13) Perl script for splitting a fasta file into several small files

This script splits a fasta file into several small fasta files, according to the specified number of sequences in each file. Upon execution, users have to input the original fasta file name (without .fasta extension) and to specify the intended number of sequences in each file.

Output: A chomped fasta file (xxx_chomped.fasta) will be produced and the small fasta files will be named as (xxx_1.fasta, xxx_2.fasta etc)

Note: Each subroutine can be run independently as a perl script by cutting and paste into another .pl file and removing the lines sub xxx { and }. If users do not want to run all of the sub-routines, just comment out those that you don't want to run, e.g. #split_fasta();

#! /usr/bin/perl

print "Please enter filename (without extension): ";

$input = <>;

chomp ($input);

print "Please enter no. of sequences you want in each file ";

$upper_limit = <>+1;

chomp ($upper_limit);

chomp_fasta();

split_fasta();

#--------------------------------------------------------------------------------

# chomp_fasta: Merges all the sequence lines in a fasta file into one line, so

#              each sequence in the fasta file will have one header line and 

#              one sequence line only

#--------------------------------------------------------------------------------

sub chomp_fasta {

open (INFILE, "$input.fasta") or die "Cannot open infile!";

open (OUT, ">"."$input"."_chomped.fasta") or die "Cannot open outfile!";

while ($line=<INFILE>) { # Please remove the spaces

if ($line=~/>/) {

print OUT "\n$line";

}

else {

chomp ($line);

print OUT "$line";

}

}

close OUT;

}

#--------------------------------------------------------------------------------

# split_fasta: Splits a fasta file into several small files according to the 

#              specified no. of sequences in each file

#--------------------------------------------------------------------------------

sub split_fasta {

$count = 0;

$number = 1;

open (INFILE, "$input"."_chomped.fasta") or die "Cannot open infile!";

open (OUT, ">"."$input"."_"."$number".".fasta") or die "Cannot open outfile!";

while ($line=<INFILE>) {

if ($line=~/>/) {

$count++;

if ($count==1) {

print OUT "$line";

}

elsif ($count<$upper_limit) { #change this value to change upper limit

print OUT "\n$line";

}

}

else {

chomp ($line);

print OUT "$line";

}

#--------------------------------------------------------------------------------

# Note: The header >xxx when $count=3 has already been evaluated in the previous

#       regex loop but is not printed out. So this if loop must print out the

#       header >xxx in a new file manually and reset the count back to 1 instead

#       of 0 

#--------------------------------------------------------------------------------

if ($count==$upper_limit) { #change this value to change upper limit

close OUT;

$number++;

open (OUT, ">"."$input"."_"."$number".".fasta") or die "Cannot open outfile!";

print OUT "$line";

$count = 1;

}

}

}