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Loop with Perl (string search)

 
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# 1  
Old 03-22-2016
Loop with Perl (string search)
I am using a perl script to reverse and complement sequences if a string is found. The script works as expected as standalone but I would like to use it in my bash file. However, I am not getting my expected result.
My test.txt file
Code:
>Sample_72
CCCCTCGCGACCTGGATGTGTCGGCGTTTGTCATGTTTTCGTCGATGGCCGGGCTGGTCGGATCGTCSREVERGGGCCAGGCCAAAA
>Sample_2
CCCCTCGCGAJOHNCCTGGATGTGTCGGCGTTTGTCATGTTTTCGTCGATGGCCGGGCTGGTCGGATCGTCSREVERGGGCCAGGCCAAAA

Standalone Perl script:
Code:
perl -ple '/JOHN/ and y/ACGT/TGCA/ and $_ = reverse unless /^>/' test.txt

I get the expected output:
Code:
>Sample_72
CCCCTCGCGACCTGGATGTGTCGGCGTTTGTCATGTTTTCGTCGATGGCCGGGCTGGTCGGATCGTCSREVERGGGCCAGGCCAAAA
>Sample_2
TTTTGGCCTGGCCCREVERSGACGATCCGACCAGCCCGGCCATCGACGAAAACATGACAAACGCCGACACATCCAGGNHOJTCGCGAGGGG

Bash file:
Code:
#!/bin/bash
Primers=( NULL 'JOHN' )
for y in {1..1}
do
	perl -ple '/${Primers[$y]}/ and y/ACGT/TGCA/ and $_ = reverse unless /^>/' test.txt
done

Unexpected output:
Code:
>Sample_72
TTTTGGCCTGGCCCREVERSGACGATCCGACCAGCCCGGCCATCGACGAAAACATGACAAACGCCGACACATCCAGGTCGCGAGGGG
>Sample_2
TTTTGGCCTGGCCCREVERSGACGATCCGACCAGCCCGGCCATCGACGAAAACATGACAAACGCCGACACATCCAGGNHOJTCGCGAGGGG

in the bash file, the script reverses and complements the sequences regardless of the presence or absence of the string (JOHN)
I guess I still do not understand the proper use of slashes
# 2  
Old 03-23-2016
try:
Code:
#!/bin/bash
Primers=( NULL 'JOHN' )
for y in {1..1}
do
        perl -ple '/'"${Primers[$y]}"'/ and y/ACGT/TGCA/ and $_ = reverse unless /^>/' test.txt
done

Last edited by rdrtx1; 03-23-2016 at 12:33 AM..
This User Gave Thanks to rdrtx1 For This Post:
Xterra
# 3  
Old 03-23-2016
The single quotes prevent the shell from expanding the shell array variable ${Primers[$y]}.
You can try:
Code:
perl -ple "/${Primers[$y]}/"' and y/ACGT/TGCA/ and $_ = reverse unless /^>/' test.txt

or pass the variable:
Code:
perl -sple '$_=~$match and y/ACGT/TGCA/ and $_ = reverse unless /^>/' -- -match="${Primers[$y]}"

--
Note that repeatedly calling an external program, like awk or perl from inside a shell loop is less efficient and detrimental to performance. It could be done more efficiently by looping inside these programs themselves...
# 4  
Old 03-23-2016
Thanks a lot!
# 5  
Old 03-23-2016
Quote:
Originally Posted by rdrtx1
try:
Code:
#!/bin/bash
Primers=( NULL 'JOHN' )
for y in {1..1}
do
        perl -ple '/'${Primers[$y]}'/ and y/ACGT/TGCA/ and $_ = reverse unless /^>/' test.txt
done

Note that by doing this anything that is in ${Primers[$y]} will be unprotected by quotes from the shell and will be subject to field splitting an globbing..

To illustrate (in an empty directory):
Code:
$ touch foo bar
$ var="a   b*"
$ echo "$var"
a   b*
$ echo ''$var''
a bar

Last edited by Scrutinizer; 03-23-2016 at 12:42 AM..
# 6  
Old 03-23-2016
Hi Xterra,

Perl is worthwhile to learn, especially if you are working with scientific data like fasta files. It does not require the help of the shell to do, efficiently, what it is required.
If you were to share a bit more of the "big picture" of what you are trying to do as a whole, maybe we could help you to just use Perl, instead.
# 7  
Old 03-23-2016
Aia
Thanks! I am chasing genes. I sequenced whole genomes and built large contigs (Example.txt). I am fishing out the contigs (sequences with > as identifiers) containing the genes of interest using conserved DNA stretches (Bait). Then, I am trimming the sequences using conserved flanking regions (Primers) to keep exclusively the nucleotide sequences coding for those genes (Gene). The sequences can be in the right direction (forward) or reversed (antisense), depending on the raw sequences generated by our MySeq sequencer. I am using a modified version of your perl one-liner script to determine if the sequence is forward or reverse (the script in this thread). If the sequence is in the right direction nothing is done; however, if the sequence is in the opposite direction, your script will reverse and complement it, outputting a forward sequence every time. Then I just proceed to name the sequence and files. Thus, this bash script outputs four different genes from the original fasta file.
My bash file is complete and working like a charm but I am interested in learning better ways to use awk and/or perl to improve my script
Thanks!
PS. My Example.txt file was trimmed to fit the size limit.
MyBash.txt.txt (1.6 KB) 
Example.txt (2.60 MB) 
 
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