Create S.salar UniProt annotations file for Shelly

See this GitHub Issue

This notebook relies on GFFutils to be installed and available in your $PATH.

List computer specs

In [1]:
%%bash
echo "TODAY'S DATE:"
date
echo "------------"
echo ""
#Display operating system info
lsb_release -a
echo ""
echo "------------"
echo "HOSTNAME: "; hostname 
echo ""
echo "------------"
echo "Computer Specs:"
echo ""
lscpu
echo ""
echo "------------"
echo ""
echo "Memory Specs"
echo ""
free -mh
TODAY'S DATE:
Tue 01 Jun 2021 07:37:57 AM PDT
------------

Distributor ID:	Ubuntu
Description:	Ubuntu 20.04.2 LTS
Release:	20.04
Codename:	focal

------------
HOSTNAME: 
computer

------------
Computer Specs:

Architecture:                    x86_64
CPU op-mode(s):                  32-bit, 64-bit
Byte Order:                      Little Endian
Address sizes:                   45 bits physical, 48 bits virtual
CPU(s):                          8
On-line CPU(s) list:             0-7
Thread(s) per core:              1
Core(s) per socket:              1
Socket(s):                       8
NUMA node(s):                    1
Vendor ID:                       GenuineIntel
CPU family:                      6
Model:                           165
Model name:                      Intel(R) Core(TM) i9-10885H CPU @ 2.40GHz
Stepping:                        2
CPU MHz:                         2400.000
BogoMIPS:                        4800.00
Hypervisor vendor:               VMware
Virtualization type:             full
L1d cache:                       256 KiB
L1i cache:                       256 KiB
L2 cache:                        2 MiB
L3 cache:                        128 MiB
NUMA node0 CPU(s):               0-7
Vulnerability Itlb multihit:     KVM: Mitigation: VMX unsupported
Vulnerability L1tf:              Not affected
Vulnerability Mds:               Not affected
Vulnerability Meltdown:          Not affected
Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl and seccomp
Vulnerability Spectre v1:        Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2:        Mitigation; Enhanced IBRS, IBPB conditional, RSB filling
Vulnerability Srbds:             Not affected
Vulnerability Tsx async abort:   Not affected
Flags:                           fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon nopl xtopology tsc_reliable nonstop_tsc cpuid pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch cpuid_fault invpcid_single ssbd ibrs ibpb stibp ibrs_enhanced fsgsbase tsc_adjust bmi1 avx2 smep bmi2 invpcid rdseed adx smap clflushopt xsaveopt xsavec xgetbv1 xsaves arat pku ospke md_clear flush_l1d arch_capabilities

------------

Memory Specs

              total        used        free      shared  buff/cache   available
Mem:           53Gi       3.6Gi        45Gi       428Mi       4.1Gi        48Gi
Swap:         2.0Gi          0B       2.0Gi
No LSB modules are available.

Set variables

  • %env indicates a bash variable; without %env is Python variable
In [1]:
# Set directories, input/output files
%env data_dir=/home/samb/data/S_salar/genomes
%env analysis_dir=/home/samb/analyses/20210601_ssal_gff-annotations
analysis_dir="/home/samb/analyses/20210601_ssal_gff-annotations"
# Input GFF
%env orig_gff=GCF_000233375.1_ICSASG_v2_genomic.gff
%env orig_gff_url=https://gannet.fish.washington.edu/metacarcinus/Salmo_Calig/GENOMES/v2/RefSeq

# UniProt batch output
%env perl_output=20210601_ssal_uniprot_batch_results.txt

# GTF extractor output
%env gtf_extractor_output=20210601_ssal_chrom-start-end-Dbxref.csv

# Gene name list for UniProt batch submission
%env gene_list=20210601_ssal_gene-list.txt

# Parsed UniProt
%env parsed_uniprot=20210601_ssal_accession-gene_id-gene-gene_description-go_ids.csv

# Final output
%env joined_output=20210601_ssal_chrom-gene_id_start-end-acc-gene-gene_description-go_ids.csv
env: data_dir=/home/samb/data/S_salar/genomes
env: analysis_dir=/home/samb/analyses/20210601_ssal_gff-annotations
env: orig_gff=GCF_000233375.1_ICSASG_v2_genomic.gff
env: orig_gff_url=https://gannet.fish.washington.edu/metacarcinus/Salmo_Calig/GENOMES/v2/RefSeq
env: perl_output=20210601_ssal_uniprot_batch_results.txt
env: gtf_extractor_output=20210601_ssal_chrom-start-end-Dbxref.csv
env: gene_list=20210601_ssal_gene-list.txt
env: parsed_uniprot=20210601_ssal_accession-gene_id-gene-gene_description-go_ids.csv
env: joined_output=20210601_ssal_chrom-gene_id_start-end-acc-gene-gene_description-go_ids.csv

Download GFF

In [3]:
%%bash
cd "${data_dir}"

# Download with wget. Use --no-check-certificate to avoid issues with Gannet certificate
# Use --quiet option to prevent wget output from printing too many lines to notebook
wget --no-check-certificate --quiet ${orig_gff_url}/${orig_gff}

ls -ltrh "${orig_gff}"
-rw-rw-r-- 1 samb samb 828M Sep 30  2020 GCF_000233375.1_ICSASG_v2_genomic.gff

Examine GFF

In [4]:
%%bash
head -n 20 "${data_dir}"/"${orig_gff}"
##gff-version 3
#!gff-spec-version 1.21
#!processor NCBI annotwriter
#!genome-build ICSASG_v2
#!genome-build-accession NCBI_Assembly:GCF_000233375.1
#!annotation-source NCBI Salmo salar Annotation Release 100
##sequence-region NC_027300.1 1 159038749
##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=8030
NC_027300.1	RefSeq	region	1	159038749	.	+	.	ID=NC_027300.1:1..159038749;Dbxref=taxon:8030;Name=ssa01;breed=double haploid;chromosome=ssa01;dev-stage=adult;gbkey=Src;genome=chromosome;isolate=Sally;mol_type=genomic DNA;sex=female;tissue-type=muscle
NC_027300.1	Gnomon	gene	5501	62139	.	-	.	ID=gene-LOC106560212;Dbxref=GeneID:106560212;Name=LOC106560212;gbkey=Gene;gene=LOC106560212;gene_biotype=protein_coding
NC_027300.1	Gnomon	mRNA	5501	62139	.	-	.	ID=rna-XM_014160784.1;Parent=gene-LOC106560212;Dbxref=GeneID:106560212,Genbank:XM_014160784.1;Name=XM_014160784.1;gbkey=mRNA;gene=LOC106560212;model_evidence=Supporting evidence includes similarity to: 99%25 coverage of the annotated genomic feature by RNAseq alignments%2C including 8 samples with support for all annotated introns;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014160784.1
NC_027300.1	Gnomon	exon	61647	62139	.	-	.	ID=exon-XM_014160784.1-1;Parent=rna-XM_014160784.1;Dbxref=GeneID:106560212,Genbank:XM_014160784.1;gbkey=mRNA;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014160784.1
NC_027300.1	Gnomon	exon	43486	43714	.	-	.	ID=exon-XM_014160784.1-2;Parent=rna-XM_014160784.1;Dbxref=GeneID:106560212,Genbank:XM_014160784.1;gbkey=mRNA;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014160784.1
NC_027300.1	Gnomon	exon	23978	24241	.	-	.	ID=exon-XM_014160784.1-3;Parent=rna-XM_014160784.1;Dbxref=GeneID:106560212,Genbank:XM_014160784.1;gbkey=mRNA;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014160784.1
NC_027300.1	Gnomon	exon	16966	17019	.	-	.	ID=exon-XM_014160784.1-4;Parent=rna-XM_014160784.1;Dbxref=GeneID:106560212,Genbank:XM_014160784.1;gbkey=mRNA;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014160784.1
NC_027300.1	Gnomon	exon	5501	5691	.	-	.	ID=exon-XM_014160784.1-5;Parent=rna-XM_014160784.1;Dbxref=GeneID:106560212,Genbank:XM_014160784.1;gbkey=mRNA;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014160784.1
NC_027300.1	Gnomon	CDS	43486	43633	.	-	0	ID=cds-XP_014016259.1;Parent=rna-XM_014160784.1;Dbxref=GeneID:106560212,Genbank:XP_014016259.1;Name=XP_014016259.1;gbkey=CDS;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;protein_id=XP_014016259.1
NC_027300.1	Gnomon	CDS	23978	24241	.	-	2	ID=cds-XP_014016259.1;Parent=rna-XM_014160784.1;Dbxref=GeneID:106560212,Genbank:XP_014016259.1;Name=XP_014016259.1;gbkey=CDS;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;protein_id=XP_014016259.1
NC_027300.1	Gnomon	CDS	16966	17019	.	-	2	ID=cds-XP_014016259.1;Parent=rna-XM_014160784.1;Dbxref=GeneID:106560212,Genbank:XP_014016259.1;Name=XP_014016259.1;gbkey=CDS;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;protein_id=XP_014016259.1
NC_027300.1	Gnomon	CDS	5501	5691	.	-	2	ID=cds-XP_014016259.1;Parent=rna-XM_014160784.1;Dbxref=GeneID:106560212,Genbank:XP_014016259.1;Name=XP_014016259.1;gbkey=CDS;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;protein_id=XP_014016259.1

Use GFFutils to extract gene features

In [7]:
%%bash
# Extract just gene features
# Extract chromosome name, start, end, and Dbxref fields
# Dbxref is the NCBI gene name, in this particular instance
# Specify input as GFF
# Use awk to format as comma-delimited output to help with downstream parsing/joining
time \
gtf_extract \
--feature gene \
--fields=chrom,start,end,Dbxref \
--gff ${data_dir}/${orig_gff} \
| awk 'BEGIN { OFS = ","; FS="[\t:]"} {print $1, $2, $3, $5}' \
> ${analysis_dir}/${gtf_extractor_output}
real	2m26.807s
user	2m26.279s
sys	0m0.468s

Check results

In [8]:
%%bash
cd "${analysis_dir}"
ls -ltrh ${gtf_extractor_output}

echo ""

head ${gtf_extractor_output}
-rw-rw-r-- 1 samb samb 2.9M Jun  1 09:49 20210601_ssal_chrom-start-end-Dbxref.csv

NC_027300.1,5501,62139,106560212
NC_027300.1,160437,198815,106607996
NC_027300.1,228330,231471,106601976
NC_027300.1,296031,297111,106560213
NC_027300.1,306942,310878,106566220
NC_027300.1,331369,346454,106571988
NC_027300.1,355675,362950,106578259
NC_027300.1,401623,416794,106583877
NC_027300.1,431662,432555,106589664
NC_027300.1,449112,490663,106596642

Confirm that GFFutils output seem okay

In [10]:
%%bash
# Count gene features via GFFutils
echo "GFFutils number of extracted genes:"
gtf_extract -f gene --fields=Dbxref --gff ${data_dir}/${orig_gff} | wc -l

echo ""

# Count gene features via awk
echo "awk number of extracted genes:"
awk '$3 == "gene" { print $0 }' ${data_dir}/${orig_gff} | wc -l
GFFutils number of extracted genes:
79030

awk number of extracted genes:
79030

Extract gene ids for batch submission to UniProt

In [11]:
%%bash
cd "${analysis_dir}"
awk -F"," '{print $4}' "${gtf_extractor_output}" > "${gene_list}"

Check gene list

In [12]:
%%bash
cd "${analysis_dir}"
head "${gene_list}"
106560212
106607996
106601976
106560213
106566220
106571988
106578259
106583877
106589664
106596642

Batch submission to UniProt

Perl script obtained from UniProt: https://www.uniprot.org/help/api_batch_retrieval

Modified to map NCIB gene ID to UniProt accession.

In [13]:
%%bash
# Print the script for viewing
cat /home/samb/programs/uniprot_mapping.pl
use strict;
use warnings;
use LWP::UserAgent;

my $list = $ARGV[0]; # File containg list of UniProt identifiers.

my $base = 'https://www.uniprot.org';
my $tool = 'uploadlists';

my $contact = '[email protected]'; # Please set a contact email address here to help us debug in case of problems (see https://www.uniprot.org/help/privacy).
my $agent = LWP::UserAgent->new(agent => "libwww-perl $contact");
push @{$agent->requests_redirectable}, 'POST';

my $response = $agent->post("$base/$tool/",
                            [ 'file' => [$list],
                              'format' => 'txt',
                              'from' => 'P_ENTREZGENEID',
                              'to' => 'ACC',
                            ],
                            'Content_Type' => 'form-data');

while (my $wait = $response->header('Retry-After')) {
  print STDERR "Waiting ($wait)...\n";
  sleep $wait;
  $response = $agent->get($response->base);
}

$response->is_success ?
  print $response->content :
  die 'Failed, got ' . $response->status_line .
    ' for ' . $response->request->uri . "\n";
In [16]:
%%bash
cd "${analysis_dir}"
time \
perl /home/samb/programs/uniprot_mapping.pl "${gene_list}" > "${perl_output}"
ls -ltrh

echo ""
echo ""
echo "--------------------------------------------------"
echo ""
echo "Line count:"
wc -l "${perl_output}"
total 354M
-rw-rw-r-- 1 samb samb 2.9M Jun  1 09:49 20210601_ssal_chrom-start-end-Dbxref.csv
-rw-rw-r-- 1 samb samb 772K Jun  1 09:58 20210601_ssal_gene-list.txt
-rw-rw-r-- 1 samb samb 350M Jun  1 10:04 20210601_ssal_uniprot_batch_results.txt


--------------------------------------------------

Line count:
7273462 20210601_ssal_uniprot_batch_results.txt
real	3m32.207s
user	0m3.099s
sys	0m9.446s

Check mapping output

In [17]:
%%bash
cd "${analysis_dir}"
head -n 30 "${perl_output}"
ID   A0A1S3NLH1_SALSA        Unreviewed;       218 AA.
AC   A0A1S3NLH1;
DT   12-APR-2017, integrated into UniProtKB/TrEMBL.
DT   12-APR-2017, sequence version 1.
DT   07-APR-2021, entry version 14.
DE   SubName: Full=fibroblast growth factor receptor 3-like {ECO:0000313|RefSeq:XP_014016259.1};
GN   Name=LOC106560212 {ECO:0000313|RefSeq:XP_014016259.1};
OS   Salmo salar (Atlantic salmon).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Actinopterygii; Neopterygii; Teleostei; Protacanthopterygii; Salmoniformes;
OC   Salmonidae; Salmoninae; Salmo.
OX   NCBI_TaxID=8030 {ECO:0000313|Proteomes:UP000087266, ECO:0000313|RefSeq:XP_014016259.1};
RN   [1] {ECO:0000313|RefSeq:XP_014016259.1}
RP   IDENTIFICATION.
RC   TISSUE=Muscle {ECO:0000313|RefSeq:XP_014016259.1};
RG   RefSeq;
RL   Submitted (OCT-2020) to UniProtKB.
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   RefSeq; XP_014016259.1; XM_014160784.1.
DR   GeneID; 106560212; -.
DR   KEGG; sasa:106560212; -.
DR   OrthoDB; 1497110at2759; -.
DR   Proteomes; UP000087266; Genome assembly.
DR   GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR   Gene3D; 2.60.40.10; -; 2.
DR   InterPro; IPR007110; Ig-like_dom.
DR   InterPro; IPR036179; Ig-like_dom_sf.

Parse out the stuff we want:

  • UniProt accession

  • Gene ID (NCBI gene ID)

  • Gene name/abbraviation

  • Gene description

  • GO terms

In [18]:
%%bash
cd "${analysis_dir}"
time \
while read -r line
do
  # Get record line descriptor
  descriptor=$(echo "${line}" | awk '{print $1}' )

  # Capture second field for evaluation
  go_line=$(echo "${line}" | awk '{print $2}')

  # Append GO IDs to array
  if [[ "${go_line}" == "GO;" ]]; then
    go_id=$(echo "${line}" | awk '{print $3}')
    go_ids_array+=("${go_id}")
  elif [[ "${go_line}" == "GeneID;" ]]; then
    # Uses sed to strip trailing semi-colon
    gene_id=$(echo "${line}" | awk '{print $3}' | sed 's/;$//')
  fi

  # Get gene description
  if [[ "${descriptor}"  == "DE" ]] && [[ "${go_line}"  == "SubName:" ]]; then
    # Uses sed to strip trailing spaces at end of line and remove commas
    gene_description=$(echo "${line}" | awk -F"[={]" '{print $2}' | sed 's/[[:blank:]]*$//' | sed 's/,//g')

  # Get gene name
  elif [[ "${descriptor}"  == "GN"  ]] && [[ $(echo "${line}" | awk -F "=" '{print $1}') == "GN   Name" ]]; then
    # Uses sed to strip trailing spaces at end of line
    gene=$(echo "${line}" | awk -F'Name=|{' '{print $2}' | sed 's/[[:blank:]]*$//')

  # Get UniProt accession
  elif [[ "${descriptor}"  == "AC" ]]; then
    # Uses sed to strip trailing semi-colon
    accession=$(echo "${line}" | awk '{print $2}' | sed 's/;$//')

  # Identify beginning on new record
  elif [[ "${descriptor}"  == "//" ]]; then

    # Prints other comma-separated variables, then GOID1;GOID2;GOIDn
    # IFS prevents spaces from being added between GO IDs
    # sed removes ";" after final GO ID
    (IFS=; printf "%s,%s,%s,%s,%s\n" "${accession}" "${gene_id}" "${gene}" "${gene_description}" "${go_ids_array[*]}" | sed 's/;$//')

    # Re-initialize variables
    accession=""  
    descriptor=""
    gene=""
    gene_description
    gene_id=""
    go_id=""
    go_ids_array=()
  fi


done < "${perl_output}" >> "${parsed_uniprot}"
IOPub data rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_data_rate_limit`.

Current values:
ServerApp.iopub_data_rate_limit=1000000.0 (bytes/sec)
ServerApp.rate_limit_window=3.0 (secs)

Despite notebook error message, if you check the time stamps on the files below, it looks like this took nearly 6.5hrs!!

Check parsed file

In [20]:
%%bash
cd "${analysis_dir}"
ls -ltrh
echo ""
head "${parsed_uniprot}"

echo ""
echo ""
echo "--------------------------------------------------"
echo ""
echo "Line count:"
wc -l "${parsed_uniprot}"
total 362M
-rw-rw-r-- 1 samb samb 2.9M Jun  1 09:49 20210601_ssal_chrom-start-end-Dbxref.csv
-rw-rw-r-- 1 samb samb 772K Jun  1 09:58 20210601_ssal_gene-list.txt
-rw-rw-r-- 1 samb samb 350M Jun  1 10:04 20210601_ssal_uniprot_batch_results.txt
-rw-rw-r-- 1 samb samb 8.0M Jun  1 16:31 20210601_ssal_accession-gene_id-gene-gene_description-go_ids.csv

A0A1S3NLH1,106560212,LOC106560212,fibroblast growth factor receptor 3-like,GO:0016021
A0A1S3SK04,106607996,LOC106607996,histone-lysine N-methyltransferase NSD2-like,GO:0005694;GO:0005634;GO:0018024;GO:0046872
A0A1S3RMY2,106601976,LOC106601976,fibroblast growth factor receptor 3-like,GO:0005524;GO:0004672
A0A1S3KV69,106560213,LOC106560213,phospholipase B1 membrane-associated-like,GO:0004620
A0A1S3LSJ1,106566220,LOC106566220,forkhead box protein I1c-like,GO:0005634;GO:0003700;GO:0043565
A0A1S3MPI8,106571988,LOC106571988,GDNF family receptor alpha-4-like,GO:0005886;GO:0038023
A0A1S3NLZ6,106578259,LOC106578259,attractin-like,
A0A1S3PJR5,106583877,LOC106583877,sodium bicarbonate transporter-like protein 11,GO:0016020;GO:0005452
A0A1S3QEI4,106589664,LOC106589664,G-protein coupled receptor 4-like,GO:0016021;GO:0004930
A0A1S3QYM9,106596642,LOC106596642,sodium bicarbonate transporter-like protein 11,GO:0016021;GO:0005452


--------------------------------------------------

Line count:
82393 20210601_ssal_accession-gene_id-gene-gene_description-go_ids.csv

Line count looks reasonable, as I know that some NCBI gene IDs are associated with multiple UniProt accessions, so we should end up with more results than were submitted.

Join parsed UniProt info with chromosome names

This will sort the both files on the columns with the NCBI gene ID for joining.

Then, it will replace the commas with tabs and re-order the columns so that the NCBI chromosome is in the first column.

In [22]:
%%bash
cd "${analysis_dir}"
join \
-t "," \
-1 4 \
-2 2 \
<(sort -t "," -k 4,4 "${gtf_extractor_output}")  \
<(sort -t "," -k2,2 "${parsed_uniprot}") \
| awk 'BEGIN {FS=","; OFS="\t"} {print $2, $1, $3, $4, $5, $6, $7, $8}' \
> "${joined_output}"
In [23]:
%%bash
cd "${analysis_dir}"
ls -ltrh

echo ""

echo "Line count:"
wc -l "${joined_output}"
total 372M
-rw-rw-r-- 1 samb samb 2.9M Jun  1 09:49 20210601_ssal_chrom-start-end-Dbxref.csv
-rw-rw-r-- 1 samb samb 772K Jun  1 09:58 20210601_ssal_gene-list.txt
-rw-rw-r-- 1 samb samb 350M Jun  1 10:04 20210601_ssal_uniprot_batch_results.txt
-rw-rw-r-- 1 samb samb 8.0M Jun  1 16:31 20210601_ssal_accession-gene_id-gene-gene_description-go_ids.csv
-rw-rw-r-- 1 samb samb  11M Jun  1 20:21 20210601_ssal_chrom-gene_id_start-end-acc-gene-gene_description-go_ids.csv

Line count:
82570 20210601_ssal_chrom-gene_id_start-end-acc-gene-gene_description-go_ids.csv

Hmmm, does this line count make sense?

Submitted to UniProt: 79030

Returned from UniProt: 82393

Joined: 82570

Look at the file. Columns will be tab-separated in this order:

| chromosome | NCBI gene ID | start | end | UniProt accession | gene abbreviation/name | gene description | GO IDs | |---|----|----|----|---|----|----|----|

In [24]:
%%bash
cd "${analysis_dir}"

head "${joined_output}"
NC_027327.1	100135779	7914675	7922535	Q7T2G8	fsh-R	neurexin-1a-like isoform X17	GO:0016323;GO:0016021;GO:0016020;GO:0004963;GO:0004996;GO:0032354;GO:0034699
NC_027321.1	100136349	24148576	24153099	Q8QHK5	dj-1	28S ribosomal protein S16 mitochondrial-like	GO:0045121;GO:0005886;GO:0006914;GO:0007338
NC_027321.1	100136351	63087382	63155499	Q2V2G8	RAF1c	Serine/threonine protein kinase RAF1c	GO:0005524;GO:0030553;GO:0106310;GO:0106311;GO:0035556
NC_027302.1	100136352	92389729	92396132	B5X240	ACTB	actin cytoplasmic 1 isoform X2	GO:0005856;GO:0097433;GO:0005925;GO:0005886
NC_027302.1	100136352	92389729	92396132	O42161	actb;	caskin-1-like	GO:0015629;GO:0005737;GO:0005634;GO:0005886;GO:0005524
NC_027318.1	100136353	42266727	42274733	O57560	LOC100136353	MBT domain-containing protein 1-like	GO:0005524;GO:0004550;GO:0006241;GO:0006183;GO:0006228
NC_027306.1	100136354	58238908	58240915	A0A1S2WYK4	LOC100136354	LIM domain only protein 3 isoform X1	GO:0005840;GO:0003735;GO:0006412
NC_027306.1	100136354	58238908	58240915	O57561	rpl18a;	LIM domain only protein 3 isoform X1	GO:0005840;GO:0003735;GO:0006412
NC_027321.1	100136355	8772597	8774381	A8YTA4	tshb	thyrotropin subunit beta precursor	GO:0005576;GO:0005179
NC_027321.1	100136355	8772597	8774381	O73824	tshb;	mitochondrial glutamate carrier 1-like isoform X1	GO:0005576;GO:0005179

Generate cheksums

Forgot to do this before closing notebook.

In [2]:
%%bash
cd "${analysis_dir}"

for file in *
do
  md5sum "${file}" | tee --append checksums.md5
done
e7d970782d7f531967dbfce01e5df549  20210601_ssal_accession-gene_id-gene-gene_description-go_ids.csv
5288ed387a6b1155cca11f25b9a9e3ca  20210601_ssal_chrom-gene_id_start-end-acc-gene-gene_description-go_ids.csv
f4182e5129978328b0e9ae2b07d0bbf7  20210601_ssal_chrom-start-end-Dbxref.csv
0d330da91260189090ba2fac1ca0340f  20210601_ssal_gene-list.txt
81f63345d2f2cfbabdc8d60c3326ba66  20210601_ssal_uniprot_batch_results.txt
In [ ]: