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#!/usr/bin/perl
#
# splitMfasta.pl
# split a multiple fasta file in smaller multiple fasta files
#
# This script is used by the braker.pl pipeline.
# Please be extremely careful when changing this script because the braker.pl
# pipeline may fail upon custom modification of this script.
# In case of doubt, contact katharina.hoff@uni-greifswald.de
#
# Mario Stanke, 2.04.2007, last modification by Katharina J. Hoff on Feb 21st 2018
#
#
use strict;
use Getopt::Long;
use File::Basename qw(basename);
use File::Spec::Functions qw(rel2abs);
my $usage = "$0 -- split a multiple fasta file in smaller multiple fasta files.\n\n";
$usage .= "Usage: $0 input.fa\n\n";
$usage .= "parameters:\n";
$usage .= "--minsize=n each split output fasta file total to at least this man base pairs.\n";
$usage .= " set this to 0 to split the input in single sequence files.\n";
$usage .= "--outputpath=s prefix to output path. Output files are\n";
$usage .= " s/input.split.1.fa\n";
$usage .= " s/input.split.2.fa\n";
$usage .= " s/input.split.3.fa\n";
$usage .= " ... \n";
$usage .= "\n";
if (@ARGV < 1) {
print $usage;
exit;
}
my ($seqfilename, $minsize, $outputpath,$cursize, $idx, $basename);
my $minsize = 0;
my $outputpath = "";
GetOptions('minsize:i'=>\$minsize,
'outputpath:s'=>\$outputpath);
$seqfilename = $ARGV[0];
if($outputpath =~ /^~/){
my $HOME = $ENV{'HOME'};
$outputpath=~s/~/$HOME/;
}
$outputpath=rel2abs($outputpath);
if ($outputpath ne "" && $outputpath !~ /\/$/){
$outputpath .= "/";
}
open(SEQ, "<$seqfilename") or die ("Could not open $seqfilename");
$idx=0;
$cursize=0;
my $basename = basename($seqfilename);
$basename =~ s/(\.fa|\.fna|\.fasta)$//;
while (<SEQ>) {
if ($idx == 0 || $cursize > $minsize && /^>/){
$idx++;
if ($idx > 1) {
close(SPLIT);
}
open (SPLIT, ">$outputpath$basename.split.$idx.fa") or die ("Could not open $basename.split.$idx.fa");
$cursize = 0;
}
print SPLIT;
if (!/^>/) {
$cursize += (length $_) - 1;
}
}
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