Create perl program

[vineetha]

Hi,

I have two sequence file.I want only the mathching sequences which is present on both files and save that output in third file...Can you please help me for creating perl program for this.??

FILE1:

>Contig1
TTCAAAAACTCATATGGGTGGTACAATGCGTCTTGGATCTAGGAGAACATATTTTCAAGTTGCAGATTGTAAATCTGCAAAATTATATGGTAACCAGAGCTTTGTAGATGAGAGGCATCGACACAGATATGAGGTGAACCCCGACATGGTGCAGC

>Contig2
GACTTGAAGATGCTGGTCTTTCTTTCACTGGCAAAGATGAAAGTGGTCATCGCATGGAGATTGTTGAGCTGCCGAGTCATCCTTACTTCATCGGAGTTCAATTTCATCCAGAATTTAAATCAAGGCCAGGAACCCCTTCAGCCCTGTTT

>Contig3
CTAGGACTTATAGCCGCAGCAACTGGGCAACTTGAAACTCTCTTGAAGAAGGGTGTTCCCAAAACATGGGGGTTGAGCAATGGTACGTCAGGACTAAAATCACATCGATATGTAAATGGGACAAAACTGTTTAATGGATCATTAGATG

>Contig4
GCATTTATTGCAATGGGAATGGTATACATGTTTAAAGGAAACAGTAACATATGTTGTGGGCGCTTGGCCCCGGATTTTTGATAATCAAATTTTGCTACTGCATTTTTTTTAAAG

>Contig5
CCCCCCCTTATTTGTCGTTTTTGATAATCAAATTTTGCTACTGCATTTTTTTTAAAG

FILE2:

>Contig1
TTCAAAAACTCATATGGGTGGTACAATGCGTCTTGGATCTAGGAGAACATATTTTCAAGTTGCAGATTGTAAATCTGCAAAATTATATGGTAACCAGAGCTTTGTAGATGAGAGGCATCGACACAGATATGAGGTGAACCCCGACATGGTGCAGC

>Contig3

CTAGGACTTATAGCCGCAGCAACTGGGCAACTTGAAACTCTCTTGAAGAAGGGTGTTCCCAAAACATGGGGGTTGAGCAATGGTACGTCAGGACTAAAATCACATCGATATGTAAATGGGACAAAACTGTTTAATGGATCATTAGATG

>Contig4
GCATTTATTGCAATGGGAATGGTATACATGTTTAAAGGAAACAGTAACATATGTTGTGGGCGCTTGGCCCCGGATTTTTGATAATCAAATTTTGCTACTGCATTTTTTTTAAAG

>Contig6
GCATTTATTGCAATGTTTTGATAATCAAATTTTGCTACTGCATTTTTTTTAAAGCCAGAGCTTTGTAGATGAGAGGCATGGTACAATGCGTCTTG

EXPECTED OUTPUT:

>Contig1
TTCAAAAACTCATATGGGTGGTACAATGCGTCTTGGATCTAGGAGAACATATTTTCAAGTTGCAGATTGTAAATCTGCAAAATTATATGGTAACCAGAGCTTTGTAGATGAGAGGCATCGACACAGATATGAGGTGAACCCCGACATGGTGCAGC

>Contig3
CTAGGACTTATAGCCGCAGCAACTGGGCAACTTGAAACTCTCTTGAAGAAGGGTGTTCCCAAAACATGGGGGTTGAGCAATGGTACGTCAGGACTAAAATCACATCGATATGTAAATGGGACAAAACTGTTTAATGGATCATTAGATG

>Contig4
GCATTTATTGCAATGGGAATGGTATACATGTTTAAAGGAAACAGTAACATATGTTGTGGGCGCTTGGCCCCGGATTTTTGATAATCAAATTTTGCTACTGCATTTTTTTTAAAG

[lindenb]

cross-posted : https://www.biostars.org/p/160027/

[GenoMax]

@vineetha: Are you looking to actually match the sequences or you just want to find matching headers? If a header matches then is the sequence always identical in both files?

[cmccabe]

@vineetha: Can awk be used to do this? A one-liner like below will work.

awk 'NR==FNR{a[$0];next}$0 in a{print $0}' file1.txt file2.txt
>Contig1
TTCAAAAACTCATATGGGTGGTACAATGCGTCTTGGATCTAGGAGAACATATTTTCAAGTTGCAGATTGTAAATCTGCAAAATTATATGGTAACCAGAGCTTTGTAGATGAGAGGCATCGACACAGATATGAGGTGAACCCCGACATGGTGCAGC

>Contig3
CTAGGACTTATAGCCGCAGCAACTGGGCAACTTGAAACTCTCTTGAAGAAGGGTGTTCCCAAAACATGGGGGTTGAGCAATGGTACGTCAGGACTAAAATCACATCGATATGTAAATGGGACAAAACTGTTTAATGGATCATTAGATG

>Contig4
GCATTTATTGCAATGGGAATGGTATACATGTTTAAAGGAAACAGTAACATATGTTGTGGGCGCTTGGCCCCGGATTTTTGATAATCAAATTTTGCTACTGCATTTTTTTTAAAG

The perl equivalent would be something like:

perl -ne 'print if ($seen{$_} .= @ARGV) =~ /10$/'  file1.txt file2.txt
>Contig1
TTCAAAAACTCATATGGGTGGTACAATGCGTCTTGGATCTAGGAGAACATATTTTCAAGTTGCAGATTGTAAATCTGCAAAATTATATGGTAACCAGAGCTTTGTAGATGAGAGGCATCGACACAGATATGAGGTGAACCCCGACATGGTGCAGC

>Contig3
CTAGGACTTATAGCCGCAGCAACTGGGCAACTTGAAACTCTCTTGAAGAAGGGTGTTCCCAAAACATGGGGGTTGAGCAATGGTACGTCAGGACTAAAATCACATCGATATGTAAATGGGACAAAACTGTTTAATGGATCATTAGATG
>Contig4
GCATTTATTGCAATGGGAATGGTATACATGTTTAAAGGAAACAGTAACATATGTTGTGGGCGCTTGGCCCCGGATTTTTGATAATCAAATTTTGCTACTGCATTTTTTTTAAAG