"""
import logging
import os
+from pprint import pformat
import sys
import types
from htsworkflow.pipelines.sequences import scan_for_sequences
from htsworkflow.pipelines import qseq2fastq
from htsworkflow.pipelines import srf2fastq
+from htsworkflow.pipelines import desplit_fastq
from htsworkflow.util.api import HtswApi
from htsworkflow.util.conversion import parse_flowcell_id
self.log_path = log_path
self.force = force
- def build_fastqs(self, library_result_map ):
+ def create_scripts(self, library_result_map ):
"""
Generate condor scripts to build any needed fastq files
Args:
library_result_map (list): [(library_id, destination directory), ...]
"""
- qseq_condor_header = self.get_qseq_condor_header()
- qseq_condor_entries = []
- srf_condor_header = self.get_srf_condor_header()
- srf_condor_entries = []
+ headers = {'srf': self.get_srf_condor_header(),
+ 'qseq': self.get_qseq_condor_header(),
+ 'split_fastq': self.get_split_fastq_condor_header(),
+ }
+
+ condor_entries = self.build_condor_arguments(library_result_map)
+
+ for script_type in headers.keys():
+ make_submit_script('{0}.condor'.format(script_type),
+ headers[script_type],
+ condor_entries[script_type])
+
+ def build_condor_arguments(self, library_result_map):
+ condor_entries = {'srf': [],
+ 'qseq': [],
+ 'split_fastq': []}
+ conversion_funcs = {'srf': self.condor_srf_to_fastq,
+ 'qseq': self.condor_qseq_to_fastq,
+ 'split_fastq': self.condor_desplit_fastq
+ }
lib_db = self.find_archive_sequence_files(library_result_map)
needed_targets = self.find_missing_targets(library_result_map, lib_db)
for target_pathname, available_sources in needed_targets.items():
LOGGER.debug(' target : %s' % (target_pathname,))
LOGGER.debug(' candidate sources: %s' % (available_sources,))
- if available_sources.has_key('qseq'):
- source = available_sources['qseq']
- qseq_condor_entries.append(
- self.condor_qseq_to_fastq(source.path,
- target_pathname,
- source.flowcell)
- )
- elif available_sources.has_key('srf'):
- source = available_sources['srf']
- mid = getattr(source, 'mid_point', None)
- srf_condor_entries.append(
- self.condor_srf_to_fastq(source.path,
- target_pathname,
- source.paired,
- source.flowcell,
- mid)
- )
+ for condor_type in available_sources.keys():
+ conversion = conversion_funcs.get(condor_type, None)
+ if conversion is None:
+ errmsg = "Unrecognized type: {0} for {1}"
+ print errmsg.format(condor_type,
+ 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)
+ )
else:
print " need file", target_pathname
- if len(srf_condor_entries) > 0:
- make_submit_script('srf.fastq.condor',
- srf_condor_header,
- srf_condor_entries)
+ return condor_entries
- if len(qseq_condor_entries) > 0:
- make_submit_script('qseq.fastq.condor',
- qseq_condor_header,
- qseq_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
+""" % {'exe': sys.executable,
+ 'log': self.log_path }
def get_qseq_condor_header(self):
return """Universe=vanilla
# end filters
if seq.paired:
- target_name = fastq_paired_template % filename_attributes
+ target_name = fastq_paired_template % \
+ filename_attributes
else:
- target_name = fastq_single_template % filename_attributes
+ target_name = fastq_single_template % \
+ filename_attributes
target_pathname = os.path.join(result_dir, target_name)
if self.force or not os.path.exists(target_pathname):
t = needed_targets.setdefault(target_pathname, {})
- t[seq.filetype] = seq
+ t.setdefault(seq.filetype, []).append(seq)
return needed_targets
- def condor_srf_to_fastq(self,
- srf_file,
- target_pathname,
- paired,
- flowcell=None,
- mid=None):
+ 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__
- args = [ py, srf_file, '--verbose']
- if paired:
+ 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
target_pathname.replace('_r1.fastq', '_r2.fastq')])
else:
args.extend(['--single', target_pathname ])
+
if flowcell is not None:
args.extend(['--flowcell', flowcell])
return script
- def condor_qseq_to_fastq(self, qseq_file, target_pathname, flowcell=None):
+ def condor_qseq_to_fastq(self, sources, target_pathname):
+ flowcell = sources[0].flowcell
py = qseq2fastq.__file__
- args = [py, '-i', qseq_file, '-o', target_pathname ]
+
+ 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
+ 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
projects / htsworkflow.git / blobdiff