# Testing Bio::Gonzales 0.082, Perl 5.026002, /usr/bin/perl t/00-load.t ................................ 1..1 ok 1 - use Bio::Gonzales; ok t/Bio-Gonzales-Align-IO.t .................. ok 1 - use Bio::Gonzales::Align::IO; ok 2 ok 3 ok 4 1..4 ok Track length: 130 Track length: 130 t/Bio-Gonzales-Align-Jalview.t ............. ok 1 - use Bio::Gonzales::Align::Jalview; ok 2 - track marks ok 3 - complete annotation 1..3 ok t/Bio-Gonzales-Domain-Group.t .............. ok 1 - use Bio::Gonzales::Domain::Group; ok 2 ok 3 ok 4 ok 5 ok 6 - pSolyc03g095680.1.1; ok 7 - pSolyc10g011940.1.1; ok 8 - pSolyc04g056400.2.1; ok 9 - pSolyc10g049740.1.1; ok 10 1..10 ok feature has no id, made artificial one: __noid_exon_0 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_exon_1 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_exon_2 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_CDS_3 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_CDS_4 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_CDS_5 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_match1_match_6 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_match2_match_7 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_match3_match_8 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_exon_9 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_exon_10 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_exon_11 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_match4_assembly_component_12 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_match5_assembly_component_13 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_match6_assembly_component_14 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_match7_assembly_component_15 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_UTR_16 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_CDS_17 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_CDS_18 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_CDS_19 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_UTR_20 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_five_prime_UTR_21 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_CDS_22 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_CDS_23 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_three_prime_UTR_24 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_three_prime_UTR_25 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_five_prime_UTR_26 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_CDS_27 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_shared_exon_CDS_28 at t/Bio-Gonzales-Feat-IO-BED.t line 23. feature has no id, made artificial one: __noid_CDS_29 at t/Bio-Gonzales-Feat-IO-BED.t line 23. t/Bio-Gonzales-Feat-IO-BED.t ............... ok 1 - use Bio::Gonzales::Feat::IO::BED; ok 2 - use Bio::Gonzales::Feat::IO::GFF3; 1..2 ok t/Bio-Gonzales-Feat-IO-GFF3.t .............. skipped: FIXME t/Bio-Gonzales-Feat-IO-SWISS.t ............. ok 1 - use Bio::Gonzales::Feat::IO::SWISS; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 1..27 ok multiple ID entries, taking the first at t/Bio-Gonzales-Feat.t line 43. multiple ID entries, taking the first at t/Bio-Gonzales-Feat.t line 62. t/Bio-Gonzales-Feat.t ...................... ok 1 - use Bio::Gonzales::Feat; ok 2 - recursion died successfully ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 1..21 ok t/Bio-Gonzales-Matrix-IO-mcl.t ............. skipped: deprecated, develop new with my mio pkg t/Bio-Gonzales-Matrix-IO.t ................. ok 1 - use Bio::Gonzales::Matrix::IO; ok 2 - first line ok 3 - second line ok 4 - last line ok 5 - first line ok 6 - second line ok 7 ok 8 a b ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 1..14 ok t/Bio-Gonzales-Matrix-Util.t ............... ok 1 - use Bio::Gonzales::Matrix::Util; ok 2 1..2 ok t/Bio-Gonzales-Project-Functions.t ......... ok 1 - use Bio::Gonzales::Project::Functions; ok 2 1..2 ok t/Bio-Gonzales-Project.t ................... # Seeded srand with seed '20190322' from local date. ok 1 1..1 ok t/Bio-Gonzales-Range-Cluster.t ............. ok 1 - use Bio::Gonzales::Range::Cluster; ok 2 - ranges ok 3 - pick up first cluster ok 4 - pick up clears the clusters of the object ok 5 ok 6 - pick up clears the clusters of the object ok 7 - empty object finished without results ok 8 - add_next_range should not accept inverted ranges ok 9 - add_next_range should not accept empty ranges ok 10 1..10 ok t/Bio-Gonzales-Range-Overlap.t ............. ok 1 - use Bio::Gonzales::Range::Overlap; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 1..19 ok empty ranges at t/Bio-Gonzales-Range-Util.t line 96. empty ranges at t/Bio-Gonzales-Range-Util.t line 99. t/Bio-Gonzales-Range-Util.t ................ ok 1 - use Bio::Gonzales::Range::Util; ok 2 - with overlap ok 3 - book ended, q after r ok 4 - book ended, r after q ok 5 - no overlap 1 ok 6 - overlap 2 ok 7 - overlap 3 ok 8 - overlap 4 ok 9 - no overlap, book ended, q after r ok 10 - no overlap, book ended, r after q ok 11 - no overlap, book ended, r after q ok 12 - offset 4a, q after r ok 13 - offset 4b, q after r ok 14 - offset 4c, q after r ok 15 - offset 4d, q after r ok 16 - offset 4e, q after r ok 17 - offset 4f, q after r ok 18 - offset 4g, q after r ok 19 - offset 4a, r after q ok 20 - offset 4b, r after q ok 21 - offset 4c, r after q ok 22 - offset 4d, r after q ok 23 - offset 4e, r after q ok 24 - offset 4f, r after q ok 25 - ranges ok 26 ok 27 ok 28 1..28 ok t/Bio-Gonzales-Role-BioPerl-Constructor.t .. ok 1 ok 2 ok 3 ok 4 1..4 ok t/Bio-Gonzales-Search-IO-HMMER3.t .......... ok 1 - use Bio::Gonzales::Search::IO::HMMER3; ok 2 - empty hmm3 search result ok 3 - starch error w/ alignments 1..3 ok t/Bio-Gonzales-Seq-Filter.t ................ ok 1 - use Bio::Gonzales::Seq::Filter; ok 2 - clean error stuff 1..2 ok Name "main::phred_fp2chr_raw" used only once: possible typo at t/Bio-Gonzales-Seq-IO-fastq.t line 67. t/Bio-Gonzales-Seq-IO-fastq.t .............. ok 1 - use Bio::Gonzales::Seq::IO::fastq; ok 2 ok 3 ok 4 ok 5 1..5 ok t/Bio-Gonzales-Seq-Util.t .................. ok 1 - use Bio::Gonzales::Seq::Util; 1..1 ok t/Bio-Gonzales-Seq-Validate-fasta.t ........ ok 1 - use Bio::Gonzales::Seq::Validate::fasta; ok 2 - validate 1..2 ok t/Bio-Gonzales-Seq.t ....................... ok 1 - use Bio::Gonzales::Seq; ok 2 ok 3 1..3 ok t/Bio-Gonzales-SummarizedExperiment.t ...... ok 1 - use Bio::Gonzales::SummarizedExperiment; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 1..32 ok t/Bio-Gonzales-Tools-SeqMask.t ............. ok 1 - use Bio::Gonzales::Tools::SeqMask; ok 2 - mask dna sequence ok 3 - mask rna sequence ok 4 - mask protein sequence ok 5 - mask dna sequence ok 6 - mask dna sequence ok 7 - mask dna sequence 1..7 ok t/Bio-Gonzales-Util-Cerial.t ............... ok 1 - use Bio::Gonzales::Util::Cerial; ok 2 ok 3 ok 4 ok 5 1..5 ok # /bin/gzip t/Bio-Gonzales-Util-File.t ................. ok 1 - use Bio::Gonzales::Util::File; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 1..19 ok t/Bio-Gonzales-Util-Log.t .................. ok 1 - use Bio::Gonzales::Util::Log; ok 2 - log debug test 1..2 ok t/Bio-Gonzales-Util-Log_threads.t .......... ok 1 - use Bio::Gonzales::Util::Log; ok 2 - log debug test 1..2 ok t/Bio-Gonzales-Util-Math.t ................. ok 1 - use Bio::Gonzales::Util::Math; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 1..11 ok t/Bio-Gonzales-Util-Text.t ................. ok 1 - use Bio::Gonzales::Util::Text; ok 2 - basic 1..2 ok t/Bio-Gonzales-Util.t ...................... ok 1 - use Bio::Gonzales::Util; ok 2 ok 3 1..3 ok # $VAR1 = [ # '0/0:10', # '1/1:11', # '2/2:22:33:44' # ]; # $VAR1 = [ # '0/0:10', # '3/3:11', # '4/4:22:33:44' # ]; # $VAR1 = [ # '0/0:10', # '3/3:11', # '4/4:22:33:44' # ]; t/Bio-Gonzales-Var-Util.t .................. ok 1 - use Bio::Gonzales::Var::Util; 1..1 ok t/boilerplate.t ............................ 1..1 ok 1 - lib/Bio/Gonzales.pm contains no boilerplate text ok t/gonz_unmap.t ............................. ok 1 ok 2 1..2 ok t/IDMapIO.t ................................ skipped: needs revision t/manifest.t ............................... skipped: Author tests not required for installation Training idx: $VAR1 = [ 1, 3 ]; (1, 0) => 1 (3, 0) => 2 0 -> $VAR1 = [ 1 ]; (1, 2) => 10 (3, 2) => 2 2 -> $VAR1 = [ 3 ]; t/Math-kNN-via-Distances.t ................. ok 1 - use Bio::Gonzales::Util::Math::kNN::via::Distances; ok 2 - basics 1..2 ok All tests successful. Files=38, Tests=253, 8 wallclock secs ( 0.09 usr 0.04 sys + 4.62 cusr 0.58 csys = 5.33 CPU) Result: PASS