def exec_deseq(self):
"""Execute the **Wedring**'s differential expression stage.
:raises: :class:WedringError
"""
if not self._qt:
wedr_report("Calculating differential expression with DESeq.")
outfile = path.join(self._o, "diffexpr.txt")
errfile = path.join(self._ld, "diffexpr.log")
de_cmd_line = "Rscript --vanilla %s %s %s %s %s" % (wedr_which("diffExprStage.R"),
self.wedring_diffexpr_parse_options(),
self._cnt_table,
self._cnd,
outfile)
de = BioSoft(de_cmd_line, errfile=errfile)
if not self._qt:
wedr_report("Command line:\n %s" % de.command)
de.run()
if 0 != de.return_code != -1:
raise WedringError(141, "%s exitted with status %d. See log file '%s' for more details." %
(de.program_name, de.return_code, de.errfile))
wedr_clean(de.errfile)
# TODO Add verification of the DESeq's output with wedr_check_path()
# \_ table (OK), graphics
wedr_check_path(outfile)
if not self._qt:
wedr_report("DESeq - Done!")
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 exec_samtools(self):
"""Executor of the SAMtools part of the pipeline.
:raises: :class:WedringError
"""
if self.mapper == "bowtie":
if not self.quiet:
wedr_report("[%s] Converting SAM file to BAM file." %
self._out_pref)
sam_in_pref = path.splitext(self.aln_file)[0]
bam_out = sam_in_pref + ".bam"
errfile = path.join(self.log_dir, self._out_pref + "_view.log")
st = BioSoft(command="samtools view -bS -o %s %s.sam" %
(bam_out, self._mapper_out), errfile=errfile)
if not self.quiet:
wedr_report("[%s] Command line:\n %s" % (self._out_pref,
st.command))
st.run()
if 0 != st.return_code != -1:
raise WedringError(141, "[%s] %s exitted with status %d. See log file '%s' for more details." %
(self._out_pref, st.program_name,
st.return_code, st.errfile))
wedr_clean(st.errfile)
wedr_clean(self.aln_file, force=True)
self.aln_file = bam_out
wedr_check_path(self.aln_file)
if not self.quiet:
wedr_report("[%s] Sorting BAM file." % self._out_pref)
errfile = path.join(self.log_dir, self._out_pref + "_sort.log")
st = BioSoft(command = "samtools sort %s %s" %
(bam_out, sam_in_pref), errfile =errfile)
if not self.quiet:
wedr_report("[%s] Command line:\n %s" % (self._out_pref,
st.command))
st.run()
if 0 != st.return_code != -1:
raise WedringError(141, "[%s] %s exitted with status %d. See log file '%s' for more details." %
(self._out_pref, st.program_name,
st.return_code, st.errfile))
wedr_clean(st.errfile)
wedr_check_path(self.aln_file)
if not self.quiet:
wedr_report("[%s] Indexing BAM file." % self._out_pref)
errfile = path.join(self.log_dir, self._out_pref + "_index.log")
st = BioSoft(command="samtools index %s" % self.aln_file,
errfile=errfile)
if not self.quiet:
wedr_report("[%s] Command line:\n %s" % (self._out_pref,
st.command))
st.run()
if 0 != st.return_code != -1:
raise WedringError(141, "[%s] %s exitted with status %d. See log file '%s' for more details." %
(self._out_pref, st.program_name, st.return_code,
st.errfile))
wedr_clean(st.errfile)
wedr_check_path(self.aln_file + ".bai")
def exec_bedtools(self):
"""Executor of the BEDTools part of the pipeline.
:raises: :class:WedringError
"""
cov_out = self.aln_file.replace(".bam", ".cov")
errfile = path.join(self.log_dir, self._out_pref + "_coverage.log")
bt = BioSoft(command="bedtools coverage -s -abam %s -b %s" %
(self.aln_file, self.annot_file),
outfile=cov_out, errfile=errfile)
if not self.quiet:
wedr_report("[%s] Command line:\n %s" % (self._out_pref,
bt.command))
bt.run()
if 0 != bt.return_code != -1:
raise WedringError(141, "[%s] %s exitted with status %d. See log file '%s' for more details." %
(self._out_pref, bt.program_name, bt.return_code,
bt.errfile))
wedr_clean(bt.errfile)
if wedr_check_path(cov_out):
self.cov_file = cov_out
def exec_mapping(self):
"""Executor of the mapping part of the pipeline.
:raises: :class:WedringError
"""
if not self.quiet:
wedr_report("[%s] Mapping reads against reference genome." %
self._out_pref)
self.parse_mapper_cmd_line()
if not self.quiet:
wedr_report("[%s] Command line:\n %s" % (self._out_pref,
self._mapper_cmd))
errfile = path.join(self.log_dir, self._out_pref + "_mapping.log")
mp = BioSoft(command=self._mapper_cmd, errfile=errfile)
mp.run()
if 0 != mp.return_code != -1:
raise WedringError(141, "[%s] %s exitted with status %d. See log file '%s' for more details." %
(self._out_pref, mp.program_name, mp.return_code,
mp.errfile))
wedr_clean(mp.errfile)
if not self.quiet:
wedr_report("[%s] Mapping - Done!." % self._out_pref)
