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maint: remove hard tabs and trailing whitespace

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1 parent 2cd1789 commit 0e0ddd3b24a2e62c837bad955b2e15484df8496f @carandraug carandraug committed Mar 28, 2013
Showing with 169 additions and 167 deletions.
  1. +115 −115 Bio/AlignIO/fasta.pm
  2. +54 −52 Bio/AlignIO/largemultifasta.pm
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@@ -12,7 +12,7 @@ Bio::AlignIO::fasta - fasta MSA Sequence input/output stream
=head1 SYNOPSIS
-Do not use this module directly. Use it via the L<Bio::AlignIO>
+Do not use this module directly. Use it via the L<Bio::AlignIO>
class.
=head1 DESCRIPTION
@@ -24,15 +24,15 @@ FastA (FastX, FastN, FastP, tFastA, etc) use the Bio::SearchIO module.
=head1 FEEDBACK
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
-rather than to the module maintainer directly. Many experienced and
-reponsive experts will be able look at the problem and quickly
-address it. Please include a thorough description of the problem
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
@@ -69,7 +69,7 @@ use Bio::LocatableSeq;
Usage : $aln = $stream->next_aln
Function: returns the next alignment in the stream.
Returns : Bio::Align::AlignI object - returns 0 on end of file
- or on error
+ or on error
Args : -width => optional argument to specify the width sequence
will be written (60 chars by default)
@@ -78,89 +78,89 @@ See L<Bio::Align::AlignI>
=cut
sub next_aln {
- my $self = shift;
- my ($width) = $self->_rearrange([qw(WIDTH)],@_);
- $self->width($width || $WIDTH);
-
- my ($start, $end, $name, $seqname, $seq, $seqchar, $entry,
- $tempname, $tempdesc, %align, $desc, $maxlen);
- my $aln = Bio::SimpleAlign->new();
-
- while (defined ($entry = $self->_readline) ) {
- chomp $entry;
- if ( $entry =~ s/^>\s*(\S+)\s*// ) {
- $tempname = $1;
- chomp($entry);
- $tempdesc = $entry;
- if ( defined $name ) {
- $seqchar =~ s/\s//g;
- $seqname = $name;
- $start = 1;
- $end = $self->_get_len($seqchar);
- $seq = Bio::LocatableSeq->new
- (
- -seq => $seqchar,
- -display_id => $seqname,
- -description => $desc,
- -start => $start,
- -end => $end,
- -alphabet => $self->alphabet,
- );
- $aln->add_seq($seq);
- $self->debug("Reading $seqname\n");
- }
- $desc = $tempdesc;
- $name = $tempname;
- $desc = $entry;
- $seqchar = "";
- next;
- }
- # removed redundant symbol validation
- # this is already done in Bio::PrimarySeq
- $seqchar .= $entry;
- }
-
- # Next two lines are to silence warnings that
- # otherwise occur at EOF when using <$fh>
- $name = "" if (!defined $name);
- $seqchar="" if (!defined $seqchar);
- $seqchar =~ s/\s//g;
-
- # Put away last name and sequence
- if ( $name =~ /(\S+)\/(\d+)-(\d+)/ ) {
- $seqname = $1;
- $start = $2;
- $end = $3;
- } else {
- $seqname = $name;
- $start = 1;
- $end = $self->_get_len($seqchar);
- }
-
- # This logic now also reads empty lines at the
- # end of the file. Skip this is seqchar and seqname is null
- unless ( length($seqchar) == 0 && length($seqname) == 0 ) {
- $seq = Bio::LocatableSeq->new
- (-seq => $seqchar,
- -display_id => $seqname,
- -description => $desc,
- -start => $start,
- -end => $end,
- -alphabet => $self->alphabet,
- );
- $aln->add_seq($seq);
- $self->debug("Reading $seqname\n");
- }
- my $alnlen = $aln->length;
- foreach my $seq ( $aln->each_seq ) {
- if ( $seq->length < $alnlen ) {
- my ($diff) = ($alnlen - $seq->length);
- $seq->seq( $seq->seq() . "-" x $diff);
- }
- }
+ my $self = shift;
+ my ($width) = $self->_rearrange([qw(WIDTH)],@_);
+ $self->width($width || $WIDTH);
+
+ my ($start, $end, $name, $seqname, $seq, $seqchar, $entry,
+ $tempname, $tempdesc, %align, $desc, $maxlen);
+ my $aln = Bio::SimpleAlign->new();
+
+ while (defined ($entry = $self->_readline) ) {
+ chomp $entry;
+ if ( $entry =~ s/^>\s*(\S+)\s*// ) {
+ $tempname = $1;
+ chomp($entry);
+ $tempdesc = $entry;
+ if ( defined $name ) {
+ $seqchar =~ s/\s//g;
+ $seqname = $name;
+ $start = 1;
+ $end = $self->_get_len($seqchar);
+ $seq = Bio::LocatableSeq->new
+ (
+ -seq => $seqchar,
+ -display_id => $seqname,
+ -description => $desc,
+ -start => $start,
+ -end => $end,
+ -alphabet => $self->alphabet,
+ );
+ $aln->add_seq($seq);
+ $self->debug("Reading $seqname\n");
+ }
+ $desc = $tempdesc;
+ $name = $tempname;
+ $desc = $entry;
+ $seqchar = "";
+ next;
+ }
+ # removed redundant symbol validation
+ # this is already done in Bio::PrimarySeq
+ $seqchar .= $entry;
+ }
+
+ # Next two lines are to silence warnings that
+ # otherwise occur at EOF when using <$fh>
+ $name = "" if (!defined $name);
+ $seqchar="" if (!defined $seqchar);
+ $seqchar =~ s/\s//g;
+
+ # Put away last name and sequence
+ if ( $name =~ /(\S+)\/(\d+)-(\d+)/ ) {
+ $seqname = $1;
+ $start = $2;
+ $end = $3;
+ } else {
+ $seqname = $name;
+ $start = 1;
+ $end = $self->_get_len($seqchar);
+ }
+
+ # This logic now also reads empty lines at the
+ # end of the file. Skip this is seqchar and seqname is null
+ unless ( length($seqchar) == 0 && length($seqname) == 0 ) {
+ $seq = Bio::LocatableSeq->new
+ (-seq => $seqchar,
+ -display_id => $seqname,
+ -description => $desc,
+ -start => $start,
+ -end => $end,
+ -alphabet => $self->alphabet,
+ );
+ $aln->add_seq($seq);
+ $self->debug("Reading $seqname\n");
+ }
+ my $alnlen = $aln->length;
+ foreach my $seq ( $aln->each_seq ) {
+ if ( $seq->length < $alnlen ) {
+ my ($diff) = ($alnlen - $seq->length);
+ $seq->seq( $seq->seq() . "-" x $diff);
+ }
+ }
# no sequences means empty alignment (possible EOF)
- return $aln if $aln->num_sequences;
+ return $aln if $aln->num_sequences;
}
=head2 write_aln
@@ -181,28 +181,28 @@ sub write_aln {
my ($seq,$desc,$rseq,$name,$count,$length,$seqsub);
foreach my $aln (@aln) {
- if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) {
- $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln");
- next;
- }
- if( $self->force_displayname_flat ) {
- $aln->set_displayname_flat(1);
- }
- foreach $rseq ( $aln->each_seq() ) {
- $name = $aln->displayname($rseq->get_nse());
- $seq = $rseq->seq();
- $desc = $rseq->description || '';
- $desc = ' '.$desc if $desc;
- $self->_print (">$name$desc\n") or return;
- $count = 0;
- $length = length($seq);
- if(defined $seq && $length > 0) {
- $seq =~ s/(.{1,$width})/$1\n/g;
- } else {
- $seq = "\n";
- }
- $self->_print($seq);
- }
+ if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) {
+ $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln");
+ next;
+ }
+ if( $self->force_displayname_flat ) {
+ $aln->set_displayname_flat(1);
+ }
+ foreach $rseq ( $aln->each_seq() ) {
+ $name = $aln->displayname($rseq->get_nse());
+ $seq = $rseq->seq();
+ $desc = $rseq->description || '';
+ $desc = ' '.$desc if $desc;
+ $self->_print (">$name$desc\n") or return;
+ $count = 0;
+ $length = length($seq);
+ if(defined $seq && $length > 0) {
+ $seq =~ s/(.{1,$width})/$1\n/g;
+ } else {
+ $seq = "\n";
+ }
+ $self->_print($seq);
+ }
}
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
@@ -211,18 +211,18 @@ sub write_aln {
=head2 _get_len
Title : _get_len
- Usage :
+ Usage :
Function: determine number of alphabetic chars
Returns : integer
Args : sequence string
=cut
sub _get_len {
- my ($self,$seq) = @_;
- my $chars = $Bio::LocatableSeq::GAP_SYMBOLS.$Bio::LocatableSeq::FRAMESHIFT_SYMBOLS;
- $seq =~ s{[$chars]+}{}gi;
- return CORE::length($seq);
+ my ($self,$seq) = @_;
+ my $chars = $Bio::LocatableSeq::GAP_SYMBOLS.$Bio::LocatableSeq::FRAMESHIFT_SYMBOLS;
+ $seq =~ s{[$chars]+}{}gi;
+ return CORE::length($seq);
}
=head2 width
@@ -231,7 +231,7 @@ sub _get_len {
Usage : $obj->width($newwidth)
$width = $obj->width;
Function: Get/set width of alignment
- Returns : integer value of width
+ Returns : integer value of width
Args : on set, new value (a scalar or undef, optional)
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