def getFromArrayByKey(cf):
"""Wrapper for the findfile_impl function."""
commentchar = cf.get_parameter('commentchar', 'string')
delimiter = cf.get_parameter('delimiter', 'string')
if delimiter == 'tab':
delimiter = '\t'
keycol = cf.get_parameter('keycol', 'int')
keysfile = cf.get_input('keys')
reader = csv.reader(open(keysfile, 'U'), delimiter=delimiter, quoting=csv.QUOTE_NONE)
#read the header
reader.next()
keys = []
for row in reader:
if not len(row) > 0 or \
(not commentchar == "" and \
row[0].startswith(commentchar)):
continue
elif keycol > len(row):
cf.write_error("Index %s out of bounds in row %s" % (keycol, row))
return constants.GENERIC_ERROR
else:
keys.append(row[keycol])
cf.write_log(str(keys))
inarray = get_array(cf, 'in_array')
outarray = AndurilOutputArray(cf, 'out_array')
for key, value in inarray:
cf.write_log("Key: %s, Value: %s" % (key, value))
if key in keys:
outarray.write(key, value)
return constants.OK
def separatePairsAndSingles(cf):
"""In an array of runs, separate the paired end reads into two separate files, and
the singles into a third."""
fastqfiles = get_array(cf, 'fastqfiles')
srafetchxml = cf.get_input('srafetchxml')
leftfh = open(cf.get_output('left'), 'w')
rightfh = open(cf.get_output('right'), 'w')
singlefh = open(cf.get_output('single'), 'w')
for accession, fastqfile in fastqfiles:
fqp = FastqParser()
fastqfh = open(fastqfile, 'U')
if isPaired(srafetchxml, accession):
iter = fqp.parse(fastqfh)
#paired end run
while True:
try:
pe1 = iter.next()
pe2 = iter.next()
leftfh.write(str(pe1) + '\n')
rightfh.write(str(pe2) + '\n')
except StopIteration:
break
else:
#single end run
for rec in fqp.parse(fastqfh):
singlefh.write(str(rec) + '\n')
leftfh.close()
rightfh.close()
singlefh.close()
return constants.OK
def fasta_merge(cf):
"""Merge an array of fastafiles."""
outfh = open(cf.get_output("output"), "w")
fastafiles = get_array(cf, "fastafiles")
cf.write_log(str(fastafiles))
for key, fastafile in fastafiles:
for rec in fasta_itr(fastafile):
outfh.write(str(rec) + "\n")
outfh.close()
return constants.OK
def fastq_merge(cf):
"""Merge an array of fastqfiles."""
outfh = open(cf.get_output('output'), 'w')
fastqfiles = get_array(cf, 'in_array')
cf.write_log(str(fastqfiles))
fqp = FastqParser()
for key, fastqfile in fastqfiles:
for rec in fqp.parse(open(fastqfile, 'U')):
outfh.write(str(rec) + '\n')
outfh.close()
return constants.OK
def sffmerge(cf):
inarray = get_array(cf, 'in_array')
outputfile = cf.get_output('output')
params = ['-o', outputfile]
for key, inputfile in inarray:
params.append(inputfile)
try:
subprocess.check_call(['sfffile'] + params)
except subprocess.CalledProcessError, e:
cf.write_log("Error running sfffile.")
cf.write_log("Error: %s" % str(e))
return constants.GENERIC_ERROR
def newbler(cf):
"""Execute a Newbler assembly."""
params = ['-o', cf.get_output('assemblydir')]
vectortrimming = cf.get_input('vectortrimming')
if vectortrimming \
and os.path.isfile(vectortrimming) \
and os.path.getsize(vectortrimming) > 0:
params += ['-vt', vectortrimming]
if cf.get_parameter('large', 'boolean'):
params.append('-large')
params += ['-cpu', str(cf.get_parameter('threads')), '-cdna', '-m', '-urt', '-force']
inputfiles = get_array(cf, 'inputfiles')
for key, inputfile in inputfiles:
params.append(inputfile)
cf.write_log("Params: %s" % str(params))
tries = cf.get_parameter('retries', 'int') + 1
return runNewblerWithRetry(cf, params, tries)
