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comparison multigps.py @ 5:7b15099378a7 draft

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author greg
date Sat, 02 Jan 2016 14:07:37 -0500
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children afba8c2a3b32
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4:32cff4d1d0ff 5:7b15099378a7
1 import argparse
2 import os
3 import shutil
4 import subprocess
5 import sys
6 import tempfile
7
8 BUFF_SIZE = 1048576
9 DESIGN_FILE = 'design.tabular'
10
11
12 def generate_design_file(input_items, filename):
13 design_file = open(filename, 'wb')
14 for items in input_items:
15 filename, ext, signal_control, condition_name, replicate_name, read_distribution_file, fixed_read = items
16 # MultiGPS version 0.5 does not support the newer scidx datatype.
17 if ext == 'scidx':
18 datatype = 'IDX'
19 else:
20 datatype = ext.upper()
21 design_file.write('%s\n' % '\t'.join([filename, signal_control, datatype, condition_name, replicate_name, read_distribution_file, fixed_read]))
22 design_file.close()
23
24
25 def get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout, include_stdout=False):
26 tmp_stderr.close()
27 # Get stderr, allowing for case where it's very large.
28 tmp_stderr = open(tmp_err, 'rb')
29 stderr_str = ''
30 buffsize = BUFF_SIZE
31 try:
32 while True:
33 stderr_str += tmp_stderr.read(buffsize)
34 if not stderr_str or len(stderr_str) % buffsize != 0:
35 break
36 except OverflowError:
37 pass
38 tmp_stderr.close()
39 if include_stdout:
40 tmp_stdout = open(tmp_out, 'rb')
41 stdout_str = ''
42 buffsize = BUFF_SIZE
43 try:
44 while True:
45 stdout_str += tmp_stdout.read(buffsize)
46 if not stdout_str or len(stdout_str) % buffsize != 0:
47 break
48 except OverflowError:
49 pass
50 tmp_stdout.close()
51 if include_stdout:
52 return 'STDOUT\n%s\n\nSTDERR\n%s\n' % (stdout_str, stderr_str)
53 return stderr_str
54
55
56 def stop_err(msg):
57 sys.stderr.write(msg)
58 sys.exit(1)
59
60 parser = argparse.ArgumentParser()
61 parser.add_argument('--input_item', dest='input_items', action='append', nargs=7, help="Input datasets and associated parameters")
62 parser.add_argument('--threads', dest='threads', type=int, default=4, help='The number of threads to run')
63 parser.add_argument('--multigps_jar', dest='multigps_jar', help='Path to the MultiGPS jar file')
64 parser.add_argument('--geninfo', dest='geninfo', help='File listing the lengths of all chromosomes')
65 parser.add_argument('--use_motif', dest='use_motif', help='Perform motif-finding or use a motif-prior')
66 parser.add_argument('--seq_dir', dest='seq_dir', default=None, help='Directory containing fasta files corresponding to every named chromosome')
67 parser.add_argument('--positional_prior', dest='positional_prior', default=None, help='Perform inter-experiment positional prior')
68 parser.add_argument('--events_shared_probability', dest='events_shared_probability', type=float, default=0.9, help='Probability that events are shared across conditions')
69 parser.add_argument('--motifs', dest='motifs', default=None, help='Perform motif-finding and motif priors')
70 parser.add_argument('--motif_finding_only', dest='motif_finding_only', default=None, help='Perform motif-finding only')
71 parser.add_argument('--num_motifs', dest='num_motifs', type=int, default=None, help='Number of motifs MEME should find for each condition')
72 parser.add_argument('--mememinw', dest='mememinw', type=int, default=None, help='Minimum motif width for MEME')
73 parser.add_argument('--mememaxw', dest='mememaxw', type=int, default=None, help='Maximum motif width for MEME')
74 parser.add_argument('--fixedpb', dest='fixedpb', type=int, default=None, help='Fixed per-base limit')
75 parser.add_argument('--poissongausspb', dest='poissongausspb', type=int, default=None, help='Poisson threshold for filtering per base')
76 parser.add_argument('--non_unique_reads', dest='non_unique_reads', default=None, help='Use non-unique reads')
77 parser.add_argument('--minqvalue', dest='minqvalue', type=int, default=None, help='Minimum Q-value (corrected p-value) of reported binding events')
78 parser.add_argument('--minfold', dest='minfold', type=int, default=None, help='Minimum event fold-change vs scaled control')
79 parser.add_argument('--diff_enrichment_tests', dest='diff_enrichment_tests', help='Run differential enrichment tests')
80 parser.add_argument('--edgerod', dest='edgerod', type=int, default=None, help='EdgeR over-dispersion parameter value')
81 parser.add_argument('--diffp', dest='diffp', type=int, default=None, help='Minimum p-value for reporting differential enrichment')
82 parser.add_argument('--noscaling', dest='noscaling', default=None, help='Do not use signal vs control scaling')
83 parser.add_argument('--medianscale', dest='medianscale', default=None, help='Use the median signal/control ratio as the scaling factor')
84 parser.add_argument('--sesscale', dest='sesscale', default=None, help='Estimate scaling factor by SES')
85 parser.add_argument('--scalewin', dest='scalewin', type=int, default=None, help='Window size for estimating scaling ratios')
86 parser.add_argument('--max_training_rounds', dest='max_training_rounds', type=int, default=None, help='Maximum number of training rounds for updating binding event read distributions')
87 parser.add_argument('--exclude_file', dest='exclude_file', default=None, help='File containing a set of regions to ignore during MultiGPS training')
88 parser.add_argument('--binding_model_updates', dest='binding_model_updates', default=None, help='Perform binding model updates')
89 parser.add_argument('--minmodelupdateevents', dest='minmodelupdateevents', type=int, default=None, help='Minimum number of events to support an update of the read distribution')
90 parser.add_argument('--binding_model_smoothing', dest='binding_model_smoothing', default=None, help='Binding model smoothing')
91 parser.add_argument('--spline_smooth', dest='spline_smooth', type=int, default=None, help='Binding model smoothing value')
92 parser.add_argument('--gauss_smooth', dest='gauss_smooth', type=int, default=None, help='Gaussian smoothing std dev')
93 parser.add_argument('--joint_in_model', dest='joint_in_model', default=None, help='Allow joint events in model updates')
94 parser.add_argument('--ml_config_not_shared', dest='ml_config_not_shared', default=None, help='Share component configs in the ML step')
95 parser.add_argument('--output_html_path', dest='output_html_path', help='Output html results file')
96 parser.add_argument('--output_html_files_path', dest='output_html_files_path', help='Output html extra files')
97 parser.add_argument('--output_process_path', dest='output_process_path', default=None, help='Output file for capturing stdout')
98 args = parser.parse_args()
99
100 try:
101 # Preparation.
102 tmp_dir = tempfile.mkdtemp(prefix="tmp-multigps-")
103 generate_design_file(args.input_items, DESIGN_FILE)
104 # Build the command line.
105 cmd_list = ['java -jar %s --verbose' % args.multigps_jar]
106 cmd_list.append('--threads %d' % args.threads)
107 cmd_list.append('--geninfo %s' % args.geninfo)
108 if args.use_motif == 'yes':
109 cmd_list.append('--seq %s' % args.seq_dir)
110 if args.positional_prior == 'no':
111 cmd_list.append('--noposprior')
112 cmd_list.append('--probshared %3f' % args.events_shared_probability)
113 if args.motifs == 'no':
114 cmd_list.append('--nomotifs')
115 if args.motif_finding_only == 'yes':
116 cmd_list.append('--nomotifprior')
117 if args.num_motifs is not None:
118 cmd_list.append('--memenmotifs %d' % args.num_motifs)
119 if args.mememinw is not None:
120 cmd_list.append('--mememinw %d' % args.mememinw)
121 if args.mememaxw is not None:
122 cmd_list.append('--mememaxw %d' % args.mememaxw)
123 if args.fixedpb is not None:
124 cmd_list.append('--fixedpb %d' % args.fixedpb)
125 if args.poissongausspb is not None:
126 cmd_list.append('--poissongausspb %d' % args.poissongausspb)
127 if args.non_unique_reads == 'yes':
128 cmd_list.append('--nonunique')
129 if args.minqvalue is not None:
130 cmd_list.append('--q %d' % args.minqvalue)
131 if args.minfold is not None:
132 cmd_list.append('--minfold %d' % args.minfold)
133 if args.diff_enrichment_tests == 'no':
134 cmd_list.append('--nodifftests')
135 if args.edgerod is not None:
136 cmd_list.append('--edgerod %d' % args.edgerod)
137 if args.diffp is not None:
138 cmd_list.append('--diffp %d' % args.diffp)
139 if args.noscaling == 'no':
140 cmd_list.append('--noscaling')
141 if args.medianscale == "yes":
142 cmd_list.append('--medianscale')
143 if args.sesscale == "yes":
144 cmd_list.append('--sesscale')
145 if args.scalewin is not None:
146 cmd_list.append('--scalewin %d' % args.scalewin)
147 if args.max_training_rounds is not None:
148 cmd_list.append('--r %d' % args.max_training_rounds)
149 if args.exclude_file not in [None, 'None']:
150 cmd_list.append('--exclude %s' % args.exclude_file)
151 if args.binding_model_updates == 'no':
152 cmd_list.append('--nomodelupdate')
153 if args.minmodelupdateevents is not None:
154 cmd_list.append('--minmodelupdateevents %d' % args.minmodelupdateevents)
155 if args.binding_model_smoothing == 'yes':
156 if args.spline_smooth is not None:
157 cmd_list.append('--splinesmoothparam %d' % args.spline_smooth)
158 else:
159 cmd_list.append('--nomodelsmoothing')
160 if args.gauss_smooth is not None:
161 cmd_list.append('--gaussmodelsmoothing')
162 cmd_list.append('--gausssmoothparam %d' % args.gauss_smooth)
163 if args.joint_in_model == 'yes':
164 cmd_list.append('--jointinmodel')
165 if args.ml_config_not_shared == 'no':
166 cmd_list.append('--mlconfignotshared')
167 cmd_list.append('--design %s' % DESIGN_FILE)
168 cmd_list.append('--out %s' % args.output_html_files_path)
169 if args.output_process_path is None:
170 cmd_list.append('2>/dev/null')
171 else:
172 cmd_list.append('2>%s' % args.output_process_path)
173 cmd = ' '.join(cmd_list)
174 # Define command response buffers.
175 tmp_out = tempfile.NamedTemporaryFile(dir=tmp_dir).name
176 tmp_stdout = open(tmp_out, 'wb')
177 tmp_err = tempfile.NamedTemporaryFile(dir=tmp_dir).name
178 tmp_stderr = open(tmp_err, 'wb')
179 tmp_filename = tempfile.NamedTemporaryFile(dir=tmp_dir).name
180 # Execute the command.
181 proc = subprocess.Popen(args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True)
182 rc = proc.wait()
183 if rc != 0:
184 error_message = get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout)
185 stop_err(error_message)
186 # Move the output HTML file to the output dataset path.
187 output_html_filename = 'multiGPS_%s_results.html' % os.path.split(args.output_html_files_path)[1]
188 shutil.move(os.path.join(args.output_html_files_path, output_html_filename), args.output_html_path)
189 except Exception, e:
190 stop_err('Error running MultiGPS\n%s\n' % str(e))
191 finally:
192 if os.path.exists(tmp_dir):
193 shutil.rmtree(tmp_dir)