Mercurial > repos > vimalkumarvelayudhan > riboseqr_wrapper

annotate riboseqr/metagene.py @ 6:5a242f289347 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Merge
author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Tue, 27 Oct 2015 12:29:39 +0000
parents c34c364ce75d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
1 #!/usr/bin/env python
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
2 import os
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
3 import sys
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
4 import glob
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
5 import argparse
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
6 import logging
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
7 import rpy2.robjects as robjects
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
8
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
9 import utils
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
10
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
11 rscript = ''
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
12 R = robjects.r
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
13
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
14
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
15 def run_rscript(command=None):
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
16 """Run R command, log it, append to rscript"""
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
17 global rscript
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
18 if not command:
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
19 return
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
20 logging.debug(command)
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
21 rscript += '{}\n'.format(command)
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
22 output = R(command)
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
23 return output
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
24
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
25
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
26 def do_analysis(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
27 rdata_load='Periodicity.rda', selected_lengths='27',
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
28 selected_frames='', hit_mean='10', unique_hit_mean='1',
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
29 ratio_check='TRUE', min5p='-20', max5p='200', min3p='-200', max3p='20',
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
30 cap='', plot_title='', plot_lengths='27', rdata_save='Metagene.rda',
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
31 html_file='Metagene-report.html', output_path=os.getcwd()):
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
32 """Metagene analysis from saved periodicity R data file. """
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
33 run_rscript('suppressMessages(library(riboSeqR))')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
34 run_rscript('load("{}")'.format(rdata_load))
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
35
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
36 logging.debug('fS\n{}\nfCs\n{}\n'.format(R['fS'], R['fCs']))
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
37 options = {}
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
38 for key, value, rtype, rmode in (
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
39 ('lengths', selected_lengths, 'int', 'charvector'),
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
40 ('frames', selected_frames, 'int', 'listvector'),
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
41 ('hit_mean', hit_mean, 'int', None),
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
42 ('unique_hit_mean', unique_hit_mean, 'int', None),
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
43 ('ratio_check', ratio_check, 'bool', None),
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
44 ('min5p', min5p, 'int', None), ('max5p', max5p, 'int', None),
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
45 ('min3p', min3p, 'int', None), ('max3p', max3p, 'int', None),
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
46 ('cap', cap, 'int', None),
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
47 ('plot_title', plot_title, 'str', 'charvector'),
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
48 ('plot_lengths', plot_lengths, 'int', 'list')):
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
49 options[key] = utils.process_args(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
50 value, ret_type=rtype, ret_mode=rmode)
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
51
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
52 cmd_args = """fCs, lengths={lengths},
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
53 frames={frames}, hitMean={hit_mean},
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
54 unqhitMean={unique_hit_mean}, fS=fS""".format(**options)
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
55
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
56 if ratio_check == 'TRUE':
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
57 cmd_args += ', ratioCheck = TRUE'
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
58
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
59 run_rscript('ffCs <- filterHits({})'.format(cmd_args))
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
60 logging.debug("ffCs\n{}\n".format(R['ffCs']))
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
61
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
62 cds_args = ('coordinates=ffCs@CDS, riboDat=riboDat, min5p={min5p}, '
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
63 'max5p={max5p}, min3p={min3p}, max3p={max3p}'.format(**options))
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
64
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
65 if options['cap']:
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
66 cds_args += ', cap={cap}'.format(**options)
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
67
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
68 if options['plot_title']:
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
69 cds_args += ', main={plot_title}'.format(**options)
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
70
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
71 html = """<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 3.2//EN">
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
72 <html>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
73 <head>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
74 <title>Metagene Analysis - Report</title>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
75 </head>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
76 <body>
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
77 """
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
78 html += '<h2>Metagene analysis - results</h2>\n<hr>\n'
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
79 html += ('<p>\nLengths of footprints used in analysis - <strong>'
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
80 '<code>{0}</code></strong><br>\nLengths of footprints '
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
81 'selected for the plot - <strong><code>{1}</code></strong>'
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
82 '\n</p>\n'.format(selected_lengths, plot_lengths))
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
83 for count, length in enumerate(options['plot_lengths']):
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
84 count += 1
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
85 html += '<h3>Length: {0}</h3>\n'.format(length)
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
86 plot_file = os.path.join(output_path,
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
87 'Metagene-analysis-plot{0}'.format(count))
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
88 for fmat in ('pdf', 'png'):
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
89 if fmat == 'png':
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
90 cmd = 'png(file="{0}_%1d.png", type="cairo")'
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
91 else:
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
92 cmd = 'pdf(file="{0}.pdf")'
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
93 run_rscript(cmd.format(plot_file))
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
94 run_rscript('plotCDS({0},{1})'.format(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
95 cds_args, 'lengths={}'.format(length)))
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
96 run_rscript('dev.off()')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
97 for image in sorted(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
98 glob.glob('{}*.png'.format(plot_file))):
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
99 html += '<p><img border="1" src="{0}" alt="{0}"></p>\n'.format(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
100 os.path.basename(image))
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
101 html += '<p><a href="{0}.pdf">PDF version</a></p>\n'.format(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
102 os.path.basename(plot_file))
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
103 run_rscript('save("ffCs", "riboDat", "fastaCDS", file="{}", '
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
104 'compress=FALSE)'.format(rdata_save))
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
105
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
106 logging.debug('\n{:#^80}\n{}\n{:#^80}\n'.format(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
107 ' R script for this session ', rscript, ' End R script '))
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
108
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
109 with open(os.path.join(output_path, 'metagene.R'), 'w') as r:
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
110 r.write(rscript)
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
111
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
112 html += ('<h4>R script for this session</h4>\n'
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
113 '<p><a href="metagene.R">metagene.R</a></p>\n'
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
114 '<p>Next step: <em>Plot Ribosome profile</em></p>\n'
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
115 '</body>\n</html>\n')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
116
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
117 with open(html_file, 'w') as f:
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
118 f.write(html)
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
119
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
120 if __name__ == '__main__':
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
121
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
122 parser = argparse.ArgumentParser(description='Metagene analysis')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
123
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
124 # required arguments
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
125 flags = parser.add_argument_group('required arguments')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
126 flags.add_argument('--rdata_load', required=True,
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
127 help='Saved riboSeqR data from Periodicity step.')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
128 flags.add_argument('--selected_lengths', required=True,
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
129 help='Select frame lengths to filter. Comma-separated',
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
130 default='27')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
131 flags.add_argument(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
132 '--selected_frames', required=True,
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
133 help='Select frames corresponding to frame lengths. Comma-separated')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
134
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
135 flags.add_argument(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
136 '--hit_mean', required=True,
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
137 help='Mean number of hits within the replicate group for filtering',
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
138 default='10')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
139
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
140 flags.add_argument(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
141 '--unique_hit_mean', required=True,
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
142 help='Mean number of unique sequences within the replicate group '
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
143 'for filtering', default='1')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
144
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
145 parser.add_argument(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
146 '--rdata_save', help='File to write R data to (default: %(default)s)',
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
147 default='Metagene.rda')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
148
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
149 parser.add_argument(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
150 '--ratio_check',
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
151 help='Check the ratios of the expected phase to maximal phase '
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
152 'within the putative coding sequence (default: %(default)s)',
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
153 choices=['TRUE', 'FALSE'], default='TRUE')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
154
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
155 parser.add_argument(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
156 '--plot_lengths',
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
157 help='Length of footprints to be plotted. Multiple values should be '
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
158 'comma-separated. In that case, multiple plots will be produced'
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
159 '(default: %(default)s)', default='27')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
160
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
161 parser.add_argument(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
162 '--min5p',
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
163 help='The distance upstream of the translation start to be plotted '
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
164 '(default: %(default)s)', default='-20')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
165
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
166 parser.add_argument(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
167 '--max5p',
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
168 help='The distance downstream of the translation start to be plotted '
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
169 '(default: %(default)s)', default='200')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
170
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
171 parser.add_argument(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
172 '--min3p',
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
173 help='The distance upstream of the translation end to be plotted '
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
174 '(default: %(default)s)', default='-200')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
175
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
176 parser.add_argument(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
177 '--max3p',
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
178 help='The distance downtream of the translation end to be plotted '
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
179 '(default: %(default)s)', default='20')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
180
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
181 parser.add_argument(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
182 '--cap', help='If given, caps the height of plotted values '
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
183 '(default: %(default)s)')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
184
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
185 parser.add_argument('--plot_title', help='Title of the plot', default='')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
186 parser.add_argument('--html_file', help='HTML file with reports')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
187 parser.add_argument('--output_path', help='Directory to save output files')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
188 parser.add_argument(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
189 '--debug', help='Produce debug output', action='store_true')
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
190
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
191 args = parser.parse_args()
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
192 if args.debug:
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
193 logging.basicConfig(format='%(module)s: %(levelname)s - %(message)s',
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
194 level=logging.DEBUG, stream=sys.stdout)
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
195 logging.debug('Supplied Arguments\n{}\n'.format(vars(args)))
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
196
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
197 if not os.path.exists(args.output_path):
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
198 os.mkdir(args.output_path)
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
199
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
200 do_analysis(
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
201 rdata_load=args.rdata_load, selected_lengths=args.selected_lengths,
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
202 selected_frames=args.selected_frames, hit_mean=args.hit_mean,
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
203 unique_hit_mean=args.unique_hit_mean, ratio_check=args.ratio_check,
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
204 min5p=args.min5p, max5p=args.max5p, min3p=args.min3p, max3p=args.max3p,
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
205 cap=args.cap, plot_title=args.plot_title,
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
206 plot_lengths=args.plot_lengths, rdata_save=args.rdata_save,
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
207 html_file=args.html_file, output_path=args.output_path)
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
208
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
209 logging.debug('Done!')