diff --git a/modules/t/circularSlice.t b/modules/t/circularSlice.t index 129cef8f4000500745d037244e6c270e0425a83d..a118d526d004c4a10c2e3d313033d88f7a991a2b 100644 --- a/modules/t/circularSlice.t +++ b/modules/t/circularSlice.t @@ -45,6 +45,28 @@ is($slice->seq_region_length, $SEQ_REGION_LENGTH, "seq_region_length == $SEQ_REGION_LENGTH"); is($slice->adaptor, $slice_adaptor, "adaptor is adaptor"); +# centrepoint method +is($slice->centrepoint, 5402639, "slice centre point"); + +# _split private method +my ($sl1, $sl2) = $slice->_split; +isa_ok($sl1, 'Bio::EnsEMBL::CircularSlice'); +is($sl1->is_circular, 1,"subslice is circular"); +is($sl1->seq_region_name, $CHR,"subslice seq region name $CHR"); +is($sl1->start, $START, "subslice start == $START"); +is($sl1->end, $SEQ_REGION_LENGTH, "subslice end == $SEQ_REGION_LENGTH"); + +isa_ok($sl2, 'Bio::EnsEMBL::CircularSlice'); +is($sl2->is_circular, 1,"subslice is circular"); +is($sl2->seq_region_name, $CHR,"subslice seq region name $CHR"); +is($sl2->start, 1, "subslice start == 1"); +is($sl2->end, $END, "subslice end == $END"); + +# seq method +my $seq = $slice->seq; +is(length $seq, 205278, "sequence length"); +exit; + my $slstart = $slice_adaptor->fetch_by_region($COORD_SYSTEM, $CHR, 1, $END); my $slend = $slice_adaptor->fetch_by_region($COORD_SYSTEM, $CHR, $START, $SEQ_REGION_LENGTH); diff --git a/modules/t/gtfSerialiser.t b/modules/t/gtfSerialiser.t index c66b9b1623da4301b4d3af08b35de48b221eadb0..6ed0ede5e704334d66536941c28f99e009e99094 100644 --- a/modules/t/gtfSerialiser.t +++ b/modules/t/gtfSerialiser.t @@ -54,9 +54,10 @@ 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\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\"; +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\"; ", +# 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\"; @@ -72,12 +73,11 @@ 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\"; @@ -87,6 +87,7 @@ 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();