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

.travis.yml

@@ -6,8 +6,27 @@ perl:
   - "5.16"
   - "5.14"
 
+matrix:
+  include:
+    - perl: 5.18
+      env: COVERAGE=1 TEST_PARTITION=1
+    - perl: 5.18
+      env: COVERAGE=1 TEST_PARTITION=2
+    - perl: 5.18
+      env: COVERAGE=1 TEST_PARTITION=3
+    - perl: 5.18
+      env: COVERAGE=1 TEST_PARTITION=4
+    - perl: 5.18
+      env: COVERAGE=1 TEST_PARTITION=5
+    - perl: 5.18
+      env: COVERAGE=1 TEST_PARTITION=6
+
 sudo: false
-env: PERL_CPANM_OPT="--notest --force --skip-satisfied"
+env:
+  global:
+    - PERL_CPANM_OPT="--notest --force --skip-satisfied"
+    - BIOPERL_NETWORK_TESTING=0   # disables the network tests
+    - TEST_PARTITIONS=6
 
 addons:
   apt:
@@ -17,37 +36,33 @@ addons:
       - libgd2-xpm-dev
       - libxml2-dev
 
+before_install:
+  - git clone git://github.com/travis-perl/helpers ~/travis-perl-helpers
+  - source ~/travis-perl-helpers/init
+  - build-perl
+  - perl -V
+  - cpanm DBD::mysql DBD::Pg DBD::SQLite 2>&1 | tail -n 1
+  - cpanm Test::Pod 2>&1 | tail -n 1
+  - cpanm Bio::ASN1::EntrezGene 2>&1 | tail -n 1
+  - if [ "$BIOPERL_NETWORK_TESTING" = "1" ]; then
+      export TRAVIS_AUTHOR_TESTING=1;
+      export TRAVIS_RELEASE_TESTING=1;
+      cpanm LWP::UserAgent LWP::Protocol::https 2>&1 | tail -n 1;
+    fi
+  - build-dist
+  - cd $BUILD_DIR
 install:
-    #These are recommended or required Perl libraries:
-    - "cpanm GD 2>&1 CGI | tail -n 1"
-    - "cpanm HTML::TableExtract DBI Data::Stag DB_File 2>&1 | tail -n 1"
-    - "cpanm DBD::mysql DBD::Pg DBD::SQLite 2>&1 | tail -n 1"
-    - "cpanm Algorithm::Munkres Array::Compare Convert::Binary::C Error 2>&1 | tail -n 1"
-    - "cpanm Graph SVG SVG::Graph GraphViz 2>&1 | tail -n 1"
-    - "cpanm XML::DOM::XPath XML::Parser XML::Parser::PerlSAX 2>&1 | tail -n 1"
-    - "cpanm XML::SAX XML::SAX::Writer XML::Simple XML::LibXML XML::Twig XML::Writer 2>&1 | tail -n 1"
-    - "cpanm PostScript::TextBlock Set::Scalar Sort::Naturally YAML | tail -n 1"
-    - "cpanm Math::Random Spreadsheet::ParseExcel | tail -n 1"
-    - "cpanm Bio::Phylo | tail -n 1"
-    - "cpanm Test::Weaken | tail -n 1"
-    - "cpanm Test::Memory::Cycle | tail -n 1"
-    #Test coverage from Coveralls
-    #- cpanm --quiet --notest Devel::Cover::Report::Coveralls
-    #for some reason tests and deps aren't skipped here.  Will have to look into it more...
-    #git repos, seems to only work for simple checkouts, so pure perl only (TODO: look into before_script for more detail)
-    #- "git clone https://github.com/bioperl/Bio-Root.git; export PERL5LIB=$( pwd )/Bio-Root/lib:$PERL5LIB"
-    #This installs BioPerl itself:
-    - "perl ./Build.PL --accept"
-
+  - cpan-install --deps
+  - cpan-install --coverage
+before_script:
+  - coverage-setup
 script:
-    - "./Build test"
-    #Devel::Cover coverage options are: statement, branch, condition, path, subroutine, pod, time, all and none
-    #- "./Build build && cover -test -report coveralls" #complete version coverage test
-    #- PERL5OPT=-MDevel::Cover=+ignore,prove,-coverage,statement,subroutine prove -lr t #limited version coverage test
-    #- cover -report coveralls
-
+  - export AUTHOR_TESTING=${TRAVIS_AUTHOR_TESTING:=0}
+  - export RELEASE_TESTING=${TRAVIS_RELEASE_TESTING:=0}
+  - prove -l -j$(test-jobs) $(test-files)
 after_success:
-    - ./travis_scripts/trigger-dockerhub.sh
+  - coverage-report
+  - ./travis_scripts/trigger-dockerhub.sh
 
 #TODO - send emails to bioperl-guts-l
 notifications:

Bio/Tools/PrositeScan.pm

@@ -8,24 +8,47 @@ Bio::Tools::PrositeScan - Parser for ps_scan result
   use Bio::Tools::PrositeScan;
 
   my $factory = Bio::Tools::PrositeScan->new(
-      -file => 'out.PrositeScan'
+      -file   => 'out.PrositeScan',
+      -format => 'fasta'
   );
 
   while(my $match = $factory->next_prediction){
-      #  $match is of Bio::SeqFeature::FeaturePair
-      my $q_id = $fatch->feature1->seq_id;
-      my $h_id = $fatch->feature2->seq_id;
+      #  $match is a Bio::SeqFeature::FeaturePair
+
+      # Sequence ID
+      my $seq_id = $match->seq_id;
+
+      # PROSITE accession number
+      my $psac = $match->hseq_id;
+
+      # Coordinates
+      my @coords = ( $match->start, $match->end );
+
+      # Subsequence
+      my $seq = $match->feature1->seq;
   }
 
 =head1 DESCRIPTION
 
-This is the parser of the output of ps_scan program. It takes either a file
-handler or a file name, and returns a Bio::SeqFeature::FeaturePair object.
+This is a parser of the output of the ps_scan program. It takes either a file
+handle or a file name, and returns a L<Bio::SeqFeature::FeaturePair> object.
+
+Note that the current implementation parses the entire file at once.
 
 =head1 AUTHOR
 
 Juguang Xiao, juguang@tll.org.sg
 
+=head1 SEE ALSO
+
+=over
+
+=item * L<ps_scan software|ftp://ftp.expasy.org/databases/prosite/ps_scan>
+
+=item * L<PROSITE User Manual|http://prosite.expasy.org/prosuser.html>
+
+=back
+
 =cut
 
 # Let the code begin...
@@ -46,6 +69,12 @@ use base qw(Bio::Root::Root Bio::Root::IO);
   Usage   : Bio::Tools::PrositeScan->new(-file => 'out.PrositeScan');
             Bio::Tools::PrositeScan->new(-fh => \*FH);
   Returns : L<Bio::Tools::PrositeScan>
+  Args    : -format => string representing the format type for the
+                       ps_scan output, REQUIRED
+
+The C<-format> argument must currently be set to C<fasta> since this is the
+only parser implemented. This corresponds with using the ps_scan arguments
+C<-o fasta>.
 
 =cut
 
@@ -72,12 +101,15 @@ sub format {
 =head2 next_prediction
 
   Title   : new
-  Usage   : 
+  Usage   :
       while($result = $factory->next_prediction){
           ;
       }
 
-  Returns : a Bio::SeqFeature::FeaturePair object
+  Returns : a Bio::SeqFeature::FeaturePair object where
+            feature1 is the matched subsequence and
+            feature2 is the PROSITE accession number.
+            See <http://prosite.expasy.org/prosuser.html#conv_ac>.
 
 =cut
 
@@ -153,7 +185,6 @@ sub _parse_fasta {
         push @matches, $fp;
     }
     push @{$self->{_matches}}, @matches;
-
 }
 
 sub _attach_seq {

t/RemoteDB/Taxonomy.t

@@ -474,7 +474,7 @@ SKIP: {
 
 # tests for #212
 SKIP: {
-        test_skip( -tests => 12, -requires_networking => 0 );
+        test_skip( -tests => 6, -requires_networking => 1 );
 
         my $db = Bio::DB::Taxonomy->new( -source => "entrez" );
 
@@ -487,16 +487,17 @@ SKIP: {
         # 'Phygadeuon ovatus'    | "No hit"      | 666060
         # 'Trimorus ovatus'      | "No hit"      | 666060
 
-        my @ids = $db_entrez->get_taxonids('Lissotriton vulgaris');
+        my @ids;
+        @ids = $db->get_taxonids('Lissotriton vulgaris');
         is $ids[0], 8324, 'Correct: Lissotriton vulgaris';
-        my @ids = $db_entrez->get_taxonids('Chlorella vulgaris');
+        @ids = $db->get_taxonids('Chlorella vulgaris');
         is $ids[0], 3077, 'Correct: Chlorella vulgaris';
-        my @ids = $db_entrez->get_taxonids('Phygadeuon solidus');
+        @ids = $db->get_taxonids('Phygadeuon solidus');
         is $ids[0], 1763951, 'Correct: Phygadeuon solidus';
-        my @ids = $db_entrez->get_taxonids('Ovatus');
+        @ids = $db->get_taxonids('Ovatus');
         is $ids[0], 666060, 'Correct: Ovatus';
-        my @ids = $db_entrez->get_taxonids('Phygadeuon ovatus');
+        @ids = $db->get_taxonids('Phygadeuon ovatus');
         is $ids[0], 'No hit', 'Correct: No hit';
-        my @ids = $db_entrez->get_taxonids('Trimorus ovatus');
+        @ids = $db->get_taxonids('Trimorus ovatus');
         is $ids[0], 'No hit', 'Correct: No hit';
 }

t/Tools/PrositeScan.t

@@ -0,0 +1,44 @@
+use strict;
+
+BEGIN {
+    use lib '.';
+    use Bio::Root::Test;
+
+    test_begin(-tests => 3);
+
+    use_ok('Bio::Tools::PrositeScan');
+    use_ok('Bio::SeqFeature::FeaturePair');
+}
+
+# Note: data generated by running
+#
+#   ./ps_scan.pl --pfscan ./pfscan -d prosite.dat -o fasta \
+#       t/data/test.fasta > t/data/ps_scan/out.PrositeScan
+#
+# followed by a manual removal of some of the output to simplify the test.
+
+subtest "Predictions" => sub {
+    my $factory = Bio::Tools::PrositeScan->new(
+          '-file'   => test_input_file('ps_scan/out.PrositeScan'),
+          '-format' => 'fasta'
+    );
+
+    my $expected_matches = [
+        { seq_id => 'roa1_drome', coords => [253, 256], psac => 'PS00001', subseq => 'NNSF' },
+        { seq_id => 'roa1_drome', coords => [270, 273], psac => 'PS00001', subseq => 'NNSW' },
+        { seq_id => 'roa2_drome', coords => [344, 349], psac => 'PS00008', subseq => 'GNNQGF' },
+        { seq_id => 'roa2_drome', coords => [217, 355], psac => 'PS50321', subseq => re(qr/NR.{135}NN/) },
+    ];
+
+    my $actual_matches = [];
+    while( my $match = $factory->next_prediction ) {
+        push @$actual_matches, {
+            seq_id  =>   $match->seq_id,
+            coords  => [ $match->start, $match->end ],
+            psac    =>   $match->hseq_id,
+            subseq  =>   $match->feature1->seq->seq,
+        };
+    }
+
+    cmp_deeply( $actual_matches, $expected_matches, 'Comparing parsed prediction input' );
+};

t/data/ps_scan/out.PrositeScan

@@ -0,0 +1,10 @@
+>roa1_drome/253-256 : PS00001 ASN_GLYCOSYLATION 
+NNSF
+>roa1_drome/270-273 : PS00001 ASN_GLYCOSYLATION 
+NNSW
+>roa2_drome/344-349 : PS00008 MYRISTYL 
+GNNQGF
+>roa2_drome/217-355 : PS50321 ASN_RICH L=0 
+NRGNMGGGNYGNQNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNN
+NPWDNGNGGGNFGGGGNNWNGGNDFGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAG
+GGNQGNYGNNQGFNNGGNN