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#!/usr/local/bin/perl -w
use strict;
use Bio::SeqIO;
use Bio::Root::IO;
use Algorithm::Diff qw(diff LCS);
use IO::ScalarArray;
use IO::String;
my %files = (
#'test.embl' => 'embl',
# 'test.ace' => 'ace',
'test.fasta' => 'fasta',
# 'test.game' => 'game',
'test.gcg' => 'gcg',
# 'test.genbank' => 'genbank',
'test.raw' => 'raw',
# 'test_badlf.gcg' => 'gcg'
);
while( my ($file, $type) = each %files ) {
my $filename = Bio::Root::IO->catfile('t','data',$file);
print "processing file $filename\n";
open(FILE, "< $filename") or die("cannot open $filename");
my @datain = <FILE>;
my $in = new IO::String(join('', @datain));
my $seqin = new Bio::SeqIO( -fh => $in,
-format => $type);
my $out = new IO::String;
my $seqout = new Bio::SeqIO( -fh => $out,
-format => $type);
my $seq;
while( defined($seq = $seqin->next_seq) ) {
$seqout->write_seq($seq);
}
$seqout->close();
$seqin->close();
my $strref = $out->string_ref;
my @dataout = map { $_."\n"} split(/\n/, $$strref );
my @diffs = &diff( \@datain, \@dataout);
foreach my $d ( @diffs ) {
foreach my $diff ( @$d ) {
chomp($diff->[2]);
print $diff->[0], $diff->[1], "\n>", $diff->[2], "\n";
}
}
if( @diffs ) {
print "in is \n", join('', @datain), "\n";
print "out is \n", join('',@dataout), "\n";
}
}
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