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sestaton · Jun 5, 2017 · 6fd2b5a · 6fd2b5a
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Showing 23 changed files with 61 additions and 44 deletions.
diff --git a/bin/transposome b/bin/transposome
@@ -15,11 +15,11 @@ transposome - A toolkit for annotation of transposable element families from una
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 #$VERSION = eval $VERSION;
 
 =head1 SYNOPSIS

diff --git a/lib/Transposome.pm b/lib/Transposome.pm
@@ -14,11 +14,11 @@ Transposome - Investigate the repeat strucuture of a genome through unassembled
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 #$VERSION = eval $VERSION;
 
 =head1 SYNOPSIS

diff --git a/lib/Transposome/Annotation.pm b/lib/Transposome/Annotation.pm
@@ -24,11 +24,11 @@ Transposome::Annotation - Annotate clusters for repeat types.
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 $VERSION = eval $VERSION;
 
 =head1 SYNOPSIS

diff --git a/lib/Transposome/Annotation/Mapping.pm b/lib/Transposome/Annotation/Mapping.pm
@@ -12,11 +12,11 @@ Transposome::Annotation::Mapping - Map BLAST hits to the full repeat taxonomy
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 $VERSION = eval $VERSION;
 
 =head1 SYNOPSIS

diff --git a/lib/Transposome/Annotation/Methods.pm b/lib/Transposome/Annotation/Methods.pm
@@ -14,11 +14,11 @@ Transposome::Annotation::Methods - An interface role to simplify importing all a
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 $VERSION = eval $VERSION;
 
 =head1 SYNOPSIS

diff --git a/lib/Transposome/Annotation/Search.pm b/lib/Transposome/Annotation/Search.pm
@@ -14,11 +14,11 @@ Transposome::Annotation::Search - Run the BLAST search on the clusters and singl
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 $VERSION = eval $VERSION;
 
 =head1 SYNOPSIS

diff --git a/lib/Transposome/Annotation/Summary.pm b/lib/Transposome/Annotation/Summary.pm
@@ -14,11 +14,11 @@ Transposome::Annotation::Summary - Generate an annotation summary for the whole
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 $VERSION = eval $VERSION;
 
 =head1 SYNOPSIS

diff --git a/lib/Transposome/Annotation/Typemap.pm b/lib/Transposome/Annotation/Typemap.pm
@@ -12,11 +12,11 @@ Transposome::Annotation::Typemap - Create a map of repeats to the family level.
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 $VERSION = eval $VERSION;
 
 =head1 SYNOPSIS

diff --git a/lib/Transposome/Cluster.pm b/lib/Transposome/Cluster.pm
@@ -27,11 +27,11 @@ Transposome::Cluster - Clustering and cluster analysis routines in Transposome.
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 $VERSION = eval $VERSION;
 
 =head1 SYNOPSIS

diff --git a/lib/Transposome/PairFinder.pm b/lib/Transposome/PairFinder.pm
@@ -21,11 +21,11 @@ Transposome::PairFinder - Parse mgblast and find best scoring unique matches.
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 $VERSION = eval $VERSION;
 
 =head1 SYNOPSIS

diff --git a/lib/Transposome/Role/Config.pm b/lib/Transposome/Role/Config.pm
@@ -9,11 +9,11 @@ Transposome::Role::Config - Attributes and routines for parsing Transposome conf
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 $VERSION = eval $VERSION;
 
 =head1 SYNOPSIS

diff --git a/lib/Transposome/Role/File.pm b/lib/Transposome/Role/File.pm
@@ -14,11 +14,11 @@ Transposome::Role::File - File handling methods for Transposome.
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 $VERSION = eval $VERSION;
 
 =head1 SYNOPSIS

diff --git a/lib/Transposome/Role/Types.pm b/lib/Transposome/Role/Types.pm
@@ -12,11 +12,11 @@ Transposome::Types - Types used by Transposome. Not meant to be used directly.
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 $VERSION = eval $VERSION;
 
 =head1 SYNOPSIS

diff --git a/lib/Transposome/Role/Util.pm b/lib/Transposome/Role/Util.pm
@@ -9,11 +9,11 @@ Transposome::Role::Util - Numerous utility routines for Transposome.
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 $VERSION = eval $VERSION;
 
 =head1 SYNOPSIS

diff --git a/lib/Transposome/Run/Blast.pm b/lib/Transposome/Run/Blast.pm
@@ -27,11 +27,11 @@ Transposome::Run::Blast - Run all vs. all BLAST to generate graph edges.
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 $VERSION = eval $VERSION;
 
 =head1 SYNOPSIS

diff --git a/lib/Transposome/SeqFactory.pm b/lib/Transposome/SeqFactory.pm
@@ -23,11 +23,11 @@ Transposome::SeqFactory - Class for constructing a Transposome::SeqIO object for
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 
 =head1 SYNOPSIS
 

diff --git a/lib/Transposome/SeqIO.pm b/lib/Transposome/SeqIO.pm
@@ -13,11 +13,11 @@ Transposome::SeqIO - Base class for reading FASTA/Q data.
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 
 =head1 SYNOPSIS
 

diff --git a/lib/Transposome/SeqIO/fasta.pm b/lib/Transposome/SeqIO/fasta.pm
@@ -12,11 +12,11 @@ Transposome::SeqIO::fasta - Class for reading FASTA data.
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 
 =head1 SYNOPSIS
 

diff --git a/lib/Transposome/SeqIO/fastq.pm b/lib/Transposome/SeqIO/fastq.pm
@@ -12,11 +12,11 @@ Transposome::SeqIO::fastq - Class for reading FASTQ data.
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 
 =head1 SYNOPSIS
 

diff --git a/lib/Transposome/SeqUtil.pm b/lib/Transposome/SeqUtil.pm
@@ -18,11 +18,11 @@ Transposome::SeqUtil - Utilities for handling Fasta/q sequence files.
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 $VERSION = eval $VERSION;
 
 =head1 SYNOPSIS

diff --git a/lib/Transposome/Test/TestFixture.pm b/lib/Transposome/Test/TestFixture.pm
@@ -14,11 +14,11 @@ Transposome::Test::TestFixture - Methods for mocking data or data structures for
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 $VERSION = eval $VERSION;
 
 =head1 SYNOPSIS

diff --git a/lib/Transposome/Test/TestFixture/TestConfig.pm b/lib/Transposome/Test/TestFixture/TestConfig.pm
@@ -13,11 +13,11 @@ Transposome::Test::TestFixture::TestConfig - Methods for mocking configuration d
 
 =head1 VERSION
 
-Version 0.11.1
+Version 0.11.2
 
 =cut
 
-our $VERSION = '0.11.1';
+our $VERSION = '0.11.2';
 $VERSION = eval $VERSION;
 
 =head1 SYNOPSIS

diff --git a/testio.pl b/testio.pl
@@ -0,0 +1,17 @@
+use strict;
+use warnings;
+use 5.010;
+use blib;
+use Transposome::SeqFactory;
+
+my $seqio_fa = Transposome::SeqFactory->new( file => shift, format => 'fastq' )->make_seqio_object;
+#say STDERR "can? ",$seqio_fa->can->get_seqtype;
+while ( my $seq = $seqio_fa->next_seq ) {
+    #say STDERR "id ->", $seq->get_id;
+    #ok( $seq->has_id,  "Fasta sequence $seq_num has an ID" );
+    #ok( $seq->get_id =~ /\/\d$/,  "Fasta sequence $seq_num has an ID in the expected format" );
+    #ok( $seq->has_seq, "Fasta sequence $seq_num has a sequence" );
+    #ok( !$seq->has_qual,
+    #"Fasta sequence $seq_num does not have quality scores" );
+    say join "\n", "@".$seq->get_id, $seq->get_seq, '+', $seq->get_qual;
+}