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#!/usr/bin/perl
#Copyright (C) 2006-2008 Keio University
#(Kris Popendorf) <comp@bio.keio.ac.jp> (2006)
#
#This file is part of Murasaki.
#
#Murasaki is free software: you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation, either version 3 of the License, or
#(at your option) any later version.
#
#Murasaki is distributed in the hope that it will be useful,
#but WITHOUT ANY WARRANTY; without even the implied warranty of
#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#GNU General Public License for more details.
#
#You should have received a copy of the GNU General Public License
#along with Murasaki. If not, see <http://www.gnu.org/licenses/>.
use File::Basename;
use Getopt::Long;
use Pod::Usage;
use Roman;
BEGIN {
unshift(@INC,(fileparse($0))[1].'perlmodules');
}
use Murasaki;
my $forceRoman;
my $noRoman;
GetOptions('help|?' => \$help, man => \$man, 'output=s' => \$outfile, 'sortall' => \$sortall,
'noroman'=>\$noRoman,'roman'=>\$forceRoman);
pod2usage(1) if $help or $#ARGV<1;
pod2usage(-exitstatus => 0, -verbose => 2) if $man;
my $geneparse="$root/geneparse";
$geneparse="$root/geneparse.pl" unless -x $geneparse;
$geneparse=`geneparse.pl` unless -x $geneparse;
if(!$outfile){ #not yet specified by getopt
$outfile=shift(@ARGV); #snag first arg
}
foreach $arg (@ARGV){
die "File not found: $arg" if !-e $arg;
die "File not readable: $arg" if !-R $arg;
if(-d $arg) { #directory parsing mojo
print "Reading directory: $arg\n";
chop($arg) if $arg=~m!/$!; #chomp final / if there is one
opendir(DIR,$arg);
@files=grep {!/^\.|~$|^#.*#$|\.sml$|^README|\.stitch$|\.bin|\.p?hmask$/ and -T "$arg/$_"} readdir(DIR);
@files=sort chrNameCmp @files;
push(@srcfiles,map {"$arg/$_"} @files);
closedir(DIR);
}if(-r $arg) {
push(@srcfiles,$arg);
}else{
die "Can't read file: $arg";
}
}
$noRoman=grep {numbered($_)=~m/\d+/} @srcfiles unless $forceRoman;
@srcfiles=sort chrNameCmp @srcfiles if $sortall;
open(OUTF,">$outfile");
$pos=1;
foreach $file (@srcfiles){
$length=genomeLength($file);
print OUTF join("\t",$file,$length,$pos,$pos+$length)."\n";
$pos+=$length+10;
}
sub chrNameCmp {
my ($ca,$cb)=(map {numbered($_)} $a,$b);
my ($na,$nb)=(chrNum($ca),chrNum($cb));
return -1 if $na and !$nb;
return 1 if $nb and !$na;
return $na<=>$nb unless !($ca<=>$b);
return $ca cmp $cb; #last resort is lexical compare
}
sub parseEnsemblName {
my ($file)=@_;
my ($filename,$dir)=fileparse($file);
my ($species,$assembly,$release,$type,$chrom,$gz)=($filename=~m/([^.]+)\.(.+)\.(\d+)\.(dna(?:_rm)?)\.chromosome\.([^.]+)\.fa(\.gz)?/) or return undef;
return {file=>$filename,
species=>$species,
assembly=>$assembly,
release=>$release,
type=>$type,
chrom=>$chrom,
compressed=>$gz};
}
sub chrNum {
my ($chrom)=@_;
return arabic($chrom) if !$noRoman and isroman($chrom);
return $1 if $chrom=~m/^(\d+)/;
}
sub numbered {
local $_=pop;
my $ensembl=parseEnsemblName($_);
return $ensembl->{chrom} if parseEnsemblName($_);
return $1 if m/(\d+)(?:\.[a-zA-Z]+)+?$/;
return $1 if m/chr(?:omosome)(?:\W)*([ivxIVX0-9]+)/;
return undef;
}
sub genomeLength {
$file=pop;
print $indent."Finding length of $file ...\n";
# print $indent."Command: $geneparse -c -l $file\n";
open(PARSE,"-|","$geneparse -c -l $file");
$seq=<PARSE>;
close(PARSE);
chomp($seq); #thou beist an int!
return $seq; #omph
}
__END__
=head1 NAME
chromostitch.pl - Makes stitch files for feeding to geneparse.pl to allow feeding of multiple chromosomes to programs like murasaki
=head1 SYNOPSIS
chromostitch.pl [options] <stitch file> <chromosome1 chromosome2 ... >
=item Options:
=item --sort sorts everything
=item --output=<file> altnerate way of specifying an output file
=head1 PARAMETERS
=over 8
=item B<stitch file>
output file (overwrites)
=item B<chromosome1 chromosome2 ...>
List of chromosome input files
=item B--output=<file>
Alternate way of specifying an output file
=item B--sort
Always sort EVERYTHING. (Allows for nicely sorted lists from sloppy input
of filenames from like multiple directories of *.gbk or something)
=back
=head1 DESCRIPTION
Makes stitch files for feeding to geneparse.pl to allow feeding of multiple chromosomes to programs like murasaki
=cut
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