Mercurial > repos > yating-l > jbrowse_hub
changeset 28:5580dbf2a31c draft
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit e81fecac281f299db00cfc88a068e056b031ae9d-dirty
| author | yating-l |
|---|---|
| date | Wed, 15 Mar 2017 11:36:09 -0400 |
| parents | e025fa070c8d |
| children | d917e081decd |
| files | jbrowse_hub.py trackObject.py |
| diffstat | 2 files changed, 5 insertions(+), 3 deletions(-) [+] |
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--- a/jbrowse_hub.py Wed Mar 15 10:54:24 2017 -0400 +++ b/jbrowse_hub.py Wed Mar 15 11:36:09 2017 -0400 @@ -44,8 +44,6 @@ # BAM format parser.add_argument('--bam', action='append', help='BAM format from HISAT') - # put bam index file at the same directory with bam file - parser.add_argument('--bai', action='append', help='BAM index format from HISAT') # BIGWIG format parser.add_argument('--bigwig', action='append', help='BIGWIG format to show rnaseq coverage') @@ -73,7 +71,6 @@ chrom_size = utils.getChromSizes(reference, tool_directory) all_tracks = trackObject.trackObject(chrom_size.name, genome, extra_files_path) #store converted files in the array: all_tracks.tracks array_inputs_bam = args.bam - array_inputs_bai = args.bai array_inputs_bed_simple_repeats = args.bedSimpleRepeats array_inputs_bed_splice_junctions = args.bedSpliceJunctions array_inputs_bigwig = args.bigwig
--- a/trackObject.py Wed Mar 15 10:54:24 2017 -0400 +++ b/trackObject.py Wed Mar 15 11:36:09 2017 -0400 @@ -30,16 +30,21 @@ Convert gff3, BED, blastxml and gtf files into gff3 files and store converted files in folder 'raw' ''' + 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 == 'bam': + # JBrowse will raise error: not a BAM file if the filename hasn't .bam extension + fileName = os.path.basename(dataFile) + '.bam' + des_path = os.path.join(self.raw_folder, fileName) bam_index = utils.createBamIndex(dataFile) indexname = os.path.basename(bam_index) des_path_for_index = os.path.join(self.raw_folder, indexname) shutil.copyfile(bam_index, des_path_for_index) track['index'] = indexname + try: shutil.copyfile(dataFile, des_path) except shutil.Error as err1: