Surabhi Chaudhary
A Bioinformatician
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Perl script to extract lines with matching ids !!
By Surabhi Chaudhary 3076 days ago
#!/usr/bin/perl
use strict;
use warnings;
my %patterns;
#USAGE: perl extactByIds.pl Idsfile1 file2 > Result
# Open file and get patterns to search for
open(my $fh2,"<","$ARGV[0]")|| die "ERROR: Could not open file2";
while (<$fh2>)
{
chop;
$patterns{$_}=1;
}
# Now read data file
open(my $fh1,"<","$ARGV[1]")|| die "ERROR: Could not open file1";
while (<$fh1>)
{
# You might need to adjust this place according to your file type
#(undef,$srch,undef)=split;
my @ids=split (/\t/, $_);
print $_ if defined $patterns{$ids[0]};
}
