Étienne Mollier pushed to branch master at Debian Med / bioperl-run
Commits: 86ba0c47 by Étienne Mollier at 2020-12-04T23:57:46+01:00 flag tests needing adaptations These adaptations are due to the use of a dataset different from the reference data in use by bioperl-run upstream. - - - - - 1 changed file: - debian/patches/alternate-data.patch Changes: ===================================== debian/patches/alternate-data.patch ===================================== @@ -30,3 +30,26 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ ($gene_bed) = `find /usr -name 'knownGene.hg18.chr21.bed' 2>/dev/null`; ($mm8_genome) = `find /usr -name 'mouse.mm8.genome' 2>/dev/null`; ($mm9_genome) = `find /usr -name 'mouse.mm9.genome' 2>/dev/null`; +@@ -326,7 +326,10 @@ + open (FILE, $file); + my $lines =()= <FILE>; + close FILE; ++ TODO: { ++ local $TODO = "maybe adapt reference results to Debian specific dataset"; + is( $lines, $result_lookup{$command}, " - number of lines"); ++ } + } else { + $v && diag(" check can get internal result format matches result file"); + my $guesser = Bio::Tools::GuessSeqFormat->new( -file => $file ); +@@ -356,8 +359,11 @@ + isa_ok( $objres, 'Bio::SeqFeature::Collection', + "returned object is correct for command '$command'" ); + $v && diag(" - correct number of features"); ++ TODO: { ++ local $TODO = "maybe adapt reference results to Debian specific dataset"; + is( scalar $objres->get_all_features, $result_lookup{$command}, + "correct number of features for command '$command'" ); ++ } + last; + }; + m/^fasta$/ && do { View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/commit/86ba0c476be5118a5cec3cc3e1c2bb62c6f93ff4 -- View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/commit/86ba0c476be5118a5cec3cc3e1c2bb62c6f93ff4 You're receiving this email because of your account on salsa.debian.org.
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