Methods to support testing

modules/t/gtfSerialiser.t

@@ -2,36 +2,127 @@ use strict;
 use warnings;
 
 use Test::More;
+use Data::Dumper;
+
+use Bio::EnsEMBL::ApiVersion qw/software_version/;
+use Bio::EnsEMBL::Utils::IO qw/gz_work_with_file iterate_lines/;
 use Bio::EnsEMBL::Test::MultiTestDB;
 use Bio::EnsEMBL::Utils::IO::GTFSerializer;
 use IO::String;
+use Net::FTP;
 
-my $db = Bio::EnsEMBL::Test::MultiTestDB->new();
-my $dba = $db->get_DBAdaptor('core');
+my $current_release = software_version();
+my $last_release = $current_release - 1;
+my $release = $last_release;
 
-my $id = 'ENSG00000131044';
+SKIP: {
+  my $ftp = eval { ensembl_ftp_connect() };
+  skip "Cannot login to Ensembl FTP site. We cannot continue with the tests"
+    if $@;
 
-my $ga = $dba->get_GeneAdaptor();
-my $gene = $ga->fetch_by_stable_id($id);
+  my $species_list = eval { get_species_list($ftp, $release) };
+  skip "Cannot retrieve GTF species list from FTP site (release $release). We cannot continue with the tests." 
+    if $@;
+  skip "Empty GTF species list from FTP site (release $release). We cannot continue with the tests" 
+    unless scalar $species_list;
 
-SKIP: {
-  my $fh = IO::String->new();
-  my $ser = Bio::EnsEMBL::Utils::IO::GTFSerializer->new($fh);
-  # $ser->print_main_header([$gene->feature_Slice()]);
-  $ser->print_feature($gene);
-  
-  my $expected = <<'OUT';
-##gff-version 3
-##sequence-region   20 30274334 30300924
-OUT
-  #Have to do this outside of the HERETO thanks to tabs
-  $expected .= join("\t", 
-    qw/20  EnsEMBL feature 30274334  30300924  . + ./,
-    'ID=ENSG00000131044;logic_name=ensembl;external_name=C20orf125;description=DJ310O13.1.2 (NOVEL PROTEIN SIMILAR DROSOPHILA PROTEIN CG7474%2C ISOFORM 2 ) (FRAGMENT). [Source:SPTREMBL%3BAcc:Q9BR18];biotype=protein_coding' 
-  );
-  $expected .= "\n";
-
-  is(${$fh->string_ref()}, $expected, 'Gene serialises to GFF3 as expected');
+  foreach my $species (@{$species_list}) {
+    my $species_gtf = 
+      retrieve_gtf_for_species($ftp, $release, $species);  
+
+    skip "Cannot retrieve GTF for $species. We cannot continue with the tests"
+      unless $species_gtf;
+
+    note "Fetching GTF for 10 transcripts randomly chosen";
+    my $transcripts_gtf = get_random_transcripts_gtf($species_gtf, 10);
+    
+    
+    unlink $species_gtf;
+  } 
+
+
+}
+
+done_testing();
+
+sub get_random_transcripts_gtf {
+  my ($gtf_file, $how_many_transcripts) = @_;
+  my $transcripts_gtf;
+
+  gz_work_with_file($gtf_file, 'r', sub {
+    my ($fh) = @_;
+    while( my $line = <$fh> and scalar keys %{$transcripts_gtf} < $how_many_transcripts) {
+      if(random > .5) {
+        chomp($line);
+        $line =~ /transcript_id \"(.+?)\"/; # double quotes?
+  	$transcripts_gtf->{$1} = $line;
+      }
+    }
+  });
+
+  return $transcripts_gtf;
 }
 
-done_testing();
\ No newline at end of file
+
+sub retrieve_gtf_for_species {
+  my ($ftp, $release, $species) = @_;
+
+  $ftp->cwd("/pub/release-$release/gtf/$species");
+  my @gtf_files = grep { $_ =~ /gtf/ } @{$ftp->ls()};
+
+  throw("More than one GTF file detected for $species")
+    if scalar @gtf_files > 1;
+
+  $ftp->binary;
+  return $ftp->get($gtf_files[0]);
+}
+
+sub get_species_list {
+  my ($ftp, $release) = @_;
+  $ftp->cwd("/pub/release-$release/gtf") 
+    or die "Cannot cd to pub/release-$release/gtf";
+
+  return $ftp->ls();
+}
+
+sub ensembl_ftp_connect {
+  my $ftp = Net::FTP->new("ftp.ensembl.org", Debug => 0) or
+    die "Cannot connect to ensembl.org: $@";
+  $ftp->login("anonymous",'-anonymous@') or die "Cannot login ", $ftp->message;
+
+  return $ftp;
+}
+
+
+
+
+
+# my $db = Bio::EnsEMBL::Test::MultiTestDB->new();
+# my $dba = $db->get_DBAdaptor('core');
+
+# my $id = 'ENSG00000131044';
+
+# my $ga = $dba->get_GeneAdaptor();
+# my $gene = $ga->fetch_by_stable_id($id);
+
+# SKIP: {
+#   my $fh = IO::String->new();
+#   my $ser = Bio::EnsEMBL::Utils::IO::GTFSerializer->new($fh);
+#   # $ser->print_main_header([$gene->feature_Slice()]);
+#   $ser->print_feature($gene);
+  
+#   my $expected = <<'OUT';
+# ##gff-version 3
+# ##sequence-region   20 30274334 30300924
+# OUT
+#   #Have to do this outside of the HERETO thanks to tabs
+#   $expected .= join("\t", 
+#     qw/20  EnsEMBL feature 30274334  30300924  . + ./,
+#     'ID=ENSG00000131044;logic_name=ensembl;external_name=C20orf125;description=DJ310O13.1.2 (NOVEL PROTEIN SIMILAR DROSOPHILA PROTEIN CG7474%2C ISOFORM 2 ) (FRAGMENT). [Source:SPTREMBL%3BAcc:Q9BR18];biotype=protein_coding' 
+#   );
+#   $expected .= "\n";
+
+#   is(${$fh->string_ref()}, $expected, 'Gene serialises to GFF3 as expected');
+# }
+
+# done_testing();
\ No newline at end of file