Mercurial > repos > rmarenco > hubarchivecreator

comparison util/subtools.py @ 21:884ee2a71680 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
author yating-l
date Wed, 12 Apr 2017 15:05:33 -0400
parents 3233451a3bd6
children fcc1021bd496
comparison
equal deleted inserted replaced
20:40469b265ddb 21:884ee2a71680
8 8
9 import logging 9 import logging
10 import os 10 import os
11 import subprocess 11 import subprocess
12 import sys 12 import sys
13 import string
13 14
14 class PopenError(Exception): 15 class PopenError(Exception):
15 def __init__(self, cmd, error, return_code): 16 def __init__(self, cmd, error, return_code):
16 self.cmd = cmd 17 self.cmd = cmd
17 self.error = error 18 self.error = error
241 # The command to send 242 # The command to send
242 array_call = ['pslToBigPsl', input_psl_file_name, output_bed12_file_name] 243 array_call = ['pslToBigPsl', input_psl_file_name, output_bed12_file_name]
243 244
244 p = _handleExceptionAndCheckCall(array_call) 245 p = _handleExceptionAndCheckCall(array_call)
245 return p 246 return p
247
248 #santitize trackName. Because track name must begin with a letter and
249 # contain only the following chars: [a-zA-Z0-9_].
250 # See the "track" Common settings at:
251 #https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html#bigPsl_-_Pairwise_Alignments
252 def fixName(filename):
253 valid_chars = "_%s%s" % (string.ascii_letters, string.digits)
254 sanitize_name = ''.join([c if c in valid_chars else '_' for c in filename])
255 sanitize_name = "gonramp_" + sanitize_name
256 return sanitize_name