def run(self):
"""Execute *bowtie-build*.
:raises: :class:WedringError
"""
if not self.quiet:
wedr_report("[%s] Building Bowtie BW index '%s'." % (self._out_pref,
self.index))
self.parse_bb_cmd_line()
if not self.quiet:
wedr_report("[%s] Command line:\n %s" % (self._out_pref,
self._bb_cmd))
wedr_prepare_directory(self.out_dir)
wedr_prepare_directory(self.log_dir)
outfile = path.join(self.log_dir, self._out_pref + "_build.log")
bb = BioSoft(command=self._bb_cmd, outfile=outfile)
bb.run()
if 0 != bb.return_code != -1:
raise WedringError(141, "[%s] %s exitted with status %d. See log file '%s' for more details." %
(self._out_pref, bb.program_name,
bb.return_code, bb.outfile))
wedr_clean(outfile)
if not self.quiet:
wedr_report("[%s] BW index build - Done!." % self._out_pref)
def run(self):
"""Execute all steps of the **Wedring** pipeline."""
# This method will execute according to the self._wb value:
# The value are set after the command line options --just-indexbuild,
# --just-map, --just-counttable, --just-de, and the possible values are
# defined in the globals TTL_PIPELINE, JUST_INDEX, JUST_MAP, JUST_TABLE
# and JUST_DE, which mean:
# TTL_PIPELINE -- execute all steps of the pipeline
# JUST_INDEX -- just execute the indexing stage
# JUST_MAP -- execute the indexing stage (if needed) and the mapping
# stage
# JUST_TABLE -- just build the count table
# JUST_DE -- just execute the differential expression stage
if self._wb in (TTL_PIPELINE, JUST_INDEX, JUST_MAP):
self.wedring_indexbuilder_parse_params()
if self._indexbldr is not None:
self._indexbldr.run()
self._i = self._indexbldr.index
if self._wb != JUST_INDEX:
wedr_prepare_directory(self._o)
wedr_prepare_directory(self._ld)
self.wedring_mapping_parse_params()
p = Pool(self._num_threads)
self._wedr_list = p.map(WedringMast.exec_mapping_stage,
self._wedr_list)
if self._wb != JUST_MAP:
feats_file = path.join(self._o, "genomic_features.txt")
tbl_file = path.join(self._o, "count_table.txt")
if not self._qt:
wedr_report("Writing genomic features to disk.")
write_genomic_features_to_file(self._a, feats_file)
if wedr_check_path(feats_file):
if not self._qt:
wedr_report("Writing genomic features - Done!")
cov_f = [wedrmast.cov_file for wedrmast in self._wedr_list]
if not self._qt:
wedr_report("Writing count table to disk.")
write_count_table_to_file(self._a, cov_f, self._cnd,
tbl_file)
if wedr_check_path(tbl_file):
self._cnt_table = tbl_file
if not self._qt:
wedr_report("Writing count table - Done!")
self.exec_deseq()
elif self._wb == JUST_TABLE:
self.wedring_mapping_parse_params()
wedr_prepare_directory(self._o)
feats_file = path.join(self._o, "genomic_features.txt")
tbl_file = path.join(self._o, "count_table.txt")
if not self._qt:
wedr_report("Writing genomic features to disk.")
write_genomic_features_to_file(self._a, feats_file)
if wedr_check_path(feats_file):
if not self._qt:
wedr_report("Writing genomic features - Done!")
cov_f = [wedrmast.cov_file for wedrmast in self._wedr_list]
if not self._qt:
wedr_report("Writing count table to disk.")
write_count_table_to_file(self._a, cov_f, self._cnd, tbl_file)
if wedr_check_path(tbl_file):
self._cnt_table = tbl_file
if not self._qt:
wedr_report("Writing count table - Done!")
elif self._wb == JUST_DE:
wedr_prepare_directory(self._o)
wedr_prepare_directory(self._ld)
self.exec_deseq()