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Bowtie tests needs Bio::DB::Sam (+extratab cleaning)
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@fangly
fangly committed Feb 28, 2012
1 parent d587561 commit 7ba2e1a
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Showing 2 changed files with 170 additions and 169 deletions.
338 changes: 169 additions & 169 deletions Bio/Assembly/IO/bowtie.pm
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Expand Up @@ -123,7 +123,7 @@ BEGIN {
# check requirements
eval "require Bio::Tools::Run::Bowtie; \$HAVE_BOWTIE = 1";
unless ( eval "require IO::Uncompress::Gunzip; \$HAVE_IO_UNCOMPRESS = 1") {
Bio::Root::Root->warn("IO::Uncompress::Gunzip is not available; you'll have to do your decompression by hand.");
Bio::Root::Root->warn("IO::Uncompress::Gunzip is not available; you'll have to do your decompression by hand.");
}
}

Expand All @@ -145,188 +145,188 @@ BEGIN {
=cut

sub new {
my $class = shift;
my @args = @_;
my $self = $class->SUPER::new(@args);
$self->_initialize(@args);
$self->{'_tempdir'} = $self->tempdir(CLEANUP=>1);
my ($file, $index, $no_head, $no_sq) = $self->_rearrange([qw(FILE INDEX NO_HEAD NO_SQ)], @args);
$file =~ s/^<//;
$self->{'_no_head'} = $no_head;
$self->{'_no_sq'} = $no_sq;

# get the sequence so Bio::DB::Sam can work with it
my $refdb;
my $inspector;
if (-e $index && -r _ ) {
$refdb = ($index =~ m/\.gz[^.]*$/) ? $self->_uncompress($index) : $index;
my $guesser = Bio::Tools::GuessSeqFormat->new(-file=>$refdb);
$self->throw("'$index' is not a fasta file.")
unless $guesser->guess =~ m/^fasta$/;
} elsif ($HAVE_BOWTIE) {
$inspector = Bio::Tools::Run::Bowtie->new( -command => 'inspect' );
$refdb = $inspector->run($index);
} else {
$self->throw("Bio::Tools::Run::Bowtie is not available - cannot extract refdb from index.");
}

my $bam_file = $self->_make_bam($self->_bowtie_to_sam($file, $refdb));
my $sam = Bio::Assembly::IO->new( -file => "<$bam_file", -refdb => $refdb , -format => 'sam' );

return $sam;
my $class = shift;
my @args = @_;
my $self = $class->SUPER::new(@args);
$self->_initialize(@args);
$self->{'_tempdir'} = $self->tempdir(CLEANUP=>1);
my ($file, $index, $no_head, $no_sq) = $self->_rearrange([qw(FILE INDEX NO_HEAD NO_SQ)], @args);
$file =~ s/^<//;
$self->{'_no_head'} = $no_head;
$self->{'_no_sq'} = $no_sq;

# get the sequence so Bio::DB::Sam can work with it
my $refdb;
my $inspector;
if (-e $index && -r _ ) {
$refdb = ($index =~ m/\.gz[^.]*$/) ? $self->_uncompress($index) : $index;
my $guesser = Bio::Tools::GuessSeqFormat->new(-file=>$refdb);
$self->throw("'$index' is not a fasta file.")
unless $guesser->guess =~ m/^fasta$/;
} elsif ($HAVE_BOWTIE) {
$inspector = Bio::Tools::Run::Bowtie->new( -command => 'inspect' );
$refdb = $inspector->run($index);
} else {
$self->throw("Bio::Tools::Run::Bowtie is not available - cannot extract refdb from index.");
}

my $bam_file = $self->_make_bam($self->_bowtie_to_sam($file, $refdb));
my $sam = Bio::Assembly::IO->new( -file => "<$bam_file", -refdb => $refdb , -format => 'sam' );

return $sam;
}

sub _bowtie_to_sam {
my ($self, $file, $refdb) = @_;

$self->throw("'$file' does not exist or is not readable.")
unless ( -e $file && -r _ );

if ($file =~ m/\.gz[^.]*$/) {
$file = $self->_uncompress($file);
$self->close;
open (my $fh,$file);
$self->file($file);
$self->_fh($fh);
}

my $guesser = Bio::Tools::GuessSeqFormat->new(-file=>$file);
$self->throw("'$file' is not a bowtie formatted file.") unless $guesser->guess =~ m/^bowtie$/;

my %SQ;
my $mapq = 255;
my $in_pair;
my @mate_line;
my $mlen;

# create temp file for working
my ($sam_tmp_h, $sam_tmp_f) = $self->tempfile( -dir => $self->{'_tempdir'}, -suffix => '.sam' );
while (my $line = $self->_readline) {
chomp($line);
my ($qname,$strand,$rname,$pos,$seq,$qual,$m,$details)=split("\cI",$line);
$SQ{$rname} = 1;
my $paired_f = ($qname =~ m#/[12]#) ? 0x03 : 0;
my $strand_f = ($strand eq '-') ? 0x10 : 0;
my $op_strand_f = ($strand eq '+' && $paired_f) ? 0x20 : 0;
my $first_f = ($qname =~ m#/1#) ? 0x40 : 0;
my $second_f = ($qname =~ m#/2#) ? 0x80 : 0;
my $flag = $paired_f | $strand_f | $op_strand_f | $first_f | $second_f;

$pos++;
my $len = length $seq;
die unless $len == length $qual;
my $cigar = $len.'M';
my @detail = split(',',$details);
my $dist = 'NM:i:'.scalar @detail;
my @mismatch;
my $last_pos = 0;
for (@detail) {
m/(\d+):(\w)>\w/;
my $err = ($1-$last_pos);
$last_pos = $1+1;
push @mismatch,($err,$2);
}
push @mismatch, $len-$last_pos;
@mismatch = reverse @mismatch if $strand eq '-';
my $mismatch = join('',('MD:Z:',@mismatch));

if ($paired_f) {
my $mrnm = '=';
if ($in_pair) {
my $mpos = $mate_line[3];
$mate_line[7] = $pos;
my $isize = $mpos-$pos-$len;
$mate_line[8] = -$isize;
print $sam_tmp_h join("\t",@mate_line),"\n";
print $sam_tmp_h join("\t",$qname, $flag, $rname, $pos, $mapq, $cigar, $mrnm, $mpos, $isize, $seq, $qual, $mismatch, $dist),"\n";
$in_pair = 0;
} else {
$mlen = $len;
@mate_line = ($qname, $flag, $rname, $pos, $mapq, $cigar, $mrnm, undef, undef, $seq, $qual, $mismatch, $dist);
$in_pair = 1;
}
} else {
my $mrnm = '*';
my $mpos = 0;
my $isize = 0;
print $sam_tmp_h join("\t",$qname, $flag, $rname, $pos, $mapq, $cigar, $mrnm, $mpos, $isize, $seq, $qual, $mismatch, $dist),"\n";
}
}

$sam_tmp_h->close;
return $sam_tmp_f if $self->{'_no_head'};

my ($samh, $samf) = $self->tempfile( -dir => $self->{'_tempdir'}, -suffix => '.sam' );

# print header
print $samh $HD;
# print sequence dictionary
unless ($self->{'_no_sq'}) {
my $db = Bio::SeqIO->new( -file => $refdb, -format => 'fasta' );
while ( my $seq = $db->next_seq() ) {
$SQ{$seq->id} = $seq->length if $SQ{$seq->id};
}
map { print $samh join("\t", ('@SQ', "SN:$_", "LN:$SQ{$_}")), "\n" } keys %SQ;
}
# print program
print $samh $PG;
# print alignments
open($sam_tmp_h, $sam_tmp_f) or
$self->throw("Can not open '$sam_tmp_f' for reading: $!");

print $samh $_ while (<$sam_tmp_h>);
close($sam_tmp_h);
$samh->close;
return $samf;
my ($self, $file, $refdb) = @_;

$self->throw("'$file' does not exist or is not readable.")
unless ( -e $file && -r _ );

if ($file =~ m/\.gz[^.]*$/) {
$file = $self->_uncompress($file);
$self->close;
open (my $fh,$file);
$self->file($file);
$self->_fh($fh);
}

my $guesser = Bio::Tools::GuessSeqFormat->new(-file=>$file);
$self->throw("'$file' is not a bowtie formatted file.") unless $guesser->guess =~ m/^bowtie$/;

my %SQ;
my $mapq = 255;
my $in_pair;
my @mate_line;
my $mlen;

# create temp file for working
my ($sam_tmp_h, $sam_tmp_f) = $self->tempfile( -dir => $self->{'_tempdir'}, -suffix => '.sam' );
while (my $line = $self->_readline) {
chomp($line);
my ($qname,$strand,$rname,$pos,$seq,$qual,$m,$details)=split("\cI",$line);
$SQ{$rname} = 1;
my $paired_f = ($qname =~ m#/[12]#) ? 0x03 : 0;
my $strand_f = ($strand eq '-') ? 0x10 : 0;
my $op_strand_f = ($strand eq '+' && $paired_f) ? 0x20 : 0;
my $first_f = ($qname =~ m#/1#) ? 0x40 : 0;
my $second_f = ($qname =~ m#/2#) ? 0x80 : 0;
my $flag = $paired_f | $strand_f | $op_strand_f | $first_f | $second_f;

$pos++;
my $len = length $seq;
die unless $len == length $qual;
my $cigar = $len.'M';
my @detail = split(',',$details);
my $dist = 'NM:i:'.scalar @detail;

my @mismatch;
my $last_pos = 0;
for (@detail) {
m/(\d+):(\w)>\w/;
my $err = ($1-$last_pos);
$last_pos = $1+1;
push @mismatch,($err,$2);
}
push @mismatch, $len-$last_pos;
@mismatch = reverse @mismatch if $strand eq '-';
my $mismatch = join('',('MD:Z:',@mismatch));

if ($paired_f) {
my $mrnm = '=';
if ($in_pair) {
my $mpos = $mate_line[3];
$mate_line[7] = $pos;
my $isize = $mpos-$pos-$len;
$mate_line[8] = -$isize;
print $sam_tmp_h join("\t",@mate_line),"\n";
print $sam_tmp_h join("\t",$qname, $flag, $rname, $pos, $mapq, $cigar, $mrnm, $mpos, $isize, $seq, $qual, $mismatch, $dist),"\n";
$in_pair = 0;
} else {
$mlen = $len;
@mate_line = ($qname, $flag, $rname, $pos, $mapq, $cigar, $mrnm, undef, undef, $seq, $qual, $mismatch, $dist);
$in_pair = 1;
}
} else {
my $mrnm = '*';
my $mpos = 0;
my $isize = 0;
print $sam_tmp_h join("\t",$qname, $flag, $rname, $pos, $mapq, $cigar, $mrnm, $mpos, $isize, $seq, $qual, $mismatch, $dist),"\n";
}
}

$sam_tmp_h->close;

return $sam_tmp_f if $self->{'_no_head'};

my ($samh, $samf) = $self->tempfile( -dir => $self->{'_tempdir'}, -suffix => '.sam' );

# print header
print $samh $HD;

# print sequence dictionary
unless ($self->{'_no_sq'}) {
my $db = Bio::SeqIO->new( -file => $refdb, -format => 'fasta' );
while ( my $seq = $db->next_seq() ) {
$SQ{$seq->id} = $seq->length if $SQ{$seq->id};
}
map { print $samh join("\t", ('@SQ', "SN:$_", "LN:$SQ{$_}")), "\n" } keys %SQ;
}
# print program
print $samh $PG;
# print alignments
open($sam_tmp_h, $sam_tmp_f) or
$self->throw("Can not open '$sam_tmp_f' for reading: $!");

print $samh $_ while (<$sam_tmp_h>);
close($sam_tmp_h);
$samh->close;
return $samf;
}

sub _uncompress {
my ($self, $file) = @_;

unless ($HAVE_IO_UNCOMPRESS) {
croak( "IO::Uncompress::Gunzip not available, can't expand '$file'" );
}
my ($tfh, $tf) = $self->tempfile( -dir => $self->{'_tempdir'} );
my $z = IO::Uncompress::Gunzip->new($file);
while (my $block = $z->getline) { print $tfh $block }
close $tfh;
$file = $tf;

return $file
my ($self, $file) = @_;

unless ($HAVE_IO_UNCOMPRESS) {
croak( "IO::Uncompress::Gunzip not available, can't expand '$file'" );
}
my ($tfh, $tf) = $self->tempfile( -dir => $self->{'_tempdir'} );
my $z = IO::Uncompress::Gunzip->new($file);
while (my $block = $z->getline) { print $tfh $block }
close $tfh;
$file = $tf;

return $file
}

sub _make_bam {
my ($self, $file) = @_;
$self->throw("'$file' does not exist or is not readable")
unless ( -e $file && -r _ );
my ($self, $file) = @_;
$self->throw("'$file' does not exist or is not readable")
unless ( -e $file && -r _ );

# make a sorted bam file from a sam file input
my ($bamh, $bamf) = $self->tempfile( -dir => $self->{'_tempdir'}, -suffix => '.bam' );
my ($srth, $srtf) = $self->tempfile( -dir => $self->{'_tempdir'}, -suffix => '.srt' );
$_->close for ($bamh, $srth);
my $samt = Bio::Tools::Run::Samtools->new( -command => 'view',
-sam_input => 1,
-bam_output => 1 );
# make a sorted bam file from a sam file input
my ($bamh, $bamf) = $self->tempfile( -dir => $self->{'_tempdir'}, -suffix => '.bam' );
my ($srth, $srtf) = $self->tempfile( -dir => $self->{'_tempdir'}, -suffix => '.srt' );
$_->close for ($bamh, $srth);
my $samt = Bio::Tools::Run::Samtools->new( -command => 'view',
-sam_input => 1,
-bam_output => 1 );

$samt->run( -bam => $file, -out => $bamf );
$samt->run( -bam => $file, -out => $bamf );

$samt = Bio::Tools::Run::Samtools->new( -command => 'sort' );
$samt = Bio::Tools::Run::Samtools->new( -command => 'sort' );

$samt->run( -bam => $bamf, -pfx => $srtf);
$samt->run( -bam => $bamf, -pfx => $srtf);

return $srtf.'.bam'
return $srtf.'.bam'
}

1;
1 change: 1 addition & 0 deletions t/Assembly/IO/bowtie.t
View file
Expand Up @@ -9,6 +9,7 @@ BEGIN {
test_begin( -tests => 796,
-requires_modules => [
'DB_File',
'Bio::DB::Sam',
'Bio::Tools::Run::Samtools',
],
);
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