Merge branch 'master' of github.com:bioperl/bioperl-live

bioperl · Jun 11, 2017 · 0feb41e · 0feb41e
2 parents 1eb9fbc + e1ac582
commit 0feb41e
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diff --git a/Bio/SeqIO/pir.pm b/Bio/SeqIO/pir.pm
@@ -1,9 +1,7 @@
 #
 # BioPerl module for Bio::SeqIO::PIR
 #
-# Please direct questions and support issues to <bioperl-l@bioperl.org> 
-#
-# Cared for by Aaron Mackey <amackey@virginia.edu>
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
 #
 # Copyright Aaron Mackey
 #
@@ -43,15 +41,15 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
-=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
@@ -110,39 +108,42 @@ sub next_seq {
     my ($self) = @_;
     local $/ = "\n>";
     return unless my $line = $self->_readline;
-    if( $line eq '>' ) {	# handle the very first one having no comment
-	return unless $line = $self->_readline;
+    if ( $line eq '>' ) {    # handle the very first one having no comment
+        return unless $line = $self->_readline;
+    }
+    my ( $top, $desc, $seq ) = ( $line =~ /^(.+?)\n(.*?)\n([^>]*)/s )
+        or $self->throw("Cannot parse entry PIR entry [$line]");
+
+    my ( $type, $id );
+    if ( $top =~ /^>?(\S{2});(\S+)\s*$/ ) {
+        ( $type, $id ) = ( $1, $2 );
+        if ( ! exists $VALID_TYPE{$type} ) {
+            $self->throw(
+                "PIR stream read attempted without proper two-letter sequence code [ $type ]"
+            );
+        }
+    } else {
+        $self->throw("Line does not match PIR format [ $line ]");
     }
-    my ($top, $desc,$seq) = ( $line =~ /^(.+?)\n(.+?)\n([^>]*)/s )  or
-	$self->throw("Cannot parse entry PIR entry [$line]");
-
-    my ( $type,$id );
-	if ( $top =~ /^>?(\S{2});(\S+)\s*$/ ) {
-	  ( $type,$id ) = ($1, $2);
-	  if (!exists $VALID_TYPE{$type} ) {
-		$self->throw("PIR stream read attempted without proper two-letter sequence code [ $type ]");
-	  }
-	} else {
-	  $self->throw("Line does not match PIR format [ $line ]");
-	}
 
     # P - indicates complete protein
     # F - indicates protein fragment
     # not sure how to stuff these into a Bio object
     # suitable for writing out.
     $seq =~ s/\*//g;
     $seq =~ s/[\(\)\.\/\=\,]//g;
-    $seq =~ s/\s+//g;		# get rid of whitespace
+    $seq =~ s/\s+//g;    # get rid of whitespace
 
     my ($alphabet) = ('protein');
+
     # TODO - not processing SFS data
-    return $self->sequence_factory->create
-	(-seq        => $seq,
-	 -primary_id => $id,
-	 -id         => $id,
-	 -desc       => $desc,
-	 -alphabet   => $alphabet
-	 );
+    return $self->sequence_factory->create(
+        -seq        => $seq,
+        -primary_id => $id,
+        -id         => $id,
+        -desc       => $desc,
+        -alphabet   => $alphabet
+    );
 }
 
 =head2 write_seq

diff --git a/t/SeqIO/pir.t b/t/SeqIO/pir.t
@@ -1,30 +1,46 @@
 # -*-Perl-*- Test Harness script for Bioperl
-# $Id$
 
 use strict;
 
 BEGIN {
-	use lib '.';
+    use lib '.';
     use Bio::Root::Test;
-    
-    test_begin(-tests => 9);
-	
-	use_ok('Bio::SeqIO::pir');
+
+    test_begin( -tests => 12 );
+
+    use_ok('Bio::SeqIO::pir');
 }
 
 my $verbose = test_debug();
 
-my $str = Bio::SeqIO->new(-file => test_input_file('seqfile.pir'),
-								  -verbose => $verbose,
-								  -format => 'pir');
+my $in = Bio::SeqIO->new(
+    -file    => test_input_file('seqfile.pir'),
+    -verbose => $verbose,
+    -format  => 'pir'
+);
 
-ok ( defined $str, 'new instance is defined ');
-isa_ok ($str, 'Bio::SeqIO');
+ok( defined $in, 'new instance is defined ' );
+isa_ok( $in, 'Bio::SeqIO' );
 
-my $out = Bio::SeqIO->new(-format => 'pir',
-								 -fh => \*STDOUT);
+my $out = Bio::SeqIO->new(
+    -format => 'pir',
+    -fh     => \*STDOUT
+);
 
-while (my $seq = $str->next_seq()) {
-	ok( $seq->length > 1, 'checked length');
-	$out->write_seq($seq) if $verbose > 0;
+while ( my $seq = $in->next_seq() ) {
+    ok( $seq->length > 1, 'checked length' );
+    $out->write_seq($seq) if $verbose > 0;
 }
+
+# Empty description line
+$in = Bio::SeqIO->new(
+    -file    => test_input_file('seqfile-no-desc.pir'),
+    -verbose => $verbose,
+    -format  => 'pir'
+);
+my $seq = $in->next_seq();
+ok( $seq->seq =~ /^MGD/, 'Correct start' );
+$seq = $in->next_seq();
+ok( $seq->seq =~ /^GDV/, 'Correct start' );
+$seq = $in->next_seq();
+ok( $seq->seq =~ /^GDV/, 'Correct start' );
diff --git a/t/data/seqfile-no-desc.pir b/t/data/seqfile-no-desc.pir
@@ -0,0 +1,9 @@
+>P1;CCHU
+
+MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE*
+>P1;CCCZ
+
+GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE*
+>P1;CCST
+
+GDVEK.GKKIF.VQKCAQCHTVEKGGKH.KTGPNLNGL.IGRKTGQAEGF.SYTEANKN.KGITWG.EETLM.EY.LENPKKY.IPGTKM.IF.AGIKKKAERADL.IAY.LKDATSK*