+def create_qseq_patterns(bustard_dir):
+ """
+ Scan a bustard directory for qseq files and determine a glob pattern
+ """
+ # grab one tile for each lane.
+ qseqs = glob(os.path.join(bustard_dir, '*_0001_qseq.txt'))
+ qseqs = [ os.path.split(x)[-1] for x in qseqs ]
+ if len(qseqs[0].split('_')) == 4:
+ # single ended
+ return [(None,"s_%d_[0-9][0-9][0-9][0-9]_qseq.txt")]
+ elif len(qseqs[0].split('_')) == 5:
+ # more than 1 read
+ # build a dictionary of read numbers by lane
+ # ( just in case we didn't run all 8 lanes )
+ lanes = {}
+ for q in qseqs:
+ sample, lane, read, tile, extension = q.split('_')
+ lanes.setdefault(lane, []).append(read)
+ qseq_patterns = []
+ # grab a lane from the dictionary
+ # I don't think it matters which one.
+ k = lanes.keys()[0]
+ # build the list of patterns
+ for read in lanes[k]:
+ read = int(read)
+ qseq_patterns.append((read, 's_%d_' + '%d_[0-9][0-9][0-9][0-9]_qseq.txt' % (read,)))
+ return qseq_patterns
+ else:
+ raise RuntimeError('unrecognized qseq pattern, not a single or multiple read pattern')
+
+def make_qseq_commands(run_name, bustard_dir, lanes, site_name, destdir, cmdlevel=ILLUMINA2SRF11):
+ """
+ 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
+ """
+ # clean up pathname
+ logging.info("run_name %s" % ( run_name, ))
+
+ cmd_list = []
+ for lane in lanes:
+ name_prefix = '%s_%%l_%%t_' % (run_name,)
+ destdir = os.path.normpath(destdir)
+ qseq_patterns = create_qseq_patterns(bustard_dir)
+
+ for read, pattern in qseq_patterns:
+ if read is None:
+ destname = '%s_%s_l%d.tar.bz2' % (site_name, run_name, lane)
+ dest_path = os.path.join(destdir, destname)
+ else:
+ destname = '%s_%s_l%d_r%d.tar.bz2' % (site_name, run_name, lane, read)
+ dest_path = os.path.join(destdir, destname)
+
+ cmd = " ".join(['tar', 'cjf', dest_path, pattern % (lane,) ])
+ logging.info("Generated command: " + cmd)
+ cmd_list.append(cmd)
+
+ return cmd_list
+
+def run_commands(new_dir, cmd_list, num_jobs):
+ logging.info("chdir to %s" % (new_dir,))