4 from optparse import OptionParser
9 from htsworkflow.pipelines import gerald
10 from htsworkflow.pipelines.eland import extract_eland_sequence
11 from htsworkflow.pipelines import runfolder
13 def make_query_filename(eland_obj, output_dir):
14 query_name = '%s_%s_eland_query.txt'
15 query_name %= (eland_obj.sample_name, eland_obj.lane_id)
17 query_pathname = os.path.join(output_dir, query_name)
19 if os.path.exists(query_pathname):
20 logging.warn("overwriting %s" % (query_pathname,))
24 def make_result_filename(eland_obj, output_dir):
25 result_name = '%s_%s_eland_result.txt'
26 result_name %= (eland_obj.sample_name, eland_obj.lane_id)
28 result_pathname = os.path.join(output_dir, result_name)
30 if os.path.exists(result_pathname):
31 logging.warn("overwriting %s" % (result_pathname,))
33 return result_pathname
35 def extract_sequence(inpathname, query_pathname, length, dry_run=False):
36 logging.info('extracting %d bases' %(length,))
37 logging.info('extracting from %s' %(inpathname,))
38 logging.info('extracting to %s' %(query_pathname,))
42 instream = open(inpathname, 'r')
43 outstream = open(query_pathname, 'w')
44 extract_eland_sequence(instream, outstream, 0, length)
49 def run_eland(length, query_name, genome, result_name, multi=False, dry_run=False):
50 cmdline = ['eland_%d' % (length,), query_name, genome, result_name]
52 cmdline += ['--multi']
54 logging.info('running eland: ' + " ".join(cmdline))
56 return subprocess.Popen(cmdline)
61 def rerun(gerald_dir, output_dir, length=25, dry_run=False):
63 look for eland files in gerald_dir and write a subset to output_dir
65 logging.info("Extracting %d bp from files in %s" % (length, gerald_dir))
66 g = gerald.gerald(gerald_dir)
68 # this will only work if we're only missing the last dir in output_dir
69 if not os.path.exists(output_dir):
70 logging.info("Making %s" %(output_dir,))
71 if not dry_run: os.mkdir(output_dir)
74 for lane_id, lane_param in g.lanes.items():
75 eland = g.eland_results[lane_id]
77 inpathname = eland.pathname
78 query_pathname = make_query_filename(eland, output_dir)
79 result_pathname = make_result_filename(eland, output_dir)
81 extract_sequence(inpathname, query_pathname, length, dry_run=dry_run)
85 lane_param.eland_genome,
95 usage = '%prog: [options] runfolder'
97 parser = OptionParser(usage)
99 parser.add_option('--gerald',
100 help='specify location of GERALD directory',
102 parser.add_option('-o', '--output',
103 help='specify output location of files',
105 parser.add_option('-l', '--read-length', type='int',
106 help='specify new eland length',
109 parser.add_option('--dry-run', action='store_true',
110 help='only pretend to run',
112 parser.add_option('-v', '--verbose', action='store_true',
113 help='increase verbosity',
119 def main(cmdline=None):
120 logging.basicConfig(level=logging.WARNING)
122 parser = make_parser()
123 opts, args = parser.parse_args(cmdline)
125 if opts.length < 16 or opts.length > 32:
126 parser.error("eland can only process reads in the range 16-32")
129 parser.error("Can only process one runfolder directory")
131 runs = runfolder.get_runs(args[0])
133 parser.error("Not a runfolder")
134 opts.gerald = runs[0].gerald.pathname
135 if opts.output is None:
136 opts.output = os.path.join(
139 # pythons 0..n ==> elands 1..n+1
140 'C1-%d' % (opts.length+1,)
143 elif opts.gerald is None:
144 parser.error("need gerald directory")
146 if opts.output is None:
147 parser.error("specify location for the new eland files")
150 root_logger = logging.getLogger()
151 root_logger.setLevel(logging.INFO)
153 rerun(opts.gerald, opts.output, opts.length, dry_run=opts.dry_run)
157 if __name__ == "__main__":
158 sys.exit(main(sys.argv[1:]))