Mercurial > repos > yating-l > jbrowsearchivecreator

comparison util/subtools.py @ 46:061da5d3a219 draft

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 3160592f4119e684ab5843dd28a2e6cf11df0121-dirty
author yating-l
date Tue, 19 Jun 2018 16:28:36 -0400
parents 4a69515eed63
children 1eb4adefd747
comparison
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45:d56955fc4c75 46:061da5d3a219
380 createFastaIndex(fastaFile) 380 createFastaIndex(fastaFile)
381 array_call = ['prepare-refseqs.pl', '--indexed_fasta', fastaFile, '--out', outputFolder] 381 array_call = ['prepare-refseqs.pl', '--indexed_fasta', fastaFile, '--out', outputFolder]
382 p = _handleExceptionAndCheckCall(array_call) 382 p = _handleExceptionAndCheckCall(array_call)
383 return p 383 return p
384 384
385 def generate_names(outputFolder, hashBits=4): 385 def generate_names(outputFolder, nameIndexTrackList, hashBits=4):
386 array_call = ['generate-names.pl', '--hashBits', '4', '-v', '--out', outputFolder] 386 array_call = ['generate-names.pl', '--hashBits', hashBits, '-v', '--completionLimit', '0', '--out', outputFolder]
387 if nameIndexTrackList:
388 array_call.append('--tracks')
389 array_call.append(','.join(nameIndexTrackList))
387 p = _handleExceptionAndCheckCall(array_call) 390 p = _handleExceptionAndCheckCall(array_call)
388 return p 391 return p
389 392
390 def validateFiles(input_file, chrom_sizes_file_name, file_type, options=None): 393 def validateFiles(input_file, chrom_sizes_file_name, file_type, options=None):
391 """ 394 """