In [5]:
%%bash
date
Thu Aug 31 13:07:47 PDT 2017
In [6]:
%%bash
hostname
friedman-Studio-XPS-7100
In [7]:
%%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

Format Ava's Master Sheet

Look at beginning of file
In [8]:
%%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												

Want to create new header line that does not contain 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" }).

In [9]:
%%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)

In [10]:
%%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.

In [11]:
%%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
In [12]:
%%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.

In [13]:
%%bash
awk -F "\t" 'BEGIN { OFS = "\t" } \
NR==1' \
ava_master_ab_list.tsv | \
cut -f1,3- > ava_master_ab_list_formatted.tsv
In [14]:
%%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
In [15]:
%%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.

In [16]:
%%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
In [17]:
%%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												
In [18]:
%%bash
awk -F "\t" 'BEGIN { OFS = "\t" } \
NR==1' \
ava_master_ab_list.tsv | \
cut -f1,3- > ava_master_ab_list_formatted.tsv
In [19]:
%%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
In [20]:
%%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												
In [21]:
%%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
In [22]:
%%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.

In [23]:
%%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
In [24]:
%%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												

Format Extraction List from 20170502

Perform same actions to this file as I did to Ava's Master List above.

In [25]:
%%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		
In [26]:
%%bash
awk -F "\t" 'BEGIN { OFS = "\t" } \
NR==1 \
{print NF}' 20170502_Ava_Ab_List.tsv
19
In [27]:
%%bash
awk -F "\t" 'BEGIN { OFS = "\t" } \
NR==1' \
ava_master_ab_list.tsv | \
cut -f1,3- > 20170502_Ava_Ab_List_formatted.tsv
In [28]:
%%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
In [29]:
%%bash
awk -F "\t" 'BEGIN { OFS = "\t" } \
{print NF}' 20170502_Ava_Ab_List_formatted.tsv
18
In [30]:
%%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		
In [31]:
%%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
In [32]:
%%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
In [33]:
%%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		

Format My Other Extraction File

In [34]:
%%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
In [35]:
%%bash
awk -F "\t" 'NR==1 {print NF}' Ava_WS_Transmission_DNA_Extractions.tsv
18
In [36]:
%%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.

In [37]:
%%bash
awk -F "\t" 'NR==1' Ava_WS_Transmission_DNA_Extractions.tsv > Ava_WS_Transmission_DNA_Extractions_formatted.tsv
In [38]:
%%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
In [39]:
%%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.

In [40]:
%%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.

In [41]:
%%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.

In [42]:
%%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
In [43]:
%%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

In [44]:
%%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.
In [45]:
%%bash
cp Ava_WS_Transmission_DNA_Extractions_formatted.tsv Ava_WS_Transmission_DNA_Extractions_all.tsv
In [46]:
%%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
In [47]:
%%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.

In [48]:
%%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.

In [49]:
%%bash
wc -l Ava_WS_Transmission_DNA_Extractions_all.tsv
317 Ava_WS_Transmission_DNA_Extractions_all.tsv

Join the master list with the extraction list to identify samples that still need to be processed.

In [50]:
%%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
In [51]:
%%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												
In [52]:
%%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
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
		
In [53]:
%%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
In [54]:
%%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												
In [55]:
%%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												
In [56]:
%%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