from htsworkflow.util.api import HtswApi
from htsworkflow.util.conversion import parse_flowcell_id
+from django.conf import settings
+from django.template import Context, loader
+
LOGGER = logging.getLogger(__name__)
class CondorFastqExtract(object):
Args:
library_result_map (list): [(library_id, destination directory), ...]
"""
- headers = {'srf': self.get_srf_condor_header(),
- 'qseq': self.get_qseq_condor_header(),
- 'split_fastq': self.get_split_fastq_condor_header(),
- }
+ template_map = {'srf': 'srf.condor',
+ 'qseq': 'qseq.condor',
+ 'split_fastq': 'split_fastq.condor'}
condor_entries = self.build_condor_arguments(library_result_map)
+ for script_type in template_map.keys():
+ template = loader.get_template(template_map[script_type])
+ variables = {'python': sys.executable,
+ 'logdir': self.log_path,
+ 'env': os.environ.get('PYTHONPATH', None),
+ 'args': condor_entries[script_type],
+ }
+
+ context = Context(variables)
- for script_type in headers.keys():
- make_submit_script('{0}.condor'.format(script_type),
- headers[script_type],
- condor_entries[script_type])
+ with open(script_type + '.condor','w+') as outstream:
+ outstream.write(template.render(context))
def build_condor_arguments(self, library_result_map):
condor_entries = {'srf': [],
pformat(available_sources))
continue
sources = available_sources.get(condor_type, None)
+
if sources is not None:
condor_entries.setdefault(condor_type, []).append(
- conversion(sources, target_pathname)
- )
+ conversion(sources, target_pathname))
else:
print " need file", target_pathname
return condor_entries
- def get_split_fastq_condor_header(self):
- return """Universe=vanilla
-executable=%(exe)s
-error=%(log)s/fastq.$(process).out
-output=%(log)s/fastq.$(process).out
-log=%(log)s/fastq.log
-environment="PYTHONPATH=%(env)s"
-
-""" % {'exe': sys.executable,
- 'log': self.log_path,
- 'env': os.environ.get('PYTHONPATH', '')
- }
-
- def get_qseq_condor_header(self):
- return """Universe=vanilla
-executable=%(exe)s
-error=%(log)s/qseq2fastq.$(process).out
-output=%(log)s/qseq2fastq.$(process).out
-log=%(log)s/qseq2fastq.log
-environment="PYTHONPATH=%(env)s"
-
-""" % {'exe': sys.executable,
- 'log': self.log_path,
- 'env': os.environ.get('PYTHONPATH','')
- }
-
- def get_srf_condor_header(self):
- return """Universe=vanilla
-executable=%(exe)s
-output=%(log)s/srf_pair_fastq.$(process).out
-error=%(log)s/srf_pair_fastq.$(process).out
-log=%(log)s/srf_pair_fastq.log
-environment="PYTHONPATH=%(env)s"
-
-""" % {'exe': sys.executable,
- 'log': self.log_path,
- 'env': os.environ.get('PYTHONPATH', '')
- }
-
def find_archive_sequence_files(self, library_result_map):
"""
Find archived sequence files associated with our results.
def condor_srf_to_fastq(self, sources, target_pathname):
if len(sources) > 1:
raise ValueError("srf to fastq can only handle one file")
- source = sources[0]
- py = srf2fastq.__file__
- flowcell = source.flowcell
- mid = getattr(source, 'mid_point', None)
- args = [ py, source.path, '--verbose']
- if source.paired:
- args.extend(['--left', target_pathname])
- # this is ugly. I did it because I was pregenerating the target
- # names before I tried to figure out what sources could generate
- # those targets, and everything up to this point had been
- # one-to-one. So I couldn't figure out how to pair the
- # target names.
- # With this at least the command will run correctly.
- # however if we rename the default targets, this'll break
- # also I think it'll generate it twice.
- args.extend(['--right',
- target_pathname.replace('_r1.fastq', '_r2.fastq')])
- else:
- args.extend(['--single', target_pathname ])
-
- if flowcell is not None:
- args.extend(['--flowcell', flowcell])
-
- if mid is not None:
- args.extend(['-m', str(mid)])
-
- if self.force:
- args.extend(['--force'])
-
- script = """arguments="%s"
-queue
-""" % (" ".join(args),)
-
- return script
+ return {
+ 'sources': [sources[0].path],
+ 'pyscript': srf2fastq.__file__,
+ 'flowcell': sources[0].flowcell,
+ 'ispaired': sources[0].paired,
+ 'target': target_pathname,
+ 'target_right': target_pathname.replace('_r1.fastq', '_r2.fastq'),
+ 'mid': getattr(sources[0], 'mid_point', None),
+ 'force': self.force,
+ }
def condor_qseq_to_fastq(self, sources, target_pathname):
- flowcell = sources[0].flowcell
- py = qseq2fastq.__file__
-
- args = [py, '-o', target_pathname ]
- if flowcell is not None:
- args.extend(['-f', flowcell])
- if len(sources) == 1:
- args += (['-i', sources[0].path])
- else:
- for source in sources:
- args += source.path
- script = """arguments="%s"
-queue
-""" % (" ".join(args))
-
- return script
+ paths = []
+ for source in sources:
+ paths.append(source.path)
+ paths.sort()
+ return {
+ 'pyscript': qseq2fastq.__file__,
+ 'flowcell': sources[0].flowcell,
+ 'target': target_pathname,
+ 'sources': paths,
+ 'ispaired': sources[0].paired,
+ 'istar': len(sources) == 1,
+ }
def condor_desplit_fastq(self, sources, target_pathname):
- py = desplit_fastq.__file__
- args = [py, '-o', target_pathname, ]
paths = []
for source in sources:
paths.append(source.path)
paths.sort()
- args += paths
- script = 'arguments="%s"\nqueue\n' % ( ' '.join(args))
- return script
-
-def make_submit_script(target, header, body_list):
- """
- write out a text file
-
- this was intended for condor submit scripts
-
- Args:
- target (str or stream):
- if target is a string, we will open and close the file
- if target is a stream, the caller is responsible.
-
- header (str);
- header to write at the beginning of the file
- body_list (list of strs):
- a list of blocks to add to the file.
- """
- if type(target) in types.StringTypes:
- f = open(target,"w")
- else:
- f = target
- f.write(header)
- for entry in body_list:
- f.write(entry)
- if type(target) in types.StringTypes:
- f.close()
+ return {
+ 'pyscript': desplit_fastq.__file__,
+ 'target': target_pathname,
+ 'sources': paths,
+ 'ispaired': sources[0].paired,
+ }
def make_lane_dict(lib_db, lib_id):
"""
projects / htsworkflow.git / blobdiff