Using awk to extract two separate strings - bash

Question

MacOS, Unix
So I have a file in the following stockholm format:
# STOCKHOLM 1.0
#=GS WP_002855993.1/5-168 DE [subseq from] MULTISPECIES: AAC(3) family N-acetyltransferase [Campylobacter]
#=GS WP_002856586.1/5-166 DE [subseq from] MULTISPECIES: aminoglycoside N(3)-acetyltransferase [Campylobacter]
WP_002855993.1/5-168 ------LEHNGKKYSDKDLIDAFYQLGIKRGDILCVHTELmkfgKALLT.K...NDFLKTLLECFFKVLGKEGTLLMP-TF---TYSF------CKNE------VYDKVHSKG--KVGVLNEFFRTSGgGVRRTSDPIFSFAVKGAKADIFLKEN--SSCFGKDSVYEILTREGGKFMLLGLNYG-HALTHYAEE-----
#=GR WP_002855993.1/5-168 PP ......6788899999***********************9333344455.6...8999********************.33...3544......4555......799999975..68********98626999****************999865..689*********************9875.456799996.....
WP_002856586.1/5-166 ------LEFENKKYSTYDFIETFYKLGLQKGDTLCVHTEL....FNFGFpLlsrNEFLQTILDCFFEVIGKEGTLIMP-TF---TYSF------CKNE------VYDKINSKT--KMGALNEYFRKQT.GVKRTNDPIFSFAIKGAKEELFLKDT--TSCFGENCVYEVLTKENGKYMTFGGQG--HTLTHYAEE-----
#=GR WP_002856586.1/5-166 PP ......5566677788889999******************....**9953422246679*******************.33...3544......4455......799998876..589**********.******************99999886..689******************999765..5666***96.....
#=GC PP_cons ......6677788899999999*****************9....77675.5...68889*******************.33...3544......4455......799999976..689*******998.8999**************99999876..689******************9998765.466699996.....
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxx.x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
WP_002855993.1/5-168 -----------------------------------------------------------------------------------------------------
#=GR WP_002855993.1/5-168 PP .....................................................................................................
WP_002856586.1/5-166 -----------------------------------------------------------------------------------------------------
#=GR WP_002856586.1/5-166 PP .....................................................................................................
#=GC PP_cons .....................................................................................................
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
//
And I've created a script to extract the IDs I want, in this case, WP_002855993.1 and WP_002856586.1, and search through another file to extract DNA sequences with the appropriate IDs. The script is as follows:
#!/bin/bash
for fileName in *.sto;
do
protID=$(grep -o "WP_.\{0,11\}" $fileName | sort | uniq)
echo $protID
file=$(echo $fileName | cut -d '_' -f 1,2,3)
file=$(echo $file'_protein.faa')
echo $file
if [ -n "$protID" ]; then
gawk "/^>/{N=0}/^.*$protID/{N=1} {if(N)print}" $file >>
sequence_protein.file
fi
done
And here's an example of the type of file I'm looking through:
>WP_002855993.1 MULTISPECIES: AAC(3) family N-acetyltransferase [Campylobacter]
MKYFLEHNGKKYSDKDLIDAFYQLGIKRGDILCVHTELMKFGKALLTKNDFLKTLLECFFKVLGKEGTLLMPTFT
>WP_002856586.1 MULTISPECIES: aminoglycoside N(3)-acetyltransferase [Campylobacter]
MKYLLEFENKKYSTYDFIETFYKLGLQKGDTLCVHTELFNFGFPLLSRNEFLQTILDCFFEVIGKEGTLIMPTFT
YSFCKNEVYDKINSKTKMGALNEYFRKQTGVKRTNDPIFSFAIKGAKEELFLKDTTSCFGENCVYEVLTKENGKY
>WP_002856595.1 MULTISPECIES: acetyl-CoA carboxylase biotin carboxylase subunit [Campylobacter]
MNQIHKILIANRAEIAVRVIRACRDLHIKSVAVFTEPDRECLHVKIADEAYRIGTDAIRGYLDVARIVEIAKACG
This script works if I have one ID, but in some cases I get two IDs, and I get an error, because I think it's looking for an ID like "WP_002855993.1 WP_002856586.1". Is there a way to modify this script so it looks for two separate occurrences? I guess it's something with the gawk command, but I'm not sure what exactly. Thanks in advance!

Answer 1

an update to the original script:
#!/usr/bin/env bash
for file_sto in *.sto; do
file_faa=$(echo $file_sto | cut -d '_' -f 1,2,3)
file_faa=${file_faa}"_protein.faa"
awk '(NR==FNR) { match($0,/WP_.\{0,11\}/);
if (RSTART > 0) a[substr($0,RSTART,RLENGTH)]++
next; }
($1 in a){ print RS $0 }' $file_sto RS=">" $file_faa >> sequence_protein.file
done
The awk part can probably even be reduced to :
awk '(NR==FNR) { if ($0 ~ /^WP_/) a[$1]++; next }
($1 in a) { print RS $0 }' FS='/' $file_sto FS=" " RS=">" $file_faa
This awk script does the following:
Set the field separator FS to / and read file $file_sto.
When reading $file_sto the record number NR is the same as the file record number FNR.
(NR==FNR) { if ($0 ~ /^WP_/) a[$1]++; next }: this line works only one $file_sto due to the condition in the front. It checks if the line starts with WP_. If it does, it stores the first field $1 (separated by FS which is a /) in an array a; it then skips to the next record in the file (next).
If we finished reading file $file_sto, we set the field separator back to a single space FS=" " (see section Regular expression) and the record separator RS to > and start reading file $file_faa The latter implies that $0 will contain all lines between > and the first field $1 is the protID.
Reading $file_faa, the file record number FNR is restarted from 1 while NR is not reset. Hence the first awk line is skipped.
($1 in a){ print RS $0 } if the first field is in the array a, print the record with the record separator in front of it.
fixing the original script:
If you want to keep your original script, you could store the protID in a list and then loop the list :
#!/bin/bash
for fileName in *.sto; do
protID_list=( $(grep -o "WP_.\{0,11\}" $fileName | sort | uniq) )
echo ${protID_list[#]}
file=$(echo $fileName | cut -d '_' -f 1,2,3)
file=$(echo $file'_protein.faa')
echo $file
for protID in ${protID_list[#]}; do
if [ -n "$protID" ]; then
gawk "/^>/{N=0}/^.*$protID/{N=1} {if(N)print}" $file >>
sequence_protein.file
fi
done
done

Answer 2

Considering your output file is test.
Using following command gives you only file names:
>>cat text | awk '{print $1}' | grep -R 'WP*' | cut -d":" -f2
gives me output:
WP_002855993.1/5-168
WP_002856586.1/5-166
WP_002855993.1/5-168
WP_002856586.1/5-166
Do you want output like that?