Extract specific FASTA sequences from a file using Perl - perl

Question

I have written a Perl script to retrieve a hypothetical protein list from a FASTA file. I'm able to get only the header line with all hypothetical proteins, but I want to have all the sequences along with protein IDs.
The script is as follows.
#!/usr/bin/perl
use strict;
use warnings;
my $line;
open $fh, '<', '/home/Desktop/hypo_proteins/testprotein.fasta' or die "Cannot open file $fh, $!";
open OUT, ">output.txt";
while ( $line = <$fh> ) {
chomp $line;
if ( $line =~ /hypothetical protein/ ) {
print OUT "$line\n";
}
}
close $fh;
The output the I got from the above script is as follows
>gi|113461928|ref|YP_718205.1| hypothetical protein HS_1792 [Haemophilus somnus 129PT]
>gi|113460158|ref|YP_718214.1| hypothetical protein HS_0009 [Haemophilus somnus 129PT]
>gi|113460165|ref|YP_718221.1| hypothetical protein HS_0016 [Haemophilus somnus 129PT]
But I need the output as follows:
>gi|113461928|ref|YP_718205.1| hypothetical protein HS_1792 [Haemophilus somnus 129PT]
MFKSLIQFFKSKSNTSNIKKENAVQRQERQDIEGWITPYSGQELLNTELRQHHLGLLWQQVSMTREMFEH
LYQKPIERYAEMVQLLPASESHHHSHLGGMLDHGLEVISFAAKLRQNYVLPLNAAPEDQAKQKDAWTAAV
IYLALVHDIGKSIVDIEIQLQDGKRWLAWHGIPTLPYKFRYIKQRDYELHPVLGGFIANQLIAKETFDWL
ATYPEVFSALMYAMAGHYDKANVLAEIVQKADQNSVALALGGDITKLVQKPVISFAKQLILALRYLISQK
FKISSKGPGDGWLTEDGLWLMSKTTADQIRAYLMGQGISVPSDNRKLFDEMQAHRVIESTSEGNAIWYCQ
LSADAGWKPKDKFSLLRIKPEVIWDNIDDRPELFAGTICVVEKENEAEEKISNTVNEVQDTVPINKKENI
ELTSNLQEENTALQSLNPSQNPEVVVENCDNNSVDFLLNMFSDNNEQQVMNIPSADAEAGTTMILKSEPE
NLNTHIEVEANAIPKLPTNDDTHLKSEGQKFVDWLKDKLFKKQLTFNDRTAKVHIVNDCLFIVSPSSFEL
YLQEKGESYDEECINNLQYEFQALGLHRKRIIKNDTINFWRCKVIGPKKESFLVGYLVPNTRLFFGDKIL
INNRHLLLEE

Answer 1

This will do as you ask
#!/usr/bin/perl
use strict;
use warnings;
use constant INPUT => '/home/Desktop/hypo_proteins/testprotein.fasta';
use constant OUTPUT => 'output.txt';
open my $in_fh, '<', INPUT or die "Cannot open input file: $!";
open my $out_fh, '>', OUTPUT or die "Cannot open output file: $!";
select $out_fh;
my $print;
while ( <$in_fh> ) {
if ( /^>/ ) {
$print = /hypothetical protein/;
}
print if $print;
}
Regarding your (deleted) question about this solution, it uses the implicit variable $_ in several places. It is equivalent to this program
#!/usr/bin/perl
use strict;
use warnings;
use constant INPUT => '/home/Desktop/hypo_proteins/testprotein.fasta';
use constant OUTPUT => 'output.txt';
open my $in_fh, '<', INPUT or die "Cannot open input file: $!";
open my $out_fh, '>', OUTPUT or die "Cannot open output file: $!";
select $out_fh;
my $print;
while ( defined( $_ = <$in_fh>) ) {
if ( $_ =~ /^>/ ) {
$print = ( $_ =~ /hypothetical protein/ );
}
print $_ if $print;
}
So I hope you can see that $print = $_ =~ /hypothetical protein/ checks whether the current line (in $_) contains the string hypothetical protein and sets $print to a true value if so.
Because $print is defined outside the loop it keeps its value across iterations of the loop, and as you can see it is only changed on header lines, when the current line begins with >, and will stay true until the next header line, so that print if $print will output the header containing hypothetical protein and all following lines until the next header
I hope that helps