#!/usr/bin/python
-from glob import glob
import logging
import optparse
import os
-import subprocess
import sys
-from htsworkflow.util import queuecommands
-
-def make_commands(run_name, lanes, site_name, destdir):
- """
- make a subprocess-friendly list of command line arguments to run solexa2srf
- generates files like:
- woldlab:080514_HWI-EAS229_0029_20768AAXX:8.srf
- site run name lane
-
- run_name - most of the file name (run folder name is a good choice)
- lanes - list of integers corresponding to which lanes to process
- site_name - name of your "sequencing site" or "Individual"
- destdir - where to write all the srf files
- """
- cmd_list = []
- for lane in lanes:
- name_prefix = '%s_%%l_%%t_' % (run_name,)
- destname = '%s_%s_%d.srf' % (site_name, run_name, lane)
- destdir = os.path.normpath(destdir)
- dest_path = os.path.join(destdir, destname)
- seq_pattern = 's_%d_*_seq.txt' % (lane,)
-
- cmd = ['solexa2srf',
- '-N', name_prefix,
- '-n', '%3x:%3y',
- '-o', dest_path,
- seq_pattern]
-
- cmd_list.append(" ".join(cmd))
- return cmd_list
-
-def pathname_to_run_name(base):
- """
- Convert a pathname to a base runfolder name
- handle the case with a trailing /
- """
- name = ""
- while len(name) == 0:
- base, name = os.path.split(base)
- if len(base) == 0:
- return None
- return name
-
-def find_bustard_dir(pathname):
- # fixme: for don't repeat yourself this should some how be related
- # fixme: to pipelines.runfolder
-
- datadir = os.path.join(pathname, 'Data')
- logging.info("searching in %s" % (datadir,))
-
- bustard_dirs = []
- for firecrest_pathname in glob(os.path.join(datadir,"*Firecrest*")):
- bustard_glob = os.path.join(firecrest_pathname, "Bustard*")
- for bustard_pathname in glob(bustard_glob):
- bustard_dirs.append(bustard_pathname)
- return bustard_dirs
-
-
+from htsworkflow.pipelines import runfolder
+from htsworkflow.pipelines.srf import make_srf_commands, make_qseq_commands, \
+ run_commands, pathname_to_run_name
+from htsworkflow.pipelines.srf import ILLUMINA2SRF10, ILLUMINA2SRF11, SOLEXA2SRF
def make_parser():
usage = '%prog: [options] runfolder -l 1,2,3 [runfolder -l 5,6 ...]'
)
parser.add_option('-j', '--jobs', default=1, type='int',
help='how many jobs to run simultaneously')
+ parser.add_option('-r', '--runfolder-version', default=ILLUMINA2SRF11, type='int',
+ help='Which class of srf file should we attempt to create\n'
+ '0 = Solexa pipeline 0.2.6 - 0.3\n'
+ '1 = illumina pipeline 1.0\n'
+ '2 = illumina pipeline 1.1rc1 and later \n')
-
+ parser.add_option('-v', '--verbose', dest='verbose',
+ default=False, action='store_true',
+ help='report more about internals (INFO)')
+ parser.add_option('--debug', dest='debug',
+ default=False, action='store_true',
+ help='report even more about internals (DEBUG)')
+
return parser
def parse_lane_arg(lane_arg):
def main(cmdline=None):
parser = make_parser()
opts, args = parser.parse_args(cmdline)
-
+
+ if opts.debug:
+ logging.basicConfig(level=logging.DEBUG)
+ elif opts.verbose:
+ logging.basicConfig(level=logging.INFO)
+ else:
+ logging.basicConfig(level=logging.WARNING)
+
if len(args) == 0:
parser.error('need runfolder arguments')
parser.error(
"Number of lane arguments must match number of runfolders"
)
-
+
+ make_commands = make_qseq_commands
# build list of commands
cmds = {}
for runfolder_path, lanes in zip(args, lanes_list):
# normalize paths, either relative to home dirs or current dir
runfolder_path = os.path.abspath(runfolder_path)
- # the last part of the path should be a runfolder name
- name = pathname_to_run_name(runfolder_path)
+ run_name = pathname_to_run_name(runfolder_path)
# so any bustard directories?
- bustard_dir = find_bustard_dir(runfolder_path)
- # give up if there are anything other than 1 bustard dir
- if len(bustard_dir) > 1:
- print 'ERROR: Too many bustard directories',
- print "\n ".join(bustard_dir)
+ runs = runfolder.get_runs(runfolder_path)
+ # give up if there are anything other than 1 run
+ if len(runs) > 1:
+ print 'ERROR: Too many run directories in %s' %(runfolder_path,)
return 1
-
- elif len(bustard_dir) == 1:
- bustard_dir = bustard_dir[0]
- cmds[bustard_dir] = make_commands(name, lanes, opts.site, opts.dest_dir)
+ elif len(runs) == 1:
+ bustard_dir = runs[0].bustard.pathname
+ cmds[bustard_dir] = make_commands(run_name,
+ bustard_dir,
+ lanes,
+ opts.site,
+ opts.dest_dir,
+ opts.runfolder_version)
else:
print "ERROR: Couldn't find a bustard directory in", runfolder_path
return 1
if not opts.dry_run:
for cwd, cmd_list in cmds.items():
- curdir = os.getcwd()
- os.chdir(cwd)
- q = queuecommands.QueueCommands(cmd_list, opts.jobs)
- q.run()
- os.chdir(curdir)
+ run_commands(cwd, cmd_list, opts.jobs)
else:
for cwd, cmd_list in cmds.items():
print cwd
return 0
if __name__ == "__main__":
- logging.basicConfig(level=logging.DEBUG)
sys.exit(main(sys.argv[1:]))
projects / htsworkflow.git / blobdiff