Mercurial > repos > yating-l > jbrowsearchivecreator

comparison util/subtools.py @ 16:8bcec8dbb8be draft

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 0648e2769587d7fd544b3c6dacfa2b5c15a4c4a9
author yating-l
date Mon, 25 Jun 2018 15:39:39 -0400
parents 43a700afd457
children 315a40b0b694
comparison
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15:6464399df918 16:8bcec8dbb8be
292 fileType = 'bed' 292 fileType = 'bed'
293 sortedFile = tempfile.NamedTemporaryFile(bufsize=0) 293 sortedFile = tempfile.NamedTemporaryFile(bufsize=0)
294 bedSort(inputFile, sortedFile) 294 bedSort(inputFile, sortedFile)
295 elif "gff" in dataType: 295 elif "gff" in dataType:
296 fileType = 'gff' 296 fileType = 'gff'
297 filteredFile = tempfile.NamedTemporaryFile(bufsize=0) 297 #filteredFile = tempfile.NamedTemporaryFile(bufsize=0)
298 remove_gene_lines(inputFile, filteredFile.name) 298 #remove_gene_lines(inputFile, filteredFile.name)
299 sortedFile = tempfile.NamedTemporaryFile(bufsize=0) 299 sortedFile = tempfile.NamedTemporaryFile(bufsize=0)
300 gff3sort(filteredFile.name, sortedFile) 300 #gff3sort(filteredFile.name, sortedFile)
301 gff3sort(inputFile, sortedFile)
301 # add .gff3.gz extension to Tabix GFF3 files, in order to enable creating name index with generate-names.pl 302 # add .gff3.gz extension to Tabix GFF3 files, in order to enable creating name index with generate-names.pl
302 trackName = trackName + '.gff3.gz' 303 trackName = trackName + '.gff3.gz'
303 compressedFile = bgzip(sortedFile.name) 304 compressedFile = bgzip(sortedFile.name)
304 tabixFile = createTabix(compressedFile, fileType) 305 tabixFile = createTabix(compressedFile, fileType)
305 trackPath = os.path.join(outputFolder, trackName) 306 trackPath = os.path.join(outputFolder, trackName)