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Closed issue EI-CoreBioinformatics#23. Expanded test set, now ID tagg…
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…ing functions as intended. Sorting might still be problematic b/c we might have overlapping +/- superloci, but in general it seems to function.
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Luca Venturini authored and Luca Venturini committed Oct 5, 2015
1 parent 9bebe67 commit b1dde15
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Showing 5 changed files with 270 additions and 154 deletions.
36 changes: 36 additions & 0 deletions sample_data/class.gtf
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@@ -1,3 +1,28 @@
Chr5 CLASS transcript 26575711 26578087 1000 - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6272";exon_number "1";Abundance "2.980217";
Chr5 CLASS exon 26575711 26575797 . - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6272";
Chr5 CLASS exon 26575885 26575944 . - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6272";
Chr5 CLASS exon 26576035 26576134 . - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6272";
Chr5 CLASS exon 26576261 26577069 . - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6272";
Chr5 CLASS exon 26577163 26577288 . - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6272";
Chr5 CLASS exon 26577378 26577449 . - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6272";
Chr5 CLASS exon 26577856 26578087 . - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6272";
Chr5 CLASS transcript 26575711 26579730 1000 - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6271";exon_number "1";Abundance "1.141582";
Chr5 CLASS exon 26575711 26575797 . - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6271";
Chr5 CLASS exon 26575885 26575944 . - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6271";
Chr5 CLASS exon 26576035 26576134 . - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6271";
Chr5 CLASS exon 26576261 26577069 . - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6271";
Chr5 CLASS exon 26577163 26577288 . - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6271";
Chr5 CLASS exon 26577378 26577449 . - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6271";
Chr5 CLASS exon 26577856 26577937 . - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6271";
Chr5 CLASS exon 26578239 26578792 . - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6271";
Chr5 CLASS exon 26579079 26579161 . - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6271";
Chr5 CLASS exon 26579301 26579395 . - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6271";
Chr5 CLASS exon 26579602 26579730 . - . gene_id "Chr5.5875.gene";transcript_id "Chr5.6271";
Chr5 CLASS transcript 26581272 26583672 1000 - . gene_id "Chr5.5876.gene";transcript_id "Chr5.6273";exon_number "1";Abundance "0.847970";
Chr5 CLASS exon 26581272 26581528 . - . gene_id "Chr5.5876.gene";transcript_id "Chr5.6273";
Chr5 CLASS exon 26583335 26583672 . - . gene_id "Chr5.5876.gene";transcript_id "Chr5.6273";
Chr5 CLASS transcript 26583267 26583672 1000 . . gene_id "Chr5.5877.gene";transcript_id "Chr5.6274";exon_number "1";Abundance "0.637901";
Chr5 CLASS exon 26583267 26583672 . . . gene_id "Chr5.5877.gene";transcript_id "Chr5.6274";
Chr5 CLASS transcript 26584128 26584508 1000 - . gene_id "Chr5.5878.gene";transcript_id "Chr5.6275";exon_number "1";Abundance "0.080689";
Chr5 CLASS exon 26584128 26584278 . - . gene_id "Chr5.5878.gene";transcript_id "Chr5.6275";
Chr5 CLASS exon 26584358 26584508 . - . gene_id "Chr5.5878.gene";transcript_id "Chr5.6275";
Expand Down Expand Up @@ -67,3 +92,14 @@ Chr5 CLASS exon 26600314 26600394 . + . gene_id "Chr5.5885.gene";transcript_id "
Chr5 CLASS exon 26600497 26600616 . + . gene_id "Chr5.5885.gene";transcript_id "Chr5.6286";
Chr5 CLASS exon 26600696 26600908 . + . gene_id "Chr5.5885.gene";transcript_id "Chr5.6286";
Chr5 CLASS exon 26600987 26601137 . + . gene_id "Chr5.5885.gene";transcript_id "Chr5.6286";
Chr5 CLASS transcript 26603313 26604166 1000 - . gene_id "Chr5.5887.gene";transcript_id "Chr5.6287";exon_number "1";Abundance "85.574225";
Chr5 CLASS exon 26603313 26603638 . - . gene_id "Chr5.5887.gene";transcript_id "Chr5.6287";
Chr5 CLASS exon 26603727 26604166 . - . gene_id "Chr5.5887.gene";transcript_id "Chr5.6287";
Chr5 CLASS transcript 26612190 26614205 1000 - . gene_id "Chr5.5888.gene";transcript_id "Chr5.6289";exon_number "1";Abundance "0.230108";
Chr5 CLASS exon 26612190 26612727 . - . gene_id "Chr5.5888.gene";transcript_id "Chr5.6289";
Chr5 CLASS exon 26612846 26613194 . - . gene_id "Chr5.5888.gene";transcript_id "Chr5.6289";
Chr5 CLASS exon 26613900 26614205 . - . gene_id "Chr5.5888.gene";transcript_id "Chr5.6289";
Chr5 CLASS transcript 26612190 26614205 1000 - . gene_id "Chr5.5888.gene";transcript_id "Chr5.6288";exon_number "1";Abundance "0.228615";
Chr5 CLASS exon 26612190 26612727 . - . gene_id "Chr5.5888.gene";transcript_id "Chr5.6288";
Chr5 CLASS exon 26612846 26612932 . - . gene_id "Chr5.5888.gene";transcript_id "Chr5.6288";
Chr5 CLASS exon 26613900 26614205 . - . gene_id "Chr5.5888.gene";transcript_id "Chr5.6288";
2 changes: 1 addition & 1 deletion sample_data/configuration.yaml
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Expand Up @@ -22,7 +22,7 @@ run_options:
purge: true
remove_overlapping_fragments: true
fragments_maximal_cds: 100
subloci_from_cds_only: true
subloci_from_cds_only: false
threads: 5
preload: true
scoring_file: plants.yaml
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