Perl : Join function and arrays

Question

I combined 2 sequence file, so I have 1 file with 2 sequences. I have split these 2 sequences into an @char array- because I later have to compare them character by character. 1 of the sequences, however is on two lines. I want to use the join function to combine the 2 lines but I don't know how to.

Ex:

seq 1

ACGTATATATTATATCTGGCGCTATCGATGCTATCGAT
CGATGCGCG

seq 2

AGTGAGCGTAGCTAGCGGCGCGATCTAGCTA

my code so far

#!usr/bin/perl
use strict;
use warnings;

# open file 1
open (my $seq1, "<", "file1.fa") or die $!;
# open file 2
open (my $seq2, "<", "file2.fa") or die $!;
# open combined file
open (my $combined, ">", "combined.txt") or die $!;

# read file 1, skip header line, write to combined file
while (my $line = <$seq1>) {
        if($line =~ />/) {
                next;
}

        else {
        print $combined "$line\n";
}
}
# read file 2, skip header line, write to combined file on new line
while (my $line2 = <$seq2>) {
        if ($line2 =~ />/) {
                next;
}
        else {
        print $combined "$line2\n";
}
}
# need to open combined file for reading
open (my $combined2, "<", "combined.txt") or die $!;
# read through combined file line by line
while (my $seqs = <$combined2>) {
        chomp($seqs);
# split sequences into characters
        my @chars = split(//, $seqs);
# the sequence from file1 is on 2 separate lines. Need to join these
# lines together

How do you know when to join the sequences? How do you know they are broken between two lines and need to be combined? — Glenn
– Glenn, Commented Feb 19, 2013 at 5:55

Kenosis · Accepted Answer · 2013-02-19 07:01:25Z

Consider using Bio::SeqIO to read your fasta files, as it can handle a sequence that's on multiple lines:

use strict;
use warnings;
use Bio::SeqIO;

my $in = Bio::SeqIO->new( -file => "file1.fa", '-format' => 'Fasta' );

while ( my $seq = $in->next_seq ) {
    my $sequence = $seq->seq;
    print $sequence, "\n";
}

Contents of file1.fa:

>seq0
FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKF
>seq1
KYRTWEEFTRAAEKLYQADPMKVRVVLKYRHCDGNLCIKVTDDVVCLLYRTDQAQDVKKIEKFHSQLMRLME
LKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
>seq2
EEYQTWEEFARAAEKLYLTDPMKVRVVLKYRHCDGNLCMKVTDDAVCLQYKTDQAQDVKKVEKLHGK
>seq3
MYQVWEEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVCLQYKTDQAQDVK

Output:

FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKF
KYRTWEEFTRAAEKLYQADPMKVRVVLKYRHCDGNLCIKVTDDVVCLLYRTDQAQDVKKIEKFHSQLMRLMELKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
EEYQTWEEFARAAEKLYLTDPMKVRVVLKYRHCDGNLCMKVTDDAVCLQYKTDQAQDVKKVEKLHGK
MYQVWEEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVCLQYKTDQAQDVK

Sahil M · Accepted Answer · 2013-09-18 11:41:58Z

I am assuming that your sequences are separated by a ">" sign, and that is why you have used the if($_ =~ />/) as a skipper. If it is not, comment back and I'll change the code. Here try the following:

open (fil1, "<", "file1.fa") or die $!;
# open file 2
open (fil2, "<", "file2.fa") or die $!;
# open combined file
open (combined, ">", "combined.txt") or die $!;

# read file 1, skip header line, write to combined file
while (<fil1>) {
        if($_ =~ />/) {
                print $combined "\n";
}

        else {
        print $combined "$line";
}
}
# read file 2, skip header line, write to combined file on new line
while (<fil2>) {
        if ($_ =~ />/) {
                print $combined "\n";
}
        else {
        print $combined "$line2";
}
}

Just check out combined.txt, if there are sequences on different lines.

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