Mercurial > repos > rmarenco > hubarchivecreator

comparison util/subtools.py @ 25:99dad5f9444c draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
author yating-l
date Fri, 02 Jun 2017 17:36:24 -0400
parents fcc1021bd496
children df42241d3731
comparison
equal deleted inserted replaced
24:fcc1021bd496 25:99dad5f9444c
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 import string
14 import tempfile
14 15
15 class PopenError(Exception): 16 class PopenError(Exception):
16 def __init__(self, cmd, error, return_code): 17 def __init__(self, cmd, error, return_code):
17 self.cmd = cmd 18 self.cmd = cmd
18 self.error = error 19 self.error = error
126 Call gff3ToGenePred and write the result into gene_pred_file_name 127 Call gff3ToGenePred and write the result into gene_pred_file_name
127 :param input_gff3_file_name: 128 :param input_gff3_file_name:
128 :param gene_pred_file_name: 129 :param gene_pred_file_name:
129 :return: 130 :return:
130 """ 131 """
131 array_call = ['gff3ToGenePred', input_gff3_file_name, gene_pred_file_name] 132 valid_gff3_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".gff3")
133 validateGff(input_gff3_file_name, valid_gff3_file.name)
134 array_call = ['gff3ToGenePred', valid_gff3_file.name, gene_pred_file_name]
132 p = _handleExceptionAndCheckCall(array_call) 135 p = _handleExceptionAndCheckCall(array_call)
133 return p 136 return p
134 137
135 def genePredToBigGenePred(gene_pred_file_name, unsorted_bigGenePred_file_name): 138 def genePredToBigGenePred(gene_pred_file_name, unsorted_bigGenePred_file_name):
136 """ 139 """
254 return filename 257 return filename
255 valid_chars = "_%s%s" % (string.ascii_letters, string.digits) 258 valid_chars = "_%s%s" % (string.ascii_letters, string.digits)
256 sanitize_name = ''.join([c if c in valid_chars else '_' for c in filename]) 259 sanitize_name = ''.join([c if c in valid_chars else '_' for c in filename])
257 sanitize_name = "gonramp_" + sanitize_name 260 sanitize_name = "gonramp_" + sanitize_name
258 return sanitize_name 261 return sanitize_name
262
263 def validateGff(orig_gff3, valid_gff3):
264 """
265 Remove extra meta line: ##gff-version 3
266 """
267 valid = open(valid_gff3, 'w')
268 num = 0
269 with open(orig_gff3, 'r') as f:
270 for line in f:
271 if '##gff-version 3' in line:
272 if num == 0:
273 num += 1
274 else:
275 continue
276 valid.write(line)
277