Create a gist now

Instantly share code, notes, and snippets.

What would you like to do?
#!/usr/bin/perl -w
my $columns = 50;
my $gapped = 0;
my $progname = $0;
$progname =~ s/^.*?([^\/]+)$/$1/;
my $usage = "Usage: $progname [<Stockholm file(s)>]\n";
$usage .= " [-h] print this help message\n";
$usage .= " [-g] write gapped FASTA output\n";
$usage .= " [-s] sort sequences by name\n";
$usage .= " [-c <cols>] number of columns for FASTA output (default is $columns)\n";
# parse cmd-line opts
my @argv;
while (@ARGV) {
my $arg = shift;
if ($arg eq "-h") {
die $usage;
} elsif ($arg eq "-g") {
$gapped = 1;
} elsif ($arg eq "-s"){
$sorted = 1;
} elsif ($arg eq "-c") {
defined ($columns = shift) or die $usage;
} else {
push @argv, $arg;
}
}
@ARGV = @argv;
my @seqorder = ();
my %seq;
while (<>) {
next unless /\S/;
next if /^\s*\#/;
if (/^\s*\/\//) { printseq() }
else {
chomp;
my ($name, $seq) = split;
$seq =~ s/[\.\-]//g unless $gapped;
push @seqorder, $name unless exists $seq{$name};
$seq{$name} .= $seq;
}
}
printseq();
sub printseq {
@seqorder = sort @seqorder if $sorted;
foreach $key (@seqorder) {
print ">$key\n";
for (my $i = 0; $i < length $seq{$key}; $i += $columns){
print substr($seq{$key}, $i, $columns), "\n";
}
}
%seq = ();
@seqorder = ();
}
Owner

mkuhn commented Aug 30, 2010

Edit 2010-08-30: Some STO files don't have the GS lines, so use the sequence names of the actual alignment.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment