def exec_mapping_stage(self):
"""Executor of the Wedring pipeline."""
if self.quiet:
wedr_check_path(self.index + '.*')
self.exec_mapping()
self.aln_file = (path.join(self._mapper_out, "accepted_hits.bam") if
self.mapper == "tophat" else
self._mapper_out + ".sam")
wedr_check_path(self.aln_file)
if wedr_check_program("samtools"):
self.exec_samtools()
if wedr_check_program("bedtools"):
self.exec_bedtools()
else:
wedr_check_path(self.index + '.*')
self.exec_mapping()
self.aln_file = (path.join(self._mapper_out, "accepted_hits.bam") if
self.mapper == "tophat" else
self._mapper_out + ".sam")
wedr_check_path(self.aln_file)
if wedr_check_program("samtools"):
wedr_report("[%s] Processing aligments with SAMtools." %
self._out_pref)
self.exec_samtools()
wedr_report("[%s] SAMtools - Done!." % self._out_pref)
if wedr_check_program("bedtools"):
wedr_report("[%s] Calculating mapping coverage with BEDTools." %
self._out_pref)
self.exec_bedtools()
wedr_report("[%s] BEDTools - Done!" % self._out_pref)
return self
def parse_args(self, out_dir="./wedr_index", ref_seq=None, index_label=None,
cfg_file=None, quiet=False):
"""This method checks the validity of :class:IndexBuilder parameters.
:param out_dir: Which output directory? (default: ./wedr_out)
:type out_dir: str
:param ref_seq: Which reference sequence(s)?
:type ref_seq: str
:param index_label: A personalized name to the index.
:type index_label: str
:param cfg_file: Which configuration file?
:type cfg_file: str
:param quiet: If True don't print anything besides errors.
:type quiet: bool
:raises: :class:WedringError
"""
if wedr_check_program("bowtie-build"):
if quiet:
self.quiet = True
if out_dir != "./wedr_index":
self.out_dir = out_dir
if cfg_file is not None:
if wedr_check_path(cfg_file):
self.cfg_file = cfg_file
if ref_seq is not None:
if wedr_check_path(self.ref_seq.split(',')):
self.ref_seq = ref_seq
else:
raise WedringError(135, "You must provide the reference sequence file(s).")
if index_label is not None:
self.index = path.join(self.out_dir, index_label)
self._out_pref = index_label
elif ',' in self.ref_seq:
index_name = [i for i in self.ref_seq.split(',') if i != ''][0]
self.index = path.join(self.out_dir,
path.split(path.splitext(index_name)[0])[1] +
"_andothers")
self._out_pref = index_name
else:
self._out_pref = path.split(path.splitext(self.ref_seq)[0])[1]
self.index = path.join(self.out_dir, self._out_pref)
def parse_args(self, out_dir="./wedr_out", mapper="bowtie", index=None,
lib_file=None, lib_mate_1=None, lib_mate_2=None,
qual_file=None, q_mate_1=None, q_mate_2=None, annot_file=None,
cov_file=None, cfg_file=None, map_label=None, quiet=False,
barrier=0):
"""This method verifies if **Wedring** parameters are set correctly and
makes other adjustments.
:param out_dir: Which output directory? (default: ./wedr_out)
:type out_dir: str -- Pathname to an existing (or not) directory.
:param mapper: Which mapper? (default: bowtie)
:type mapper: str -- "bowtie" or "tophat"
:param index: Which BW index?
:type index: str -- Pathname to *Bowtie*'s index (just the suffix)
:param lib_file: Which library file(s)?
:type lib_file: str
:param lib_mate_1: Which first mate reads file?
:type lib_mate_1: str
:param lib_mate_2: Which second mate reads file?
:type lib_mate_2: str
:param qual_file: Which quality file(s)?
:type qual_file: str
:param q_mate_1: Which quality file(s) for mate 1?
:type q_mate_1: str
:param q_mate_2: Which quality file(s) for mate 2?
:type q_mate_2: str
:param annot_file: Which annotation file?
:type q_mate_2: str
:param cfg_file: Which configuration file?
:type cfg_file: str
:param map_label: A personalized name to the mapping.
:type map_label: str
:param barrier: When the pipeline will stop?
:type barrier: int
:param quiet: If True don't print anything besides errors.
:type quiet: bool
:raises: :class:WedringError
"""
if self.wedr_barrier != 3:
mp = mapper.lower()
if mp in ("bowtie", "tophat"):
if wedr_check_program(mp):
self.mapper = mp
else:
raise WedringError(134, "Invalid mapper name: %s" % mapper)
if quiet:
self.quiet = True
if out_dir != "./wedr_out":
self.out_dir = out_dir
self.log_dir = path.join(out_dir, "log")
else:
self.log_dir = path.join(out_dir, "log")
if cfg_file is not None:
if wedr_check_path(cfg_file):
self.cfg_file = cfg_file
if index is not None:
if wedr_check_path(index + ".*"):
self.index = index
else:
raise WedringError(135, "You must provide Bowtie's BW index.")
if lib_file is not None:
lib_temp = [lf for lf in lib_file.split(',') if lf != '']
if wedr_check_path(lib_temp):
self.lib_file = ','.join(lib_temp)
self._map_mode = 2
if qual_file is not None:
qual_temp = [qf for qf in qual_file.split(',') if qf != '']
if wedr_check_path(qual_temp):
if len(lib_temp) != len(qual_temp):
raise WedringError(140, "Unbalanced number of library and quality files.")
self.qual_file = qual_file
self._map_mode += 5
else:
self._map_mode += 6
elif lib_mate_1 is not None and lib_mate_2 is not None:
lib_1_temp = [l1 for l1 in lib_mate_1.split(',') if l1 != '']
lib_2_temp = [l2 for l2 in lib_mate_2.split(',') if l2 != '']
if wedr_check_path(lib_1_temp + lib_2_temp):
if len(lib_1_temp) != len(lib_2_temp):
raise WedringError(140, "Unbalanced number of pair-mate libraries.")
if q_mate_1 is not None and q_mate_2 is not None:
qual_1_temp = [q1 for q1 in q_mate_1.split(',') if q1 != '']
qual_2_temp = [q2 for q2 in q_mate_2.split(',') if q2 != '']
if wedr_check_path(qual_1_temp + qual_2_temp):
if (len(lib_1_temp) != len(qual_1_temp) or
len(lib_1_temp) != len(qual_2_temp)):
raise WedringError(140, "Unbalanced number of pair-mate libraries and its qualities.")
self.lib_mate_1 = ','.join(lib_1_temp)
self.lib_mate_2 = ','.join(lib_2_temp)
self.q_mate_1 = ','.join(qual_1_temp)
self.q_mate_2 = ','.join(qual_2_temp)
self._map_mode = 4
elif (q_mate_1 is None) ^ (q_mate_2 is None):
raise WedringError(135, "You must set both pair-mate quality files.")
self.lib_mate_1 = ','.join(lib_1_temp)
self.lib_mate_2 = ','.join(lib_2_temp)
self._map_mode = 5
elif (lib_mate_1 is None) ^ (lib_mate_2 is None):
raise WedringError(135, "You must set both pair-mate library files.")
else:
raise WedringError(135, "You must provide the library file(s).")
if map_label is not None:
self._mapper_out = path.join(self.out_dir, map_label)
self._out_pref = map_label
elif 7 != self._map_mode != 8:
if ',' in self.lib_mate_1:
map_out_pref = (path.split(path.splitext(self.lib_mate_1[:self.lib_mate_1.index(',')])[0])[1],
path.split(path.splitext(self.lib_mate_2[:self.lib_mate_2.index(',')])[0][1]))
if map_out_pref[0][:-2] == map_out_pref[1][:-2]:
self._mapper_out = (path.join(self.out_dir,
map_out_pref[0] +
"_andothers_vs_" +
path.split(self.index)[1]))
self._out_pref = map_out_pref[0]
else:
self._mapper_out = (path.join(self.out_dir,
map_out_pref[0][:-2] + '_' +
map_out_pref[1][:-2] +
"_andothers_vs_" +
path.split(self.index)[1]))
self._out_pref = (map_out_pref[0][:-2] + '_' +
map_out_pref[1][:-2] + "_andothers_vs_")
else:
map_out_pref = (path.split(path.splitext(self.lib_mate_1)[0])[1],
path.split(path.splitext(self.lib_mate_2)[0])[1])
if map_out_pref[0][:-2] == map_out_pref[1][:-2]:
self._mapper_out = (path.join(self.out_dir,
map_out_pref[0][:-2] + "_vs_" +
path.split(self.index)[1]))
self._out_pref = map_out_pref[0][:-2]
else:
self._mapper_out = (path.join(self.out_dir,
map_out_pref[0][:-2] + '_' +
map_out_pref[1][:-2] + "_vs_" +
path.split(self.index)[1]))
self._out_pref = (map_out_pref[0][:-2] + '_' +
map_out_pref[1][:-2])
else:
if ',' in self.lib_file:
map_out_pref = path.split(path.splitext(self.lib_file[:self.lib_file.index(',')])[0])[1]
self._mapper_out = (path.join(self.out_dir, map_out_pref +
"_andothers_vs_" +
path.split(self.index)[1]))
self._out_pref = map_out_pref + "_andothers_vs_"
else:
map_out_pref = path.split(path.splitext(self.lib_file)[0])[1]
self._mapper_out = (path.join(self.out_dir, map_out_pref +
"_vs_" +
path.split(self.index)[1]))
self._out_pref = map_out_pref
if annot_file is not None:
if wedr_check_path(annot_file):
self.annot_file = annot_file
else:
raise WedringError(135, "You must provide the annotation file.")
else:
if annot_file is not None:
if wedr_check_path(annot_file):
self.annot_file = annot_file
else:
raise WedringError(135, "You must provide the annotation file.")
if cov_file is not None:
if wedr_check_path(cov_file):
self.cov_file = cov_file
else:
raise WedringError(135, "You must provide the coverage file.")