#!/usr/bin/perl
use strict;
use warnings;
my $qfn1 = "File1.txt";
my $qfn2 = "File2.txt";
my %positions;
{
open(my $fh, '<', $qfn1)
or die("Cannot open file \"$qfn1\": $!\n");
while (<$fh>) {
chomp; #line added
my ($key, $pos) = split /\s+/;
if (!$positions{$key}) {
$positions{$key} = [$pos];
} else {
my $ref = $positions{$key};
push @$ref,$pos;
}
}
}
my %sequences;
{
open(my $fh, '<', $qfn2)
or die("Cannot open file \"$qfn2\": $!\n");
my $key;
while (<$fh>) {
if ( s/^>// ) {
$key = ( split /\|/ )[1];
}
else {
chomp;
$sequences{$key} .= $_;
}
}
}
for my $key ( sort keys %positions ) {
my $ref = $positions{$key};
foreach my $value (@$ref) {
if ( ! exists( $sequences{$key} )) {
warn "KEY $key in File1 not found in File2\n";
next;
}
if ( length( $sequences{$key} ) < $positions{$key} ) {
warn "KEY $key: File2 string length too short for File1 positi
+on value\n";
next;
}
my $index = rindex( $sequences{$key}, "ATG", $positions{$key} );
if ( $index < 0 ) {
warn sprintf( "KEY %s: No ATG in File2 string prior to positio
+n %d\n",
$key, $positions{$key} );
next;
}
$index += 3 while ( ($index + 3) < $positions{$key} );
print "$key $positions{$key} " . substr($sequences{$key}, $index,
+3) . "\n";
}
}
My Input file look like this:-
File 1:-
155369268 17 A
155369268 60 C
269212605 49 G
File 2:-
>gi|155369268|ref|NM_001100917.1| some text
AAACAATGTCGATTCTATGATGCGAACGCAGCATTTCAGGGACTGGAATGGGAGCTTACGGTTTTTTACG
ACAGAATCATCAATATCTTGGAAGAAAAAGAATGTTAAGAAATAACAAAACAATAATTATTAAGTACTTT
>gi|155369268|ref|XM_001716884.1| some text
AGACAAGCTTGTCCTGATGTTCCTTGCCCTGGCAGATGTTCAGGACCATGGGAGCTTACGGTTTTTTACG
CTAAATGGCCCAAGCTTTCGGGGCTGTCATTGTCTGTTTGTCATTCAAGGGCCCAAGCTGAAGAGGGGGT
>gi|269212605|ref|XM_401716884.1| some text
AGACAAGCTTGTCCTGATGTTCCTTGCCCTGGCAGATGTTCAGGACCTTCCTTTGATTCAACCCTATGAC
CTAATTGGCCCAAGCTTTCGGGGCTGTCATTGTCTGTTTGTCATTCAAGGGCCCAAGCTGAAGAGGGGGT
|
