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comparison multigps.py @ 4:0bec3b2df784 draft

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author iuc
date Mon, 03 Apr 2017 14:07:14 -0400
parents 91127c200437
children
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3:d78ff3764fe5 4:0bec3b2df784
23 parser.add_argument('--fixedpb', dest='fixedpb', type=int, default=None, help='Fixed per-base limit') 23 parser.add_argument('--fixedpb', dest='fixedpb', type=int, default=None, help='Fixed per-base limit')
24 parser.add_argument('--fixedscaling', dest='fixedscaling', type=float, default=None, help='Multiply control counts by total tag count ratio and then by this factor') 24 parser.add_argument('--fixedscaling', dest='fixedscaling', type=float, default=None, help='Multiply control counts by total tag count ratio and then by this factor')
25 parser.add_argument('--format', dest='format', default=None, help='Input expt file data format') 25 parser.add_argument('--format', dest='format', default=None, help='Input expt file data format')
26 parser.add_argument('--gaussmodelsmoothing', dest='gaussmodelsmoothing', default=None, help='Use Gaussian model smoothing') 26 parser.add_argument('--gaussmodelsmoothing', dest='gaussmodelsmoothing', default=None, help='Use Gaussian model smoothing')
27 parser.add_argument('--gausssmoothparam', dest='gausssmoothparam', type=int, default=None, help='Smoothing factor') 27 parser.add_argument('--gausssmoothparam', dest='gausssmoothparam', type=int, default=None, help='Smoothing factor')
28 parser.add_argument('--input_item', dest='input_items', action='append', nargs=7, default=None, help="Input files, attributes and options") 28 parser.add_argument('--input_item', dest='input_items', action='append', nargs=8, default=None, help="Input files, attributes and options")
29 parser.add_argument('--jointinmodel', dest='jointinmodel', default=None, help='Allow joint events in model updates') 29 parser.add_argument('--jointinmodel', dest='jointinmodel', default=None, help='Allow joint events in model updates')
30 parser.add_argument('--mappability', dest='mappability', type=float, default=None, help='Fraction of the genome that is mappable for these experiments') 30 parser.add_argument('--mappability', dest='mappability', type=float, default=None, help='Fraction of the genome that is mappable for these experiments')
31 parser.add_argument('--maxtrainingrounds', dest='maxtrainingrounds', type=int, default=None, help='Maximum number of training rounds for updating binding event read distributions') 31 parser.add_argument('--maxtrainingrounds', dest='maxtrainingrounds', type=int, default=None, help='Maximum number of training rounds for updating binding event read distributions')
32 parser.add_argument('--medianscale', dest='medianscale', default=None, help='Use the median signal/control ratio as the scaling factor') 32 parser.add_argument('--medianscale', dest='medianscale', default=None, help='Use the median signal/control ratio as the scaling factor')
33 parser.add_argument('--meme1proc', dest='meme1proc', default=None, help='Do not run the parallel version of meme') 33 parser.add_argument('--meme1proc', dest='meme1proc', default=None, help='Do not run the parallel version of meme')
64 parser.add_argument('--threads', dest='threads', type=int, default=4, help='The number of threads to run') 64 parser.add_argument('--threads', dest='threads', type=int, default=4, help='The number of threads to run')
65 args = parser.parse_args() 65 args = parser.parse_args()
66 66
67 67
68 def generate_design_file(input_items): 68 def generate_design_file(input_items):
69 control_file_names = []
69 design_file = open(DESIGN_FILE, 'w') 70 design_file = open(DESIGN_FILE, 'w')
70 for item in input_items: 71 for item in input_items:
71 file_name, label, file_format, condition_name, replicate_name, experiment_type, fixed_read_count = item 72 experiment_file_name, control_file_name, label, file_format, condition_name, replicate_name, experiment_type, fixed_read_count = item
73 if control_file_name not in ['None', None, '']:
74 control_file_names.append(control_file_name)
72 file_format = file_format.upper() 75 file_format = file_format.upper()
73 items = [file_name, label, file_format, condition_name] 76 items = [experiment_file_name, label, file_format, condition_name]
74 if replicate_name not in ['None', None, '']: 77 if replicate_name not in ['None', None, '']:
75 items.append(replicate_name) 78 items.append(replicate_name)
76 if experiment_type not in ['None', None, '']: 79 if experiment_type not in ['None', None, '']:
77 items.append(experiment_type) 80 items.append(experiment_type)
78 if fixed_read_count not in ['None', None, '']: 81 if fixed_read_count not in ['None', None, '']:
79 items.append(fixed_read_count) 82 items.append(fixed_read_count)
80 design_file.write('%s\n' % '\t'.join(items)) 83 design_file.write('%s\n' % '\t'.join(items))
81 design_file.close() 84 design_file.close()
85 return control_file_names
82 86
83 87
84 def get_file_with_extension(dir, ext): 88 def get_file_with_extension(dir, ext):
85 file_list = [f for f in os.listdir(dir) if f.endswith(ext)] 89 file_list = [f for f in os.listdir(dir) if f.endswith(ext)]
86 if len(file_list) == 1: 90 if len(file_list) == 1:
139 if args.meme1proc is not None: 143 if args.meme1proc is not None:
140 # Do not run the parallel version of meme. 144 # Do not run the parallel version of meme.
141 cmd += ' --meme1proc' 145 cmd += ' --meme1proc'
142 # Experiment. 146 # Experiment.
143 if args.input_items is not None: 147 if args.input_items is not None:
144 generate_design_file(args.input_items) 148 control_file_names = generate_design_file(args.input_items)
145 cmd += ' --design %s' % DESIGN_FILE 149 cmd += ' --design %s' % DESIGN_FILE
150 if len(control_file_names) > 0:
151 cmd += ' --ctrl %s' % ','.join(control_file_names)
146 else: 152 else:
147 if args.expt is not None: 153 if args.expt is not None:
148 cmd += ' --expt %s' % args.expt 154 cmd += ' --expt %s' % args.expt
149 if args.format is not None: 155 if args.format is not None:
150 cmd += ' --format %s' % args.format 156 cmd += ' --format %s' % args.format