def check_command_line_args(options, args, parser):
# check command line arguments
if len(args) < 3:
parser.error("Incorrect number of command line arguments")
fastq_files = args[0:2]
output_dir = args[2]
# check that input fastq files exist
read_lengths = []
for mate, fastq_file in enumerate(fastq_files):
if not os.path.isfile(args[0]):
parser.error("mate '%d' fastq file '%s' is not valid" %
(mate, fastq_file))
logging.debug("Checking read length for file %s" % (fastq_file))
read_lengths.append(get_read_length(fastq_file))
logging.debug("Read length for file %s: %d" %
(fastq_file, read_lengths[-1]))
# check that mate read lengths are equal
if len(set(read_lengths)) > 1:
parser.error("read lengths mate1=%d and mate2=%d are unequal" %
(read_lengths[0], read_lengths[1]))
# check that seed length < read length
if any(options.segment_length > rlen for rlen in read_lengths):
parser.error("seed length %d cannot be longer than read length" %
(options.segment_length))
# check that output dir is not a regular file
if os.path.exists(output_dir) and (not os.path.isdir(output_dir)):
parser.error(
"Output directory name '%s' exists and is not a valid directory" %
(output_dir))
if check_executable(options.bowtie_build_bin):
logging.debug("Checking for 'bowtie-build' binary... found")
else:
parser.error("bowtie-build binary not found or not executable")
# check that bowtie program exists
if check_executable(options.bowtie_bin):
logging.debug("Checking for 'bowtie' binary... found")
else:
parser.error("bowtie binary not found or not executable")
# check that alignment index exists
if os.path.isdir(options.index_dir):
logging.debug("Checking for chimerascan index directory... found")
else:
parser.error("chimerascan alignment index directory '%s' not valid" %
(options.index_dir))
# check that alignment index file exists
align_index_file = os.path.join(options.index_dir,
config.BOWTIE_INDEX_FILE)
if os.path.isfile(align_index_file):
logging.debug("Checking for bowtie index file... found")
else:
parser.error("chimerascan bowtie index file '%s' invalid" %
(align_index_file))
# check for sufficient processors
if options.num_processors < config.BASE_PROCESSORS:
logging.warning(
"Please specify >=2 processes using '-p' to allow program to run efficiently"
)
def check_config(self):
# check that input fastq files exist
config_passed = True
read_lengths = []
for mate,fastq_file in enumerate(self.fastq_files):
if not os.path.isfile(fastq_file):
logging.error("mate '%d' fastq file '%s' is not valid" %
(mate, fastq_file))
config_passed = False
read_lengths.append(get_read_length(fastq_file))
logging.debug("Checking file %s" % (fastq_file))
logging.debug("File %s read length=%d" % (fastq_file, read_lengths[-1]))
# check that mate read lengths are equal
if len(set(read_lengths)) > 1:
logging.error("Unequal read lengths mate1=%d and mate2=%d" %
(read_lengths[0], read_lengths[1]))
config_passed = False
# check that seed length < read length
if any(self.segment_length > rlen for rlen in read_lengths):
logging.error("seed length %d cannot be longer than read length" %
(self.segment_length))
config_passed = False
# check that output dir is not a regular file
if os.path.exists(self.output_dir) and (not os.path.isdir(self.output_dir)):
logging.error("Output directory name '%s' exists and is not a valid directory" %
(self.output_dir))
config_passed = False
if check_executable(self.bowtie_build_bin):
logging.debug("Checking for 'bowtie-build' binary... found")
else:
logging.error("bowtie-build binary not found or not executable")
config_passed = False
# check that bowtie program exists
if check_executable(self.bowtie_bin):
logging.debug("Checking for 'bowtie' binary... found")
else:
logging.error("bowtie binary not found or not executable")
config_passed = False
# check that alignment index exists
if os.path.isdir(self.index_dir):
logging.debug("Checking for chimerascan index directory... found")
# check that alignment index file exists
align_index_file = os.path.join(self.index_dir, config.BOWTIE_INDEX_FILE)
if os.path.isfile(align_index_file):
logging.debug("Checking for bowtie index file... found")
else:
logging.error("chimerascan bowtie index file '%s' invalid" % (align_index_file))
config_passed = False
else:
logging.error("chimerascan alignment index directory '%s' not valid" %
(self.index_dir))
config_passed = False
# check for sufficient processors
if self.num_processors < config.BASE_PROCESSORS:
logging.warning("Please specify >=2 processes using '-p' to allow program to run efficiently")
return config_passed
def check_command_line_args(options, args, parser):
# check command line arguments
if len(args) < 3:
parser.error("Incorrect number of command line arguments")
fastq_files = args[0:2]
output_dir = args[2]
# check that input fastq files exist
read_lengths = []
for mate,fastq_file in enumerate(fastq_files):
if not os.path.isfile(args[0]):
parser.error("mate '%d' fastq file '%s' is not valid" %
(mate, fastq_file))
logging.debug("Checking read length for file %s" %
(fastq_file))
read_lengths.append(get_read_length(fastq_file))
logging.debug("Read length for file %s: %d" %
(fastq_file, read_lengths[-1]))
# check that mate read lengths are equal
if len(set(read_lengths)) > 1:
parser.error("read lengths mate1=%d and mate2=%d are unequal" %
(read_lengths[0], read_lengths[1]))
# check that seed length < read length
if any(options.segment_length > rlen for rlen in read_lengths):
parser.error("seed length %d cannot be longer than read length" %
(options.segment_length))
# check that output dir is not a regular file
if os.path.exists(output_dir) and (not os.path.isdir(output_dir)):
parser.error("Output directory name '%s' exists and is not a valid directory" %
(output_dir))
if check_executable(options.bowtie_build_bin):
logging.debug("Checking for 'bowtie-build' binary... found")
else:
parser.error("bowtie-build binary not found or not executable")
# check that bowtie program exists
if check_executable(options.bowtie_bin):
logging.debug("Checking for 'bowtie' binary... found")
else:
parser.error("bowtie binary not found or not executable")
# check that alignment index exists
if os.path.isdir(options.index_dir):
logging.debug("Checking for chimerascan index directory... found")
else:
parser.error("chimerascan alignment index directory '%s' not valid" %
(options.index_dir))
# check that alignment index file exists
align_index_file = os.path.join(options.index_dir, config.BOWTIE_INDEX_FILE)
if os.path.isfile(align_index_file):
logging.debug("Checking for bowtie index file... found")
else:
parser.error("chimerascan bowtie index file '%s' invalid" % (align_index_file))
# check for sufficient processors
if options.num_processors < config.BASE_PROCESSORS:
logging.warning("Please specify >=2 processes using '-p' to allow program to run efficiently")
def main():
logging.basicConfig(
level=logging.DEBUG,
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
parser = argparse.ArgumentParser(
description="Build alignment indexes for use with chimerascan")
parser.add_argument("ref_fasta_file", help="reference genome FASTA file")
parser.add_argument("transcript_feature_file", help="transcript features")
parser.add_argument("output_dir",
help="directory where indexes will be created")
args = parser.parse_args()
# check that input files exist
if not os.path.isfile(args.ref_fasta_file):
parser.error("Reference fasta file '%s' not found" %
(args.ref_fasta_file))
if not os.path.isfile(args.transcript_feature_file):
parser.error("Gene feature file '%s' not found" %
(args.transcript_feature_file))
# check that output dir is not a regular file
if os.path.exists(
args.output_dir) and (not os.path.isdir(args.output_dir)):
parser.error("Output directory name '%s' exists and is not a valid "
"directory" % (args.output_dir))
# check that bowtie2-build program exists
if check_executable(config.BOWTIE2_BUILD_BIN):
logging.debug("Checking for '%s' binary... found" %
(config.BOWTIE2_BUILD_BIN))
else:
parser.error("%s binary not found or not executable" %
(config.BOWTIE2_BUILD_BIN))
# run main index creation function
retcode = create_chimerascan_index(args.output_dir, args.ref_fasta_file,
args.transcript_feature_file)
return retcode
def main():
logging.basicConfig(level=logging.DEBUG,
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
parser = argparse.ArgumentParser(description="Build alignment indexes for use with chimerascan")
parser.add_argument("ref_fasta_file", help="reference genome FASTA file")
parser.add_argument("transcript_feature_file", help="transcript features")
parser.add_argument("output_dir", help="directory where indexes will be created")
args = parser.parse_args()
# check that input files exist
if not os.path.isfile(args.ref_fasta_file):
parser.error("Reference fasta file '%s' not found" % (args.ref_fasta_file))
if not os.path.isfile(args.transcript_feature_file):
parser.error("Gene feature file '%s' not found" % (args.transcript_feature_file))
# check that output dir is not a regular file
if os.path.exists(args.output_dir) and (not os.path.isdir(args.output_dir)):
parser.error("Output directory name '%s' exists and is not a valid "
"directory" % (args.output_dir))
# check that bowtie2-build program exists
if check_executable(config.BOWTIE2_BUILD_BIN):
logging.debug("Checking for '%s' binary... found" % (config.BOWTIE2_BUILD_BIN))
else:
parser.error("%s binary not found or not executable" % (config.BOWTIE2_BUILD_BIN))
# run main index creation function
retcode = create_chimerascan_index(args.output_dir, args.ref_fasta_file,
args.transcript_feature_file)
return retcode
def main():
logging.basicConfig(level=logging.DEBUG,
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
parser = OptionParser("usage: %prog [options] <reference_genome.fa> "
"<genepred_genes.txt> <index_output_dir>")
parser.add_option("--bowtie-dir", dest="bowtie_dir", default="",
help="Path to the 'bowtie' software (by default, "
"expects the 'bowtie' and 'bowtie-build' "
"binaries to be in current PATH)")
options, args = parser.parse_args()
# check command line arguments
if len(args) < 3:
parser.error("Incorrect number of command line arguments")
ref_fasta_file = args[0]
gene_feature_file = args[1]
output_dir = args[2]
# check that input files exist
if not os.path.isfile(ref_fasta_file):
parser.error("Reference fasta file '%s' not found" % (ref_fasta_file))
if not os.path.isfile(gene_feature_file):
parser.error("Gene feature file '%s' not found" % (gene_feature_file))
# check that output dir is not a regular file
if os.path.exists(output_dir) and (not os.path.isdir(output_dir)):
parser.error("Output directory name '%s' exists and is not a valid "
"directory" % (output_dir))
# check that bowtie-build program exists
bowtie_build_bin = os.path.join(options.bowtie_dir, "bowtie-build")
if check_executable(bowtie_build_bin):
logging.debug("Checking for 'bowtie-build' binary... found")
else:
parser.error("bowtie-build binary not found or not executable")
# run main index creation function
retcode = create_chimerascan_index(output_dir, ref_fasta_file,
gene_feature_file, bowtie_build_bin)
sys.exit(retcode)
def _setup_and_open_files(genome_index, transcripts, input_file, output_file,
library_type, input_sam, output_sam):
# create SAM header from genome index
logging.debug("Creating genome SAM header")
if not check_executable(config.BOWTIE2_INSPECT_BIN):
logging.error("Cannot find bowtie2-inspect binary")
return config.JOB_ERROR
# get references/lengths from bowtie2
ref_list = get_references_from_bowtie2_index(genome_index)
# open input BAM file and add to header
if input_sam:
mode = "r"
else:
mode = "rb"
infh = pysam.Samfile(input_file, mode)
header_dict = dict(infh.header)
header_dict['SQ'] = [{
'SN': seqname,
'LN': seqlen
} for seqname, seqlen in ref_list]
# open output BAM file with new header
if output_sam:
mode = "wh"
else:
mode = "wb"
outfh = pysam.Samfile(output_file, mode, header=header_dict)
# setup reference name mappings
genome_rname_tid_map = dict(
(rname, i) for i, rname in enumerate(outfh.references))
transcriptome_rname_tid_map = dict(
(rname, i) for i, rname in enumerate(infh.references))
# read transcript feature and prepare data structure for conversion
logging.debug("Creating transcript to genome map")
transcript_tid_map = {}
for t in transcripts:
exons = [(start, end) for start, end in t.exons]
negstrand = True if t.strand == "-" else False
if negstrand:
exons.reverse()
transcript_tid = transcriptome_rname_tid_map[str(t.tx_id)]
genome_tid = genome_rname_tid_map[t.chrom]
transcript_tid_map[transcript_tid] = (genome_tid, negstrand, exons)
return infh, outfh, transcript_tid_map
def main():
logging.basicConfig(
level=logging.DEBUG,
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
parser = OptionParser("usage: %prog [options] <reference_genome.fa> "
"<gene_models.txt> <index_output_dir>")
#parser.add_option('-i', '--min-fragment-size', dest="min_fragment_size", default=0)
#parser.add_option('-I', '--max-fragment-size', dest="max_fragment_size", default=700)
parser.add_option("--bowtie-dir",
dest="bowtie_dir",
default="",
help="Path to the 'bowtie' software (by default, "
"expects the 'bowtie' and 'bowtie-build' "
"binaries to be in current PATH)")
options, args = parser.parse_args()
# check command line arguments
if len(args) < 3:
parser.error("Incorrect number of command line arguments")
ref_fasta_file = args[0]
gene_feature_file = args[1]
output_dir = args[2]
# check that input files exist
if not os.path.isfile(ref_fasta_file):
parser.error("Reference fasta file '%s' not found" % (ref_fasta_file))
if not os.path.isfile(gene_feature_file):
parser.error("Gene feature file '%s' not found" % (gene_feature_file))
# check that output dir is not a regular file
if os.path.exists(output_dir) and (not os.path.isdir(output_dir)):
parser.error("Output directory name '%s' exists and is not a valid "
"directory" % (output_dir))
# check that bowtie-build program exists
bowtie_build_bin = os.path.join(options.bowtie_dir, "bowtie-build")
if check_executable(bowtie_build_bin):
logging.debug("Checking for 'bowtie-build' binary... found")
else:
parser.error("bowtie-build binary not found or not executable")
# run main index creation function
retcode = create_chimerascan_index(output_dir, ref_fasta_file,
gene_feature_file, bowtie_build_bin)
# min_fragment_size=options.min_fragment_size,
# max_fragment_size=options.max_fragment_size)
sys.exit(retcode)
def _setup_and_open_files(genome_index, transcripts,
input_file, output_file,
library_type, input_sam,
output_sam):
# create SAM header from genome index
logging.debug("Creating genome SAM header")
if not check_executable(config.BOWTIE2_INSPECT_BIN):
logging.error("Cannot find bowtie2-inspect binary")
return config.JOB_ERROR
# get references/lengths from bowtie2
ref_list = get_references_from_bowtie2_index(genome_index)
# open input BAM file and add to header
if input_sam:
mode = "r"
else:
mode = "rb"
infh = pysam.Samfile(input_file, mode)
header_dict = dict(infh.header)
header_dict['SQ'] = [{'SN': seqname, 'LN': seqlen} for seqname,seqlen in ref_list]
# open output BAM file with new header
if output_sam:
mode = "wh"
else:
mode = "wb"
outfh = pysam.Samfile(output_file, mode, header=header_dict)
# setup reference name mappings
genome_rname_tid_map = dict((rname,i) for i,rname in enumerate(outfh.references))
transcriptome_rname_tid_map = dict((rname,i) for i,rname in enumerate(infh.references))
# read transcript feature and prepare data structure for conversion
logging.debug("Creating transcript to genome map")
transcript_tid_map = {}
for t in transcripts:
exons = [(start, end) for start, end in t.exons]
negstrand = True if t.strand == "-" else False
if negstrand:
exons.reverse()
transcript_tid = transcriptome_rname_tid_map[str(t.tx_id)]
genome_tid = genome_rname_tid_map[t.chrom]
transcript_tid_map[transcript_tid] = (genome_tid, negstrand, exons)
return infh, outfh, transcript_tid_map
def main():
logging.basicConfig(
level=logging.DEBUG,
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
parser = OptionParser(
"usage: %prog [options] <reference_genome.fa> <gene_models.txt> <index_output_dir>"
)
parser.add_option("--bowtie-build-bin",
dest="bowtie_build_bin",
default="bowtie-build",
help="Path to 'bowtie-build' program")
options, args = parser.parse_args()
# check command line arguments
if len(args) < 3:
parser.error("Incorrect number of command line arguments")
ref_fasta_file = args[0]
gene_feature_file = args[1]
output_dir = args[2]
# check that input files exist
if not os.path.isfile(ref_fasta_file):
parser.error("Reference fasta file '%s' not found" % (ref_fasta_file))
if not os.path.isfile(gene_feature_file):
parser.error("Gene feature file '%s' not found" % (gene_feature_file))
# check that output dir is not a regular file
if os.path.exists(output_dir) and (not os.path.isdir(output_dir)):
parser.error(
"Output directory name '%s' exists and is not a valid directory" %
(output_dir))
# check that bowtie-build program exists
if check_executable(options.bowtie_build_bin):
logging.debug("Checking for 'bowtie-build' binary... found")
else:
parser.error("bowtie-build binary not found or not executable")
# run main index creation function
retcode = create_chimerascan_index(output_dir, ref_fasta_file,
gene_feature_file,
options.bowtie_build_bin)
sys.exit(retcode)
def check_config(self):
# check that input fastq files exist
config_passed = True
for mate, fastq_file in enumerate(self.fastq_files):
if not os.path.isfile(fastq_file):
logging.error("mate '%d' fastq file '%s' is not valid" %
(mate, fastq_file))
config_passed = False
# check read lengths with trimming applied
logging.debug("Checking read lengths")
read_lengths = [detect_read_length(fq) for fq in self.fastq_files]
total_trimming = self.trim5 + self.trim3
for i, rlen in enumerate(read_lengths):
trimmed_rlen = rlen - total_trimming
logging.debug("File %s read length: %d after trimming: %d" %
(self.fastq_files[i], rlen, trimmed_rlen))
if trimmed_rlen < config.MIN_SEGMENT_LENGTH:
logging.error(
"Trimmed read length is less than the minimum length of %d"
% (trimmed_rlen, config.MIN_SEGMENT_LENGTH))
config_passed = False
# check that mate read lengths are equal
if len(set(read_lengths)) > 1:
logging.error("Unequal read lengths mate1=%d and mate2=%d" %
(read_lengths[0], read_lengths[1]))
config_passed = False
# check that seed length < read length
if self.segment_length is not None:
if any((self.segment_length > rlen) for rlen in read_lengths):
logging.error(
"seed length %d cannot be longer than read length" %
(self.segment_length))
config_passed = False
# ensure local anchor length is larger than minimum
if self.local_anchor_length < config.LOCAL_ANCHOR_LENGTH_MIN:
logging.error(
"Local anchor length of %d < %d" %
(self.local_anchor_length, config.LOCAL_ANCHOR_LENGTH_MIN))
config_passed = False
# check that output dir is not a regular file
if os.path.exists(
self.output_dir) and (not os.path.isdir(self.output_dir)):
logging.error(
"Output directory name '%s' exists and is not a valid directory"
% (self.output_dir))
config_passed = False
if check_executable(config.BOWTIE2_BUILD_BIN):
logging.debug("Checking for '%s' binary... found" %
config.BOWTIE2_BUILD_BIN)
else:
logging.error("%s binary not found or not executable" %
config.BOWTIE2_BUILD_BIN)
config_passed = False
# check that bowtie program exists
if check_executable(os.path.join(config.BOWTIE2_BIN)):
logging.debug("Checking for '%s' binary... found" %
config.BOWTIE2_BIN)
else:
logging.error("%s binary not found or not executable" %
config.BOWTIE2_BIN)
config_passed = False
# check that alignment index exists
if os.path.isdir(self.index_dir):
logging.debug("Checking for chimerascan index directory... found")
# check that alignment index files exist
for f in config.TRANSCRIPTOME_BOWTIE2_FILES:
filename = os.path.join(self.index_dir, f)
if not os.path.isfile(filename):
logging.error("chimerascan index file '%s' invalid" %
(filename))
config_passed = False
break
for f in config.GENOME_BOWTIE2_FILES:
filename = os.path.join(self.index_dir, f)
if not os.path.isfile(filename):
logging.error("chimerascan index file '%s' invalid" %
(filename))
config_passed = False
break
else:
logging.error(
"chimerascan alignment index directory '%s' not valid" %
(self.index_dir))
config_passed = False
# check for sufficient processors
if self.num_processors < config.BASE_PROCESSORS:
logging.warning(
"Please specify >=2 processes using '-p' to allow program to run efficiently"
)
return config_passed
def check_config(self):
# check that input fastq files exist
config_passed = True
for mate,fastq_file in enumerate(self.fastq_files):
if not os.path.isfile(fastq_file):
logging.error("mate '%d' fastq file '%s' is not valid" %
(mate, fastq_file))
config_passed = False
# check read lengths with trimming applied
logging.debug("Checking read lengths")
read_lengths = [detect_read_length(fq) for fq in self.fastq_files]
total_trimming = self.trim5 + self.trim3
for i,rlen in enumerate(read_lengths):
trimmed_rlen = rlen - total_trimming
logging.debug("File %s read length: %d after trimming: %d" %
(self.fastq_files[i], rlen, trimmed_rlen))
if trimmed_rlen < config.MIN_SEGMENT_LENGTH:
logging.error("Trimmed read length is less than the minimum length of %d" %
(trimmed_rlen, config.MIN_SEGMENT_LENGTH))
config_passed = False
# check that mate read lengths are equal
if len(set(read_lengths)) > 1:
logging.error("Unequal read lengths mate1=%d and mate2=%d" %
(read_lengths[0], read_lengths[1]))
config_passed = False
# check that seed length < read length
if self.segment_length is not None:
if any((self.segment_length > rlen) for rlen in read_lengths):
logging.error("seed length %d cannot be longer than read length" %
(self.segment_length))
config_passed = False
# ensure local anchor length is larger than minimum
if self.local_anchor_length < config.LOCAL_ANCHOR_LENGTH_MIN:
logging.error("Local anchor length of %d < %d" %
(self.local_anchor_length, config.LOCAL_ANCHOR_LENGTH_MIN))
config_passed = False
# check that output dir is not a regular file
if os.path.exists(self.output_dir) and (not os.path.isdir(self.output_dir)):
logging.error("Output directory name '%s' exists and is not a valid directory" %
(self.output_dir))
config_passed = False
if check_executable(config.BOWTIE2_BUILD_BIN):
logging.debug("Checking for '%s' binary... found" % config.BOWTIE2_BUILD_BIN)
else:
logging.error("%s binary not found or not executable" % config.BOWTIE2_BUILD_BIN)
config_passed = False
# check that bowtie program exists
if check_executable(os.path.join(config.BOWTIE2_BIN)):
logging.debug("Checking for '%s' binary... found" % config.BOWTIE2_BIN)
else:
logging.error("%s binary not found or not executable" % config.BOWTIE2_BIN)
config_passed = False
# check that alignment index exists
if os.path.isdir(self.index_dir):
logging.debug("Checking for chimerascan index directory... found")
# check that alignment index files exist
for f in config.TRANSCRIPTOME_BOWTIE2_FILES:
filename = os.path.join(self.index_dir, f)
if not os.path.isfile(filename):
logging.error("chimerascan index file '%s' invalid" % (filename))
config_passed = False
break
for f in config.GENOME_BOWTIE2_FILES:
filename = os.path.join(self.index_dir, f)
if not os.path.isfile(filename):
logging.error("chimerascan index file '%s' invalid" % (filename))
config_passed = False
break
else:
logging.error("chimerascan alignment index directory '%s' not valid" %
(self.index_dir))
config_passed = False
# check for sufficient processors
if self.num_processors < config.BASE_PROCESSORS:
logging.warning("Please specify >=2 processes using '-p' to allow program to run efficiently")
return config_passed
def check_config(self):
# check that input fastq files exist
config_passed = True
read_lengths = []
for mate, fastq_file in enumerate(self.fastq_files):
if not os.path.isfile(fastq_file):
logging.error("mate '%d' fastq file '%s' is not valid" %
(mate, fastq_file))
config_passed = False
read_lengths.append(get_read_length(fastq_file))
logging.debug("Checking file %s" % (fastq_file))
logging.debug("File %s read length=%d" %
(fastq_file, read_lengths[-1]))
# check that mate read lengths are equal
if len(set(read_lengths)) > 1:
logging.error("Unequal read lengths mate1=%d and mate2=%d" %
(read_lengths[0], read_lengths[1]))
config_passed = False
# check that seed length < read length
if any(self.segment_length > rlen for rlen in read_lengths):
logging.error("seed length %d cannot be longer than read length" %
(self.segment_length))
config_passed = False
# check that output dir is not a regular file
if os.path.exists(
self.output_dir) and (not os.path.isdir(self.output_dir)):
logging.error(
"Output directory name '%s' exists and is not a valid directory"
% (self.output_dir))
config_passed = False
if check_executable(self.bowtie_build_bin):
logging.debug("Checking for 'bowtie-build' binary... found")
else:
logging.error("bowtie-build binary not found or not executable")
config_passed = False
# check that bowtie program exists
if check_executable(self.bowtie_bin):
logging.debug("Checking for 'bowtie' binary... found")
else:
logging.error("bowtie binary not found or not executable")
config_passed = False
# check that alignment index exists
if os.path.isdir(self.index_dir):
logging.debug("Checking for chimerascan index directory... found")
# check that alignment index file exists
align_index_file = os.path.join(self.index_dir,
config.BOWTIE_INDEX_FILE)
if os.path.isfile(align_index_file):
logging.debug("Checking for bowtie index file... found")
else:
logging.error("chimerascan bowtie index file '%s' invalid" %
(align_index_file))
config_passed = False
else:
logging.error(
"chimerascan alignment index directory '%s' not valid" %
(self.index_dir))
config_passed = False
# check for sufficient processors
if self.num_processors < config.BASE_PROCESSORS:
logging.warning(
"Please specify >=2 processes using '-p' to allow program to run efficiently"
)
return config_passed
