def pca_rnaseq(self, counts_table_file):
@program
def pca(counts_table_file):
outprefix = unique_filename_in()
args = ['pca.R', counts_table_file, outprefix, "rpkm"]
return {"arguments": args, "return_value": outprefix}
if not program_exists('pca.R'):
self.write_debug("Skipped PCA: pca.R not found.")
return
try:
self.write_log("* PCA")
outprefix = pca.nonblocking(self.ex,
counts_table_file,
via=self.via).wait()
except Exception as err:
self.write_debug("PCA failed: %s." % str(err))
return
if outprefix is None:
self.write_debug("PCA failed.")
return
pca_descr_pdf = set_file_descr('pca.pdf',
type='pdf',
step='pca',
ucsc=0)
self.ex.add(outprefix + '.pdf', description=pca_descr_pdf)
def _run_tool(self, tool_name, args):
if not program_exists(tool_name):
raise OSError("Program not found in $PATH: %s" % tool_name)
proc = subprocess.Popen([tool_name] + args, stderr=subprocess.PIPE)
stdout, stderr = proc.communicate()
if stderr:
raise OSError("%s exited with message: %s" % (tool_name, stderr))
def differential_analysis(self, filename):
"""Launch an analysis of differential expression on the count
values, and saves the output in the MiniLIMS."""
@program
def run_DE(data_file):
"""Run limma.R on *data_file*."""
output_file = unique_filename_in()
arguments = [
"limma.R", data_file, "-s", "$'\t'", "-o", output_file
]
return {'arguments': arguments, 'return_value': output_file}
if not program_exists('limma.R'):
self.write_debug("Skipped DE analysis: negbin.test.R not found.")
return
if filename is None:
self.write_log(
" Skipped differential analysis: empty counts file.")
return
ncond = len(self.conditions)
if ncond < 2:
self.write_log(
" Skipped differential analysis: less than two groups.")
return
else:
self.write_log("* Differential analysis")
try:
de_file = run_DE.nonblocking(self.ex, filename,
via=self.via).wait()
except Exception as err:
self.write_debug("DE analysis failed with error: %s." %
str(err))
return
if de_file is None:
self.write_debug(
"DE analysis failed (see bein 'program' table).")
return
output_files = [
f for f in os.listdir(self.ex.working_directory)
if de_file in f
]
if isinstance(de_file, Exception) or len(output_files) == 0:
self.write_debug(
"Skipped differential analysis: `de_file` has value %s." %
str(de_file))
return
self.write_log(" ....done.")
return output_files
def pca_rnaseq(self,counts_table_file):
@program
def pca(counts_table_file):
outprefix = unique_filename_in()
args = ['pca.R', counts_table_file, outprefix, "rpkm"]
return {"arguments": args, "return_value": outprefix}
if not program_exists('pca.R'):
self.write_debug("Skipped PCA: pca.R not found.")
return
try:
self.write_log("* PCA")
outprefix = pca.nonblocking(self.ex, counts_table_file, via=self.via).wait()
except Exception as err:
self.write_debug("PCA failed: %s." % str(err))
return
if outprefix is None:
self.write_debug("PCA failed.")
return
pca_descr_pdf = set_file_descr('pca.pdf', type='pdf', step='pca', ucsc=0)
self.ex.add(outprefix+'.pdf', description=pca_descr_pdf)
def differential_analysis(self, filename):
"""Launch an analysis of differential expression on the count
values, and saves the output in the MiniLIMS."""
@program
def run_DE(data_file):
"""Run limma.R on *data_file*."""
output_file = unique_filename_in()
arguments = ["limma.R", data_file, "-s","$'\t'", "-o",output_file]
return {'arguments': arguments, 'return_value': output_file}
if not program_exists('limma.R'):
self.write_debug("Skipped DE analysis: negbin.test.R not found.")
return
if filename is None:
self.write_log(" Skipped differential analysis: empty counts file.")
return
ncond = len(self.conditions)
if ncond < 2:
self.write_log(" Skipped differential analysis: less than two groups.")
return
else:
self.write_log("* Differential analysis")
try:
de_file = run_DE.nonblocking(self.ex, filename, via=self.via).wait()
except Exception as err:
self.write_debug("DE analysis failed with error: %s." % str(err))
return
if de_file is None:
self.write_debug("DE analysis failed (see bein 'program' table).")
return
output_files = [f for f in os.listdir(self.ex.working_directory) if de_file in f]
if isinstance(de_file,Exception) or len(output_files)==0:
self.write_debug("Skipped differential analysis: `de_file` has value %s." % str(de_file))
return
self.write_log(" ....done.")
return output_files
def find_junctions(self,
soapsplice_index=None,
path_to_soapsplice=None,
soapsplice_options={}):
"""
Retrieve unmapped reads from a precedent mapping and runs SOAPsplice on them.
Return the names of a .bed track indicating the junctions positions, as well as
of a bam file of the alignments attesting the junctions.
:param soapsplice_index: (str) path to the SOAPsplice index.
:param path_to_soapsplice: (str) specify the path to the program if it is not in your $PATH.
:param soapsplice_options: (dict) SOAPsplice options, e.g. {'-m':2}.
:rtype: str, str
"""
@program
def soapsplice(unmapped_R1,
unmapped_R2,
index,
output=None,
path_to_soapsplice=None,
options={}):
"""Bind 'soapsplice'. Return a text file containing the list of junctions.
:param unmapped_R1: (str) path to the fastq file containing the 'left' reads.
:param unmapped_R2: (str) path to the fastq file containing the 'right' reads.
:param index: (str) path to the SOAPsplice index.
:param output: (str) output file name.
:param path_to_soapsplice: (str) path to the SOAPsplice executable.
If not specified, the program must be in your $PATH.
:param options: (dict) SOAPsplice options, given as {opt: value}.
:rtype: str
Main options::
-p: number of threads, <= 20. [1]
-S: 1: forward strand, 2: reverse strand, 3: both. [3]
-m: maximum mismatch for one-segment alignment, <= 5. [3]
-g: maximum indel for one-segment alignment, <= 2. [2]
-i: length of tail that can be ignored in one-segment alignment. [7]
-t: longest gap between two segments in two-segment alignment. [500000]
-a: shortest length of a segment in two-segment alignment. [8]
-q: input quality type in FASTQ file (0: old Illumina, 1: Sanger). [0]
-L: maximum distance between paired-end reads. [500000]
-l: minimum distance between paired-end reads. [50]
-I: insert length of paired-end reads.
"""
if not output: output = unique_filename_in()
path_to_soapsplice = path_to_soapsplice or 'soapsplice'
args = [
path_to_soapsplice, '-d', index, '-1', unmapped_R1, '-2',
unmapped_R2, '-o', output, '-f', '2'
]
opts = []
for k, v in options.iteritems():
opts.extend([str(k), str(v)])
return {"arguments": args + opts, "return_value": output}
if not program_exists('soapsplice'):
self.write_debug("Skipped junctions search: soapsplice not found.")
return
self.assembly.set_index_path(intype=3)
soapsplice_index = soapsplice_index or self.assembly.index_path
soapsplice_options.update(
self.job.options.get('soapsplice_options', {}))
soapsplice_options.setdefault('-p', 16) # number of threads
soapsplice_options.setdefault('-q', 1) # Sanger format
unmapped_fastq = {}
for gid, group in self.job.groups.iteritems():
unmapped_fastq[gid] = []
for rid, run in group['runs'].iteritems():
unmapped = self.job.files[gid][rid].get('unmapped_fastq')
if not unmapped:
self.write_log(
"No unmapped reads found for group %s, run %d. Skip." %
(gid, rid))
continue
elif not isinstance(unmapped, tuple):
self.write_log("Pair-end reads required. Skip.")
continue
unmapped_fastq[gid].append(unmapped)
if len(unmapped_fastq[gid]) == 0:
continue
R1 = cat(zip(*unmapped_fastq[gid])[0])
R2 = cat(zip(*unmapped_fastq[gid])[1])
future = soapsplice.nonblocking(
self.ex,
R1,
R2,
soapsplice_index,
path_to_soapsplice=path_to_soapsplice,
options=soapsplice_options,
via=self.via,
memory=8,
threads=soapsplice_options['-p'])
try:
template = future.wait()
except Exception as err:
self.write_debug("SOAPsplice failed: %s." % str(err))
return
if template is None:
self.write_debug("SOAPsplice failed.")
return
junc_file = template + '.junc'
bed = self.convert_junc_file(junc_file, self.assembly)
bed_descr = set_file_descr('junctions_%s.bed' % group['name'],
groupId=gid,
type='bed',
step='junctions',
ucsc=1)
bam_descr = set_file_descr('junctions_%s.bam' % group['name'],
groupId=gid,
type='bam',
step='junctions',
ucsc=0)
sam = template + '.sam'
try:
bam = sam_to_bam(self.ex, sam, reheader=self.assembly.name)
add_and_index_bam(self.ex, bam, description=bam_descr)
self.ex.add(bam, description=bam_descr)
except Exception as e:
self.write_debug(
"%s\n(Qualities may be in the wrong format, try with '-q 0'.)"
% str(e))
self.ex.add(bed, description=bed_descr)
return bed, bam
def find_junctions(self, soapsplice_index=None, path_to_soapsplice=None, soapsplice_options={}):
"""
Retrieve unmapped reads from a precedent mapping and runs SOAPsplice on them.
Return the names of a .bed track indicating the junctions positions, as well as
of a bam file of the alignments attesting the junctions.
:param soapsplice_index: (str) path to the SOAPsplice index.
:param path_to_soapsplice: (str) specify the path to the program if it is not in your $PATH.
:param soapsplice_options: (dict) SOAPsplice options, e.g. {'-m':2}.
:rtype: str, str
"""
@program
def soapsplice(unmapped_R1, unmapped_R2, index, output=None, path_to_soapsplice=None, options={}):
"""Bind 'soapsplice'. Return a text file containing the list of junctions.
:param unmapped_R1: (str) path to the fastq file containing the 'left' reads.
:param unmapped_R2: (str) path to the fastq file containing the 'right' reads.
:param index: (str) path to the SOAPsplice index.
:param output: (str) output file name.
:param path_to_soapsplice: (str) path to the SOAPsplice executable.
If not specified, the program must be in your $PATH.
:param options: (dict) SOAPsplice options, given as {opt: value}.
:rtype: str
Main options::
-p: number of threads, <= 20. [1]
-S: 1: forward strand, 2: reverse strand, 3: both. [3]
-m: maximum mismatch for one-segment alignment, <= 5. [3]
-g: maximum indel for one-segment alignment, <= 2. [2]
-i: length of tail that can be ignored in one-segment alignment. [7]
-t: longest gap between two segments in two-segment alignment. [500000]
-a: shortest length of a segment in two-segment alignment. [8]
-q: input quality type in FASTQ file (0: old Illumina, 1: Sanger). [0]
-L: maximum distance between paired-end reads. [500000]
-l: minimum distance between paired-end reads. [50]
-I: insert length of paired-end reads.
"""
if not output: output = unique_filename_in()
path_to_soapsplice = path_to_soapsplice or 'soapsplice'
args = [path_to_soapsplice,'-d',index,'-1',unmapped_R1,'-2',unmapped_R2,'-o',output,'-f','2']
opts = []
for k,v in options.iteritems(): opts.extend([str(k),str(v)])
return {"arguments": args+opts, "return_value": output}
if not program_exists('soapsplice'):
self.write_debug("Skipped junctions search: soapsplice not found.")
return
self.assembly.set_index_path(intype=3)
soapsplice_index = soapsplice_index or self.assembly.index_path
soapsplice_options.update(self.job.options.get('soapsplice_options',{}))
soapsplice_options.setdefault('-p',16) # number of threads
soapsplice_options.setdefault('-q',1) # Sanger format
unmapped_fastq = {}
for gid, group in self.job.groups.iteritems():
unmapped_fastq[gid] = []
for rid, run in group['runs'].iteritems():
unmapped = self.job.files[gid][rid].get('unmapped_fastq')
if not unmapped:
self.write_log("No unmapped reads found for group %s, run %d. Skip." % (gid,rid))
continue
elif not isinstance(unmapped,tuple):
self.write_log("Pair-end reads required. Skip.")
continue
unmapped_fastq[gid].append(unmapped)
if len(unmapped_fastq[gid]) == 0:
continue
R1 = cat(zip(*unmapped_fastq[gid])[0])
R2 = cat(zip(*unmapped_fastq[gid])[1])
future = soapsplice.nonblocking(self.ex,R1,R2,soapsplice_index,
path_to_soapsplice=path_to_soapsplice,
options=soapsplice_options,
via=self.via, memory=8, threads=soapsplice_options['-p'])
try:
template = future.wait()
except Exception as err:
self.write_debug("SOAPsplice failed: %s." % str(err))
return
if template is None:
self.write_debug("SOAPsplice failed.")
return
junc_file = template+'.junc'
bed = self.convert_junc_file(junc_file,self.assembly)
bed_descr = set_file_descr('junctions_%s.bed' % group['name'],
groupId=gid,type='bed',step='junctions', ucsc=1)
bam_descr = set_file_descr('junctions_%s.bam' % group['name'],
groupId=gid,type='bam',step='junctions', ucsc=0)
sam = template+'.sam'
try:
bam = sam_to_bam(self.ex,sam,reheader=self.assembly.name)
add_and_index_bam(self.ex, bam, description=bam_descr)
self.ex.add(bam, description=bam_descr)
except Exception as e:
self.write_debug("%s\n(Qualities may be in the wrong format, try with '-q 0'.)" %str(e))
self.ex.add(bed, description=bed_descr)
return bed, bam
def _run_tool(self, tool_name, args):
if not program_exists(tool_name):
raise OSError("Program not found in $PATH: %s" % tool_name)
proc = subprocess.Popen([tool_name]+args, stderr=subprocess.PIPE)
stdout, stderr = proc.communicate()
if stderr: raise OSError("%s exited with message: %s" % (tool_name,stderr))
