:08-087 6 Corona 0.165 105 20170504 SJW 20170509 SJW 15:08-088 6 Corona 0.064 8.8 20170504 SJW 20170509 SJW 15:08-089 6 Corona 0.122 33.8 20170504 SJW 20170509 SJW 15:08-094 11 Corona 0.042 4.98 20170504 SJW 20170509 SJW 15:08-095 11 5.88 73 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 D4 15:08-096 11 21.4 74 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 D5 15:08-097 11 9.32 73 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 D6 15:08-098 11 62 130 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 D7 15:08-099 11 6 42 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 D8 15:08-100 1 24 106 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 D9 15:08-101 1 5.4 96 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 E1 15:08-102 1 15 91 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 E2 15:08-103 1 15.5 79 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 E3 15:08-104 1 7.34 48 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 E4 15:08-105 1 39.4 197 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 E5 15:08-118 12 Corona 0.125 36 20170504 SJW 20170509 SJW 15:09-001 Control 116 117 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 F7 15:09-002 Control 68 132 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 F8 15:09-003 Control 138 65.2 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 F9 15:09-004 108 15:09-005 148 15:09-006 172 15:09-007 112 15:09-008 180 15:09-010 Control 135 116 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 G1 15:09-011 Control 96 80.2 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 G2 15:09-012 92 15:09-013 100 15:09-014 69 15:09-015 237 15:09-016 170 15:09-022 Control 100 220 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 G3 15:09-023 Control 117 198 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 G4 15:09-032 Control 51 75 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 G5 15:09-033 Control 115 124 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 G6 15:09-034 Control 190 234 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 G7 15:09-035 148 15:09-036 155 15:09-037 161 15:09-038 214 15:09-039 67 15:09-060 26 Goleta 0.138 33.4 20170504 SJW 20170509 SJW 15:09-061 26 Goleta 0.052 3.26 20170504 SJW 20170509 SJW 15:09-062 26 Goleta 0.111 24 20170504 SJW 20170509 SJW 15:09-119 16 30 63.8 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 D9 15:09-120 16 24 9.78 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 E1 15:09-121 16 53 98.2 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 E2 15:09-122 16 155 166 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 E3 15:09-123 16 152 140 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 E4 15:09-140 23 Goleta 0.049 7.82 20170504 SJW 20170509 SJW 15:09-141 23 Goleta 0.057 3.74 20170504 SJW 20170509 SJW 15:09-142 23 Goleta 0.023 Out of range 20170504 SJW 20170509 SJW 15:09-143 23 Goleta 0.036 2.16 20170504 SJW 20170509 SJW 15:09-144 23 50 60 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 B2 15:09-145 23 51 72 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 B3 15:09-146 23 43 121 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 B4 15:09-147 23 84 159 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 B5 15:09-148 23 66 41.8 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 B6 15:09-149 23 Goleta 0.094 15.7 20170504 SJW 20170509 SJW 15:09-150 23 Goleta 0.184 6.48 20170504 SJW 20170509 SJW 15:09-173 22 Goleta 0.116 92.8 20170504 SJW 20170509 SJW 15:09-174 22 Goleta 0.102 28.2 20170504 SJW 20170509 SJW 15:09-228 18 120 117 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 E5 15:09-229 18 37 83.4 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 E6 15:09-230 18 113 43 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 E7 15:09-231 18 144 93.8 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 E8 15:09-232 18 173 43.6 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 E9 15:09-233 18 Goleta 0.119 8.3 20170504 SJW 20170509 SJW 15:09-234 18 Goleta 0.136 58.6 20170504 SJW 20170509 SJW 15:09-235 18 Goleta 0.156 64.2 20170504 SJW 20170509 SJW 15:09-236 18 Goleta 0.176 78.8 20170504 SJW 20170509 SJW 15:09-237 18 Goleta 0.169 44.8 20170504 SJW 20170509 SJW 15:09-245 19 157 60.4 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 F1 15:09-246 19 128 101 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 F2 15:09-247 19 111 114 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 F3 15:09-248 19 116 84.8 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 F4 15:09-249 19 171 91.2 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 F5 15:09-250 19 Goleta 0.168 37.2 20170504 SJW 20170509 SJW 15:09-251 19 Goleta 0.12 23.8 20170504 SJW 20170509 SJW 15:09-252 19 Goleta 0.146 38.4 20170504 SJW 20170509 SJW 15:09-253 19 Goleta 0.106 35 20170504 SJW 20170509 SJW 15:09-254 19 Goleta 0.147 58.6 20170504 SJW 20170509 SJW 15:09-269 20 Goleta 0.137 39.2 20170504 SJW 20170509 SJW 15:09-270 20 Goleta 0.114 33.4 20170504 SJW 20170509 SJW 15:09-271 20 Goleta 0.092 12.2 20170504 SJW 20170509 SJW 15:09-272 20 Goleta 0.093 3.56 20170504 SJW 20170509 SJW 15:09-273 20 Goleta 0.088 3.36 20170504 SJW 20170509 SJW 15:10-001 1 10.4 43 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 E6 15:10-002 1 69.4 187 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 E7 15:10-003 1 19.3 123 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 E8 15:10-004 1 14.4 83 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 E9 15:10-005 1 28.2 123 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 F1 15:10-006 1 Corona 0.153 41.4 20170504 SJW 20170509 SJW 15:10-007 1 Corona 0.086 10.4 20170504 SJW 20170509 SJW 15:10-008 1 Corona 0.111 6.22 20170504 SJW 20170509 SJW 15:10-009 1 Corona 0.091 27.8 20170504 SJW 20170509 SJW 15:10-010 1 Corona 0.129 9.14 20170504 SJW 20170509 SJW 15:10-019 9 Corona 0.065 18.9 20170504 SJW 20170509 SJW 15:10-020 9 Corona 0.158 105 20170504 SJW 20170509 SJW 15:10-021 9 Corona 0.094 29.6 20170504 SJW 20170509 SJW 15:10-022 9 Corona 0.063 5.9 20170504 SJW 20170509 SJW 15:10-023 9 Corona 0.084 13.6 20170504 SJW 20170509 SJW 15:10-024 9 Corona 0.071 21.4 20170504 SJW 20170509 SJW 15:10-025 9 63 226 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 C3 15:10-026 9 65 133 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 C4 15:10-027 9 37 182 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 C5 15:10-028 9 166 194 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 C6 15:10-029 9 27.2 92 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 C7 15:10-030 Control 103 163 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 G8 15:10-031 Control 83 104 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 G9 15:10-032 Control 116 174 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 H1 15:10-033 64 15:10-034 113 15:10-040 2 51.2 114 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 C8 15:10-041 2 27.6 102 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 C9 15:10-042 2 28 96 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 D1 15:10-043 2 21.4 101 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 D2 15:10-044 2 31.2 128 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 D3 15:10-045 2 Corona 0.079 13.8 20170504 SJW 20170509 SJW 15:10-046 2 Corona 0.086 19.1 20170504 SJW 20170509 SJW 15:10-047 2 Corona 0.079 19.3 20170504 SJW 20170509 SJW 15:10-048 2 Corona 0.067 6.84 20170504 SJW 20170509 SJW 15:10-049 2 Corona 0.072 21 20170504 SJW 20170509 SJW 15:10-050 10 89 102 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 B2 15:10-051 10 80 133 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 B3 15:10-052 10 54 45.8 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 B4 15:10-053 10 59 56 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 B5 15:10-054 10 68 65.6 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 B6 15:10-055 10 Corona 0.062 5.24 20170504 SJW 20170509 SJW 15:10-056 10 Corona 0.098 10.7 20170504 SJW 20170509 SJW 15:10-057 10 Corona 0.113 19.1 20170504 SJW 20170509 SJW 15:10-058 10 Corona 0.079 5.08 20170504 SJW 20170509 SJW 15:10-059 10 Corona 0.085 7.92 20170504 SJW 20170509 SJW 15:10-065 Control 190 98 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 H2 15:10-066 Control 112 182 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 H3 15:10-067 108 15:11-001 28 103 80.4 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 H9 15:11-002 28 69 78.6 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 I1 15:11-003 28 105 43.2 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 I2 15:11-004 28 60 61 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 I3 15:11-005 28 111 38.6 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 I4 15:11-006 28 Goleta 0.126 28.4 20170504 SJW 20170509 SJW 15:11-007 28 Goleta 0.072 7.5 20170504 SJW 20170509 SJW 15:11-008 28 Goleta 0.117 15.1 20170504 SJW 20170509 SJW 15:11-009 28 Goleta 0.068 11.9 20170504 SJW 20170509 SJW 15:11-013 28 Goleta 0.119 24.6 20170504 SJW 20170509 SJW 15:11-021 26 53 42.8 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 F6 15:11-022 26 110 56.4 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 F7 15:11-023 26 56 77.2 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 F8 15:11-024 26 96 107 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 F9 15:11-025 26 134 90.4 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 G1 15:11-026 26 Goleta 0.117 25 20170504 SJW 20170509 SJW 15:11-027 26 Goleta 0.113 50 20170504 SJW 20170509 SJW 15:11-028 26 Goleta 0.117 41.4 20170504 SJW 20170509 SJW 15:11-029 26 Goleta 0.075 8.34 20170504 SJW 20170509 SJW 15:11-030 27 12.8 82 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 F2 15:11-031 27 27.4 121 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 F3 15:11-032 27 10.2 83 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 F4 15:11-033 27 36 113 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 F5 15:11-034 27 19.6 66 20160725 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160725 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 F6 15:11-035 27 Goleta 0.064 6.34 20170504 SJW 20170509 SJW 15:11-042 27 Goleta 0.145 25.8 20170504 SJW 20170509 SJW 15:11-043 27 Goleta 0.098 30.6 20170504 SJW 20170509 SJW 15:11-044 27 Goleta 0.095 14.2 20170504 SJW 20170509 SJW 15:11-045 27 Goleta 0.045 6.8 20170504 SJW 20170509 SJW 15:11-046 27 Goleta 0.041 4.08 20170504 SJW 20170509 SJW 15:11-049 24 103 102 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 A1 15:11-050 24 86 53 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 A2 15:11-051 24 54 86.4 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 A3 15:11-052 24 65 142 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 A4 15:11-053 24 130 85.4 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 A5 15:11-054 24 Goleta 0.13 20.4 20170504 SJW 20170509 SJW 15:11-055 24 Goleta 0.072 10.9 20170504 SJW 20170509 SJW 15:11-056 24 Goleta 0.066 13 20170504 SJW 20170509 SJW 15:11-057 24 Goleta 0.074 11 20170504 SJW 20170509 SJW 15:11-058 24 Goleta 0.055 5.5 20170504 SJW 20170509 SJW 15:11-062 22 79 83.2 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 A6 15:11-063 22 189 87.2 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 A7 15:11-064 22 93 98 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 A8 15:11-065 22 63 109 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 A9 15:11-066 22 81 111 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 B1 15:11-067 22 Goleta 0.15 78.8 20170504 SJW 20170509 SJW 15:11-068 22 Goleta 0.128 32.4 20170504 SJW 20170509 SJW 15:11-069 22 Goleta 0.068 7.96 20170504 SJW 20170509 SJW 15:11-076 17 Goleta 0.112 27.8 20170504 SJW 20170509 SJW 15:11-077 17 Goleta 0.085 16.1 20170504 SJW 20170509 SJW 15:11-078 17 Goleta 0.148 32.8 20170504 SJW 20170509 SJW 15:11-079 17 Goleta 0.126 17 20170504 SJW 20170509 SJW 15:11-080 17 Goleta 0.111 27.8 20170504 SJW 20170509 SJW 15:11-082 17 Goleta 0.058 4.12 20170504 SJW 20170509 SJW 15:11-083 17 Goleta 0.089 4.44 20170504 SJW 20170509 SJW 15:11-084 17 57 48 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A6 15:11-085 17 40 80 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A7 15:11-086 17 85 138 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A8 15:11-087 17 74 68 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A9 15:11-088 17 125 18.2 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 B1 15:11-089 21 147 168 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A1 15:11-090 21 112 69.2 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A2 15:11-091 21 101 70.4 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A3 15:11-092 21 45 58.8 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A4 15:11-093 21 128 61.6 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 A5 15:11-094 21 Goleta 0.07 18.9 20170504 SJW 20170509 SJW 15:11-095 21 Goleta 0.052 3.12 20170504 SJW 20170509 SJW 15:11-096 21 Goleta 0.073 5.64 20170504 SJW 20170509 SJW 15:11-097 21 Goleta 0.133 26.2 20170504 SJW 20170509 SJW 15:11-098 21 Goleta 0.111 42.8 20170504 SJW 20170509 SJW 15:11-099 21 Goleta 0.072 3.94 20170504 SJW 20170509 SJW 15:11-100 20 135 29 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 B7 15:11-101 20 103 133 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 B8 15:11-102 20 143 116 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 B9 15:11-103 20 53 163 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 C1 15:11-104 20 106 162 20160721 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160721 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 C2 15:11-105 20 Goleta 0.095 21 20170504 SJW 20170509 SJW 15:11-106 20 Goleta 0.138 107 20170504 SJW 20170509 SJW 15:11-107 15 131 180 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 D4 15:11-108 15 96 224 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 D5 15:11-109 15 111 146 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 D6 15:11-110 15 127 153 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 D7 15:11-111 15 120 224 20160817 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160817 SJW Ava WS Transmission Study DNA Extractions by Sam Box 2 D8 15:11-112 15 Goleta 0.103 27.4 20170504 SJW 20170509 SJW 15:11-113 15 Goleta 0.44 Out of range 20170504 SJW 20170509 SJW 15:11-114 15 Goleta 0.057 2.78 20170504 SJW 20170509 SJW 15:11-115 15 Goleta 0.076 8.76 20170504 SJW 20170509 SJW 15:11-116 15 Goleta 0.158 26.8 20170504 SJW 20170509 SJW 15:11-123 25 30 41.8 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 I5 15:11-124 25 63 105 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 I6 15:11-125 25 67 87 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 I7 15:11-126 25 70 72.8 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 I8 15:11-127 25 185 140 20160810 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 I9 15:11-128 25 Goleta 0.152 52.2 20170504 SJW 20170509 SJW 15:11-129 25 Goleta 0.07 15.7 20170504 SJW 20170509 SJW 15:11-130 25 Goleta 0.12 49 20170504 SJW 20170509 SJW 15:11-131 25 Goleta 0.069 11.4 20170504 SJW 20170509 SJW 15:11-132 25 Goleta 0.049 4.4 20170504 SJW 20170509 SJW 15:11-142 Control 89 99.6 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 H4 15:11-143 Control 94 96 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 H5 15:11-144 Control 94 181 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 H6 15:11-145 0.045 6.06 20170509 SJW 20170509 SJW 15:11-146 0.061 8.96 20170509 SJW 20170509 SJW 15:11-147 0.056 Out of range 20170509 SJW 20170509 SJW 15:11-148 0.102 13.5 20170509 SJW 20170509 SJW 15:11-149 0.064 Out of range 20170509 SJW 20170509 SJW 15:11-153 Control 206 186 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 H7 15:11-154 Control 116 171 20160809 SJW QIAmp Fast DNA Stool Mini Kit 100 qubit 20160810 SJW Ava WS Transmission Study DNA Extractions by Sam Box 1 H8 15:11-155 211 accession_number cage_number site TW(g) SW(g) SL(mm) comments weight(mg) concentration(ng/uL) extraction_date extraction_initials extraction_method elution_volume(uL) quant_method quant_date quant_initials storage_box_name box_slot
%%bash
join -t $'\t' <(sort ava_master_ab_list_formatted.tsv) <(sort Ava_WS_Transmission_DNA_Extractions_all.tsv) | head
11 Corona 0.047 5.82 20170504 SJW 20170509 SJW 11 Corona 0.114 44.4 20170504 SJW 20170509 SJW 11 Corona 0.046 2.46 20170504 SJW 20170509 SJW 11 Corona 0.156 74 20170504 SJW 20170509 SJW 11 Corona 0.204 78.4 20170504 SJW 20170509 SJW 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 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 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 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 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
%%bash
join -a1 -t $'\t' <(sort ava_master_ab_list_formatted.tsv) <(sort Ava_WS_Transmission_DNA_Extractions_all.tsv) | head
15:08-001 11 13.15 3.81 48.2 11 Corona 0.047 5.82 20170504 SJW 20170509 SJW 11 Corona 0.114 44.4 20170504 SJW 20170509 SJW 11 Corona 0.046 2.46 20170504 SJW 20170509 SJW 11 Corona 0.156 74 20170504 SJW 20170509 SJW 11 Corona 0.204 78.4 20170504 SJW 20170509 SJW 15:08-007 10 10.04 3.18 43.5 15:08-008 10 8.25 2.67 41.6 15:08-009 10 14.09 3.76 46.6 15:08-010 10 10.9 3.36 45
%%bash
join -a1 -a2 -t $'\t' <(sort ava_master_ab_list_formatted.tsv) <(sort Ava_WS_Transmission_DNA_Extractions_all.tsv) | head
15:08-001 11 13.15 3.81 48.2 11 Corona 0.047 5.82 20170504 SJW 20170509 SJW 11 Corona 0.114 44.4 20170504 SJW 20170509 SJW 11 Corona 0.046 2.46 20170504 SJW 20170509 SJW 11 Corona 0.156 74 20170504 SJW 20170509 SJW 11 Corona 0.204 78.4 20170504 SJW 20170509 SJW 15:08-007 10 10.04 3.18 43.5 15:08-008 10 8.25 2.67 41.6 15:08-009 10 14.09 3.76 46.6 15:08-010 10 10.9 3.36 45
%%bash
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
15:08-001 11 13.15 3.81 48.2 11 Corona 0.047 5.82 20170504 SJW 20170509 SJW 11 Corona 0.114 44.4 20170504 SJW 20170509 SJW 11 Corona 0.046 2.46 20170504 SJW 20170509 SJW 11 Corona 0.156 74 20170504 SJW 20170509 SJW 11 Corona 0.204 78.4 20170504 SJW 20170509 SJW 15:08-007 10 10.04 3.18 43.5 15:08-008 10 8.25 2.67 41.6 15:08-009 10 14.09 3.76 46.6 15:08-010 10 10.9 3.36 45