import shutil
from htsworkflow.util import queuecommands
+from htsworkflow.pipelines.samplekey import SampleKey
LOGGER = logging.getLogger(__name__)
LOGGER.info("run_name %s" % (run_name,))
cmd_list = []
- for lane in lanes:
+ for key in lanes:
+ if not isinstance(key, SampleKey):
+ errmsg = "Expected %s got %s"
+ raise ValueError(errmsg % (str(SampleKey), str(type(key))))
name_prefix = '%s_%%l_' % (run_name,)
- destname = '%s_%s_%d.srf' % (site_name, run_name, lane)
+ destname = '%s_%s_%d.srf' % (site_name, run_name, key.lane)
destdir = os.path.normpath(destdir)
dest_path = os.path.join(destdir, destname)
- seq_pattern = 's_%d_*_seq.txt' % (lane,)
+ seq_pattern = 's_%d_*_seq.txt' % (key.lane,)
if cmdlevel == SOLEXA2SRF:
cmd = ['solexa2srf',
'-o', dest_path,
seq_pattern]
elif cmdlevel == ILLUMINA2SRF11:
- seq_pattern = 's_%d_*_qseq.txt' % (lane,)
+ seq_pattern = 's_%d_*_qseq.txt' % (key.lane,)
cmd = ['illumina2srf',
'-o', dest_path,
seq_pattern]
LOGGER.info("run_name %s" % (run_name,))
cmd_list = []
- for lane in lanes:
+ for key in lanes:
+ if not isinstance(key, SampleKey):
+ errmsg = "Expected %s got %s"
+ raise ValueError(errmsg % (str(SampleKey), str(type(key))))
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)
+ destname = '%s_%s_l%d.tar.bz2' % (site_name, run_name, key.lane)
dest_path = os.path.join(destdir, destname)
else:
- destname = '%s_%s_l%d_r%d.tar.bz2' % (site_name, run_name, lane, read)
+ destname = '%s_%s_l%d_r%d.tar.bz2' % (site_name, run_name, key.lane, read)
dest_path = os.path.join(destdir, destname)
- cmd = " ".join(['tar', 'cjf', dest_path, pattern % (lane,) ])
+ cmd = " ".join(['tar', 'cjf', dest_path, pattern % (key.lane,) ])
LOGGER.info("Generated command: " + cmd)
cmd_list.append(cmd)