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#!/usr/bin/perl
#
# weedMaf remove only-gap columns from a multiple alignment in MAF format
#
# input file format:
#
# a score=5037
# s chlamy4.chromosome10 5424 36280 + 6579462 ATCA-CCACAG--ACC...
# s volvox.scaffold_9 2188403 51128 + 9999999 ACCA-CCACGGGCACC...
#
#
# 10.03.2013, Mario Stanke, mario.stanke@uni-greifswald.de
use strict;
use Getopt::Long;
my @alirows; # array of all alignment rows (including gaps)
my @alidata; # array of everying up to alignment rows
my $help = 0;
my $len;
GetOptions('help!'=>\$help);
exec("perldoc $0") if ($help);
while (<>) {
if (!/^s\s/){
my $line = $_;
if (@alirows){
weed();
@alidata = @alirows = ();
}
print $line;
} elsif (/(^s\s.*\s)(\S+)$/){
push @alidata, $1;
push @alirows, $2;
}
}
if (@alirows){
weed();
}
sub weed{
$len = length($alirows[0]);
my $k = @alirows;
my @newalirows = ();
foreach my $alirow (@alirows){
if (length($alirow) != $len){
die ("Inconsistent alignment lengths");
}
push @newalirows, "";
}
for (my $i=0; $i<$len; $i++){
my $onlygaps = 1;
for (my $j=0; $j<@alirows && $onlygaps; $j++){
if (substr($alirows[$j], $i, 1) ne '-'){
$onlygaps = 0;
}
}
if (!$onlygaps){
for (my $j=0; $j<@alirows; $j++){
$newalirows[$j] .= substr($alirows[$j], $i, 1);
}
}
}
for (my $j=0; $j<@alirows; $j++){
print $alidata[$j] . $newalirows[$j] . "\n";
}
}
__END__
=head1 NAME
weedMaf.pl remove only-gap columns from a multiple alignment in MAF format
=head1 SYNOPSIS
weedMaf.pl < in.maf > out.maf
=cut
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