Mercurial > repos > rmarenco > hubarchivecreator

comparison util/subtools.py @ 13:25809f699cb3 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
author rmarenco
date Thu, 11 Aug 2016 19:02:29 -0400
parents acc233161f50
children 3233451a3bd6
comparison
equal deleted inserted replaced
12:747475757cb0 13:25809f699cb3
4 """ 4 """
5 This class handles the subprocess calls of the different tools used 5 This class handles the subprocess calls of the different tools used
6 in HubArchiveCreator 6 in HubArchiveCreator
7 """ 7 """
8 8
9 import logging
9 import os 10 import os
10 import subprocess 11 import subprocess
11 12 import sys
13
14 class PopenError(Exception):
15 def __init__(self, cmd, error, return_code):
16 self.cmd = cmd
17 self.error = error
18 self.return_code = return_code
19
20 def __str__(self):
21 message = "The subprocess {0} has returned the error: {1}.".format(self.cmd, self.return_code)
22 message = ','.join((message, "Its error message is: {0}".format(self.error)))
23 return repr(message)
12 24
13 def _handleExceptionAndCheckCall(array_call, **kwargs): 25 def _handleExceptionAndCheckCall(array_call, **kwargs):
14 """ 26 """
15 This class handle exceptions and call the tool. 27 This class handle exceptions and call the tool.
16 It maps the signature of subprocess.check_call: 28 It maps the signature of subprocess.check_call:
18 """ 30 """
19 stdin = kwargs.get('stdin') 31 stdin = kwargs.get('stdin')
20 stdout = kwargs.get('stdout') 32 stdout = kwargs.get('stdout')
21 stderr = kwargs.get('stderr') 33 stderr = kwargs.get('stderr')
22 shell = kwargs.get('shell') 34 shell = kwargs.get('shell')
35
36 cmd = array_call[0]
37
38 output = None
39 error = None
40
41 # TODO: Check the value of array_call and <=[0]
42 logging.debug("Calling {0}:".format(cmd))
43
44 logging.debug("---------")
45
46 # TODO: Use universal_newlines option from Popen?
23 try: 47 try:
24 p = subprocess.check_call(array_call, stdin=stdin, stdout=stdout, stderr=stderr, shell=shell) 48 p = subprocess.Popen(array_call, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=shell)
25 except subprocess.CalledProcessError: 49 output, error = p.communicate()
26 raise 50
51 logging.debug("\t{0}".format(output))
52 # If we detect an error from the subprocess, then we raise an exception
53 # TODO: Manage if we raise an exception for everything, or use CRITICAL etc... but not stop process
54 # TODO: The responsability of returning a sys.exit() should not be there, but up in the app.
55 if p.returncode:
56 raise PopenError(cmd, error, p.returncode)
57
58 except OSError as e:
59 message = "The subprocess {0} has encountered an OSError: {1}".format(cmd, e.strerror)
60 if e.filename:
61 message = '\n'.join((message, ", against this file: {0}".format(e.filename)))
62 logging.error(message)
63 sys.exit(-1)
64 except PopenError as p:
65 message = "The subprocess {0} has returned the error: {1}.".format(p.cmd, p.return_code)
66 message = '\n'.join((message, "Its error message is: {0}".format(p.error)))
67
68 logging.exception(message)
69
70 sys.exit(p.return_code)
71 except Exception as e:
72 message = "The subprocess {0} has encountered an unknown error: {1}".format(cmd, e)
73 logging.exception(message)
74
75 sys.exit(-1)
27 return p 76 return p
28 77
29 78
30 def twoBitInfo(two_bit_file_name, two_bit_info_file): 79 def twoBitInfo(two_bit_file_name, two_bit_info_file):
31 """ 80 """
74 """ 123 """
75 array_call = ['gff3ToGenePred', input_gff3_file_name, gene_pred_file_name] 124 array_call = ['gff3ToGenePred', input_gff3_file_name, gene_pred_file_name]
76 p = _handleExceptionAndCheckCall(array_call) 125 p = _handleExceptionAndCheckCall(array_call)
77 return p 126 return p
78 127
128 def genePredToBigGenePred(gene_pred_file_name, unsorted_bigGenePred_file_name):
129 """
130 Call genePredToBigGenePred and write the result into unsorted_bigGenePred_file_name
131 :param gene_pred_file_name:
132 :param unsorted_bigGenePred_file_name:
133 :return:
134 """
135 array_call = ['genePredToBigGenePred',
136 gene_pred_file_name,
137 unsorted_bigGenePred_file_name]
138 p = _handleExceptionAndCheckCall(array_call)
139 return p
79 140
80 def genePredToBed(gene_pred_file_name, unsorted_bed_file_name): 141 def genePredToBed(gene_pred_file_name, unsorted_bed_file_name):
81 """ 142 """
82 Call genePredToBed and write the result into unsorted_bed_file_name 143 Call genePredToBed and write the result into unsorted_bed_file_name
83 :param gene_pred_file_name: 144 :param gene_pred_file_name:
111 array_call = ['sort', '-k2rn', two_bit_info_file_name, '-o', chrom_sizes_file_name] 172 array_call = ['sort', '-k2rn', two_bit_info_file_name, '-o', chrom_sizes_file_name]
112 p = _handleExceptionAndCheckCall(array_call) 173 p = _handleExceptionAndCheckCall(array_call)
113 return p 174 return p
114 175
115 176
116 def bedToBigBed(sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name, typeOption=None, autoSql=None): 177 def bedToBigBed(sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name,
178 typeOption=None, autoSql=None, tab=False):
117 """ 179 """
118 Call bedToBigBed on sorted_bed_file_name, using chrom_sizes_file_name and write the result into big_bed_file_name 180 Call bedToBigBed on sorted_bed_file_name, using chrom_sizes_file_name and write the result into big_bed_file_name
119 :param sorted_bed_file_name: 181 :param sorted_bed_file_name:
120 :param chrom_sizes_file_name: 182 :param chrom_sizes_file_name:
121 :param big_bed_file_name: 183 :param big_bed_file_name:
122 :return: 184 :return:
123 """ 185 """
186
187 # TODO: Move this into the _handleExceptionAndCheckCall function
188 # Parse the array
189 logging.debug("sorted_bed_file_name: {0}".format(sorted_bed_file_name))
190 logging.debug("chrom_sizes_file_name: {0}".format(chrom_sizes_file_name))
191 logging.debug("big_bed_file_name: {0}".format(big_bed_file_name))
192 logging.debug("typeOption: {0}".format(typeOption))
193 logging.debug("autoSql: {0}".format(autoSql))
194 logging.debug("tab option: {0}".format(tab))
195
124 array_call = ['bedToBigBed', sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name] 196 array_call = ['bedToBigBed', sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name]
125 if typeOption: 197 if typeOption:
198 typeOption = ''.join(['-type=', typeOption])
126 array_call.append(typeOption) 199 array_call.append(typeOption)
127 if autoSql: 200 if autoSql:
201 autoSql = ''.join(['-as=', autoSql])
128 array_call.append(autoSql) 202 array_call.append(autoSql)
203 if tab:
204 array_call.append('-tab')
129 205
130 p = _handleExceptionAndCheckCall(array_call) 206 p = _handleExceptionAndCheckCall(array_call)
131 return p 207 return p
132 208
133 209