Do multiple capture groups in an array, but only respond to one group
I am trying to do a simple modification of some existing code without much luck, I want to migrate one additional capture group from FILE1: $ 2 before comparing the $ 1 as usual with the data in FILE2 and print both if a successful match occurs, Please keep an answer similar to my attempt if possible so I can understand the changes.
FILE1 data:
abc 99269 +t
abc 550 -a
abc 100 +a
gdh 126477 +t
hduf 1700 +c
FILE2 data:
517 1878 forward
2156 3289 forward
99000 100000 forward
22000 23000 backward
999555 999999 backward
Desired output:
99269 +t 99000 100000 forward
550 -a 517 1878 forward
1700 +c 517 1878 forward
Code:
#!/usr/bin/perl
use strict;
use warnings;
use autodie;
my $outputfile = "/Users/edwardtickle/Documents/CC22CDSpositive.txt";
open FILE1, "/Users/edwardtickle/Documents/CC22indelscc.txt";
open FILE2, "/Users/edwardtickle/Documents/CDS_rmmge.CC22.CORE.aln";
open (OUTPUTFILE, ">$outputfile");
my @file1list=();
my @indels=();
while (<FILE1>) {
if (/^\S+\s+(\d+)\s+(\S+)/) {
push @file1list, $1;
push @indels, $2;
}
}
close FILE1;
while ( my $line = <FILE2> ) {
if ($line =~ /^>\S+\s+\S+\s+(\d+)\s+(\d+)\s+(\S+)/) {
my $cds1 = $1;
my $cds2 = $2;
my $cds3 = $3;
for my $cc22 (@file1list) {
for my $indel (@indels) {
if ( $cc22 > $cds1 && $cc22 < $cds2 ) {
print OUTPUTFILE "$cc22 $indel $cds1 $cds2 $cds3\n";
}
}
}
}
}
close FILE2;
close OUTPUTFILE;
Thanks in advance!
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1 answer
It's frustrating that you don't seem to learn from many of the solutions and tips that are given to you.
Here's a program that will do as you ask.
use strict;
use warnings;
use 5.010;
use autodie;
chdir '/Users/edwardtickle/Documents';
open my $fh, '<', 'CDS_rmmge.CC22.CORE.aln';
my @file2;
while (<$fh>) {
next unless /\S/;
push @file2, [ split ];
}
open my $out, '>', 'CC22CDSpositive.txt';
open $fh, '<', 'CC22indelscc.txt';
while (<$fh>) {
my @line1 = split;
for my $line2 (@file2) {
if ( $line1[1] >= $line2->[0] and $line1[1] <= $line2->[1] ) {
my @out = ( @line1[1,2], @$line2 );
print $out "@out\n";
last;
}
}
}
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