Mercurial > repos > yating-l > jbrowse_hub
diff trackObject.py @ 50:3e5b6f6a9abe draft
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 6391cdb975d14b5a7060fa1665a8a575797a0eaa-dirty
| author | yating-l |
|---|---|
| date | Thu, 30 Mar 2017 16:03:16 -0400 |
| parents | a5108e5010b4 |
| children |
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--- a/trackObject.py Wed Mar 29 14:46:23 2017 -0400 +++ b/trackObject.py Thu Mar 30 16:03:16 2017 -0400 @@ -33,10 +33,12 @@ fileName = os.path.basename(dataFile) des_path = os.path.join(self.raw_folder, fileName) track = {} - if dataType == 'gff3_mrna' or dataType == 'gff3_transcript' or dataType == 'fasta' or dataType == 'bam' or dataType == 'bigwig' or dataType == 'bai': + if dataType == 'bed' or dataType == 'gff3' or dataType == 'gff3_mrna' or dataType == 'gff3_transcript' or dataType == 'fasta' or dataType == 'bam' or dataType == 'bigwig': if dataType == 'bam': # JBrowse will raise error: not a BAM file if the filename hasn't .bam extension - fileName = fileName + '.bam' + extension = os.path.splitext(fileName)[1] + if extension != '.bam': + fileName = fileName + '.bam' des_path = os.path.join(self.raw_folder, fileName) bam_index = utils.createBamIndex(dataFile) indexname = os.path.basename(bam_index)