Mercurial > repos > yating-l > jbrowse_hub
comparison trackObject.py @ 50:3e5b6f6a9abe draft
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 6391cdb975d14b5a7060fa1665a8a575797a0eaa-dirty
author | yating-l |
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date | Thu, 30 Mar 2017 16:03:16 -0400 |
parents | a5108e5010b4 |
children |
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49:193e94a43f0f | 50:3e5b6f6a9abe |
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31 """ | 31 """ |
32 false_path = os.path.abspath(dataFile) | 32 false_path = os.path.abspath(dataFile) |
33 fileName = os.path.basename(dataFile) | 33 fileName = os.path.basename(dataFile) |
34 des_path = os.path.join(self.raw_folder, fileName) | 34 des_path = os.path.join(self.raw_folder, fileName) |
35 track = {} | 35 track = {} |
36 if dataType == 'gff3_mrna' or dataType == 'gff3_transcript' or dataType == 'fasta' or dataType == 'bam' or dataType == 'bigwig' or dataType == 'bai': | 36 if dataType == 'bed' or dataType == 'gff3' or dataType == 'gff3_mrna' or dataType == 'gff3_transcript' or dataType == 'fasta' or dataType == 'bam' or dataType == 'bigwig': |
37 if dataType == 'bam': | 37 if dataType == 'bam': |
38 # JBrowse will raise error: not a BAM file if the filename hasn't .bam extension | 38 # JBrowse will raise error: not a BAM file if the filename hasn't .bam extension |
39 fileName = fileName + '.bam' | 39 extension = os.path.splitext(fileName)[1] |
40 if extension != '.bam': | |
41 fileName = fileName + '.bam' | |
40 des_path = os.path.join(self.raw_folder, fileName) | 42 des_path = os.path.join(self.raw_folder, fileName) |
41 bam_index = utils.createBamIndex(dataFile) | 43 bam_index = utils.createBamIndex(dataFile) |
42 indexname = os.path.basename(bam_index) | 44 indexname = os.path.basename(bam_index) |
43 des_path_for_index = os.path.join(self.raw_folder, indexname) | 45 des_path_for_index = os.path.join(self.raw_folder, indexname) |
44 shutil.copyfile(bam_index, des_path_for_index) | 46 shutil.copyfile(bam_index, des_path_for_index) |