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Commit ef348ffc authored by Alessandro Vullo's avatar Alessandro Vullo
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Correct expected string

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modules/t/gtfSerialiser.t
+ 4
− 5
View file @ ef348ffc
......@@ -54,10 +54,9 @@ my $transcripts_gtf =
20\tprotein_coding\texon\t30315002\t30315126\t.\t+\t.\tgene_id \"ENSG00000174873\"; transcript_id \"ENST00000252021\"; exon_number \"5\"; gene_biotype \"protein_coding\"; exon_id \"ENSE00001155819\";
20\tprotein_coding\tCDS\t30315002\t30315126\t.\t+\t1\tgene_id \"ENSG00000174873\"; transcript_id \"ENST00000252021\"; exon_number \"5\"; gene_biotype \"protein_coding\"; protein_id \"ENSP00000252021\";
20\tprotein_coding\texon\t30318805\t30318881\t.\t+\t.\tgene_id \"ENSG00000174873\"; transcript_id \"ENST00000252021\"; exon_number \"6\"; gene_biotype \"protein_coding\"; exon_id \"ENSE00001180793\";
20\tprotein_coding\tCDS\t30318805\t30318881\t.\t+\t2\tgene_id \"ENSG00000174873\"; transcript_id \"ENST00000252021\"; exon_number \"6\"; gene_biotype \"protein_coding\"; protein_id \"ENSP00000252021\";
20\tprotein_coding\tCDS\t30318805\t30318878\t.\t+\t2\tgene_id \"ENSG00000174873\"; transcript_id \"ENST00000252021\"; exon_number \"6\"; gene_biotype \"protein_coding\"; protein_id \"ENSP00000252021\";
20\tprotein_coding\tstop_codon\t30318879\t30318881\t.\t+\t0\tgene_id \"ENSG00000174873\"; transcript_id \"ENST00000252021\"; exon_number \"6\"; gene_biotype \"protein_coding\";
",
# last line 20\tprotein_coding\tstop_codon\t30318879\t30318881\t.\t+\t0\tgene_id \"ENSG00000174873\"; transcript_id \"ENST00000252021\"; exon_number \"6\"; gene_biotype \"protein_coding\";
# CDS end on previous line extended to stop_codon length, was 30318878
ENST00000202017 => "20\tprotein_coding\texon\t30327735\t30327869\t.\t-\t.\tgene_id \"ENSG00000088356\"; transcript_id \"ENST00000202017\"; exon_number \"1\"; gene_name \"C20orf126\"; gene_biotype \"protein_coding\"; transcript_name \"C20orf126\"; exon_id \"ENSE00001155739\";
20\tprotein_coding\tCDS\t30327735\t30327869\t.\t-\t0\tgene_id \"ENSG00000088356\"; transcript_id \"ENST00000202017\"; exon_number \"1\"; gene_name \"C20orf126\"; gene_biotype \"protein_coding\"; transcript_name \"C20orf126\"; protein_id \"ENSP00000202017\";
......@@ -73,11 +72,12 @@ my $transcripts_gtf =
ENST00000246203 => "20\tprotein_coding\texon\t30565065\t30566129\t.\t-\t.\tgene_id \"ENSG00000125979\"; transcript_id \"ENST00000246203\"; exon_number \"1\"; gene_name \"TSPYL3\"; gene_biotype \"protein_coding\"; transcript_name \"TSPYL3\"; exon_id \"ENSE00000859919\";
20\tprotein_coding\tCDS\t30565065\t30566129\t.\t-\t0\tgene_id \"ENSG00000125979\"; transcript_id \"ENST00000246203\"; exon_number \"1\"; gene_name \"TSPYL3\"; gene_biotype \"protein_coding\"; transcript_name \"TSPYL3\"; protein_id \"ENSP00000246203\";
20\tprotein_coding\tstart_codon\t30566127\t30566129\t.\t-\t0\tgene_id \"ENSG00000125979\"; transcript_id \"ENST00000246203\"; exon_number \"1\"; gene_name \"TSPYL3\"; gene_biotype \"protein_coding\"; transcript_name \"TSPYL3\";
",
# last line 20\tprotein_coding\tstart_codon\t30566127\t30566129\t.\t-\t0\tgene_id \"ENSG00000125979\"; transcript_id \"ENST00000246203\"; exon_number \"1\"; gene_name \"TSPYL3\"; gene_biotype \"protein_coding\"; transcript_name \"TSPYL3\";
ENST00000201961 => "20\tprotein_coding\texon\t30911297\t30911383\t.\t-\t.\tgene_id \"ENSG00000088303\"; transcript_id \"ENST00000201961\"; exon_number \"1\"; gene_name \"Q9NQF5\"; gene_biotype \"protein_coding\"; transcript_name \"Q9NQF5\"; exon_id \"ENSE00000661216\";
20\tprotein_coding\tCDS\t30911297\t30911383\t.\t-\t0\tgene_id \"ENSG00000088303\"; transcript_id \"ENST00000201961\"; exon_number \"1\"; gene_name \"Q9NQF5\"; gene_biotype \"protein_coding\"; transcript_name \"Q9NQF5\"; protein_id \"ENSP00000201961\";
20\tprotein_coding\tstart_codon\t30911381\t30911383\t.\t-\t0\tgene_id \"ENSG00000088303\"; transcript_id \"ENST00000201961\"; exon_number \"1\"; gene_name \"Q9NQF5\"; gene_biotype \"protein_coding\"; transcript_name \"Q9NQF5\";
20\tprotein_coding\texon\t30903618\t30903773\t.\t-\t.\tgene_id \"ENSG00000088303\"; transcript_id \"ENST00000201961\"; exon_number \"2\"; gene_name \"Q9NQF5\"; gene_biotype \"protein_coding\"; transcript_name \"Q9NQF5\"; exon_id \"ENSE00000661215\";
20\tprotein_coding\tCDS\t30903618\t30903773\t.\t-\t0\tgene_id \"ENSG00000088303\"; transcript_id \"ENST00000201961\"; exon_number \"2\"; gene_name \"Q9NQF5\"; gene_biotype \"protein_coding\"; transcript_name \"Q9NQF5\"; protein_id \"ENSP00000201961\";
20\tprotein_coding\texon\t30896671\t30896782\t.\t-\t.\tgene_id \"ENSG00000088303\"; transcript_id \"ENST00000201961\"; exon_number \"3\"; gene_name \"Q9NQF5\"; gene_biotype \"protein_coding\"; transcript_name \"Q9NQF5\"; exon_id \"ENSE00000560920\";
......@@ -87,7 +87,6 @@ my $transcripts_gtf =
20\tprotein_coding\texon\t30885729\t30885800\t.\t-\t.\tgene_id \"ENSG00000088303\"; transcript_id \"ENST00000201961\"; exon_number \"5\"; gene_name \"Q9NQF5\"; gene_biotype \"protein_coding\"; transcript_name \"Q9NQF5\"; exon_id \"ENSE00000661212\";
20\tprotein_coding\tCDS\t30885729\t30885800\t.\t-\t0\tgene_id \"ENSG00000088303\"; transcript_id \"ENST00000201961\"; exon_number \"5\"; gene_name \"Q9NQF5\"; gene_biotype \"protein_coding\"; transcript_name \"Q9NQF5\"; protein_id \"ENSP00000201961\";
"
# third line 20\tprotein_coding\tstart_codon\t30911381\t30911383\t.\t-\t0\tgene_id \"ENSG00000088303\"; transcript_id \"ENST00000201961\"; exon_number \"1\"; gene_name \"Q9NQF5\"; gene_biotype \"protein_coding\"; transcript_name \"Q9NQF5\";
};
my $mtdb = Bio::EnsEMBL::Test::MultiTestDB->new();
......
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