def main():
# get args and options
args = get_args()
# setup logging
log, my_name = setup_logging(args)
# get the input data
log.info("Getting input filenames and creating output directories")
input = get_input_data(args.config, args.dir)
# create the output directory if it does not exist
if not os.path.isdir(args.output):
os.makedirs(args.output)
else:
pass
# make the symlink directory within the output directory
contig_dir = os.path.join(args.output, 'contigs')
if not os.path.isdir(contig_dir):
os.makedirs(contig_dir)
else:
pass
try:
abyss_pe = which('abyss-pe')[0]
abyss_se = which('ABYSS')[0]
except:
raise EnvironmentError("Cannot find abyss-pe or ABYSS. Ensure they "
"are installed and in your $PATH")
# run abyss in (mostly) single-threaded mode for RAM and simplicity
# reasons. abyss-map will run using as many cores as user specifies.
for group in input:
sample, dir = group
# pretty print taxon status
text = " Processing {} ".format(sample)
log.info(text.center(65, "-"))
# make a directory for sample-specific assemblies
sample_dir = os.path.join(args.output, sample)
os.makedirs(sample_dir)
# determine how many files we're dealing with
reads = get_input_files(dir, args.subfolder, log)
# copy the read data over, combine singletons with read 1
# and run the assembly for PE data.
if reads.r1 and reads.r2:
output = run_abyss_pe(abyss_pe, args.kmer, reads, args.cores,
sample_dir, log)
if args.clean:
cleanup_abyss_assembly_folder(output, log)
elif reads.r1 and not reads.r2:
output = run_abyss_se(abyss_se, args.kmer, reads,
sample_dir, log)
if args.clean:
cleanup_abyss_assembly_folder(output, log, single_end=True)
contigs_file = get_contigs_file_from_output(output)
# remove degenerate bases, contigs < 100 bp, and rename
# contigs to velvet-style naming
contigs_file = convert_abyss_contigs_to_velvet(contigs_file)
# create generic link in assembly folder for covg. computation
generate_within_dir_symlink(contigs_file)
# link to the standard (non-trimmed) assembly in ../contigs
generate_symlinks(contig_dir, sample, contigs_file, log)
text = " Completed {} ".format(my_name)
log.info(text.center(65, "="))
def main():
# get args and options
args = get_args()
# setup logging
log, my_name = setup_logging(args)
# get the input data
log.info("Getting input filenames and creating output directories")
input = get_input_data(args.config, args.dir)
# create the output directory if it does not exist
if not os.path.isdir(args.output):
os.makedirs(args.output)
else:
pass
# make the symlink directory within the output directory
contig_dir = os.path.join(args.output, 'contigs')
if not os.path.isdir(contig_dir):
os.makedirs(contig_dir)
else:
pass
try:
velveth = which('velveth')[0]
velvetg = which('velvetg')[0]
except:
raise EnvironmentError("Cannot find velveth or velvetg. Ensure they "
"are installed and in your $PATH")
# run velvet in single-threaded mode for RAM and simplicity
# reasons.
for group in input:
sample, dir = group
# pretty print taxon status
text = " Processing {} ".format(sample)
log.info(text.center(65, "-"))
# make a directory for sample-specific assemblies
sample_dir = os.path.join(args.output, sample)
os.makedirs(sample_dir)
# determine how many files we're dealing with
reads = get_input_files(dir, args.subfolder, log)
# copy the read data over, combine singletons with read 1
# and run the assembly for PE data.
if reads.r1 and reads.r2:
output = run_velveth(velveth, args.kmer, reads, sample_dir, log)
output = run_velvetg(velvetg, args.kmer, output, log)
elif reads.r1 and not reads.r2 and not reads.singleton:
pass
if args.clean:
cleanup_velvet_assembly_folder(output, log)
contigs_file = get_contigs_file_from_output(output)
# create generic link in assembly folder for covg. computation
generate_within_dir_symlink(sample_dir, contigs_file)
# link to the standard (non-trimmed) assembly in ../contigs
generate_symlinks(contig_dir, sample, contigs_file, log)
text = " Completed {} ".format(my_name)
log.info(text.center(65, "="))
def get_velvet_optimiser(name='VelvetOptimiser'):
"""ensure that velvetg, velveth, VelvetOpt, and VelvetOptimiser are in $PATH"""
# ensure velvetg and velveth are in $PATH
velvetg = which("velvetg")
velveth = which("velveth")
velvet_opt = which("VelvetOpt")
# we need velvetoptimiser - ensure that is in $PATH and return
try:
velvet_optimiser = which("{}".format(name))[0]
return velvet_optimiser
except EnvironmentError, e:
velvet_optimiser = which("{}.pl".format(name))[0]
return velvet_optimiser
def main():
# get args and options
args = get_args()
# setup logging
log, my_name = setup_logging(args)
# get the input data
log.info("Getting input filenames and creating output directories")
input = get_input_data(args.config, args.dir)
# create the output directory if it does not exist
if not os.path.isdir(args.output):
os.makedirs(args.output)
else:
pass
# make the symlink directory within the output directory
contig_dir = os.path.join(args.output, 'contigs')
if not os.path.isdir(contig_dir):
os.makedirs(contig_dir)
else:
pass
# Get path to trinity. Standard name is `Trinity.pl`.
# I usually symlink to `trinity`
#TODO: Change this to system "which" - this is just to flaky in certain cases
try:
trinity = which('trinity')[0]
except EnvironmentError:
trinity = which('Trinity.pl')[0]
except:
raise EnvironmentError("Cannot find Trinity. Ensure it is installed and in your $PATH")
for group in input:
sample, dir = group
# pretty print taxon status
text = " Processing {} ".format(sample)
log.info(text.center(65, "-"))
# make a directory for sample-specific assemblies
sample_dir = os.path.join(args.output, sample)
os.makedirs(sample_dir)
# determine how many files we're dealing with
reads = get_input_files(dir, args.subfolder, log)
# copy the read data over, combine singletons with read 1
# and run the assembly for PE data.
if reads.r1 and reads.r2 and reads.singleton:
copy_read_data(reads, sample_dir, log)
combine_read_data(reads, log)
output = run_trinity_pe(trinity, reads, args.cores, args.min_kmer_coverage, log)
if args.clean:
cleanup_trinity_assembly_folder(output, log)
# we don't need to combine singleton files here. copy
# the read data over and run the assembly for PE data
elif reads.r1 and reads.r2:
copy_read_data(reads, sample_dir, log)
output = run_trinity_pe(trinity, reads, args.cores, args.min_kmer_coverage, log)
if args.clean:
cleanup_trinity_assembly_folder(output, log)
# here, we don't have PE data, so copy the file over
# and run the assembly for SE data
elif reads.r1:
copy_read_data(reads, sample_dir, log)
output = run_trinity_se(trinity, reads, args.cores, args.min_kmer_coverage, log)
if args.clean:
cleanup_trinity_assembly_folder(output, log)
# generate symlinks to assembled contigs
generate_symlinks(contig_dir, sample, reads, log)
text = " Completed {} ".format(my_name)
log.info(text.center(65, "="))
def main():
# get args and options
args = get_args()
# setup logging
log, my_name = setup_logging(args)
# get the input data
log.info("Getting input filenames")
input = get_input_data(args.assemblo_config, None)
# Get path to bwa
try:
bwa = which('bwa')[0]
except:
raise EnvironmentError("Cannot find bwa. Ensure it is installed and in your $PATH")
# make the symlink directory within the output directory
contig_dir = os.path.join(args.assemblies, 'contigs-trimmed')
if not os.path.isdir(contig_dir):
os.makedirs(contig_dir)
else:
pass
for group in input:
sample, reads = group
# pretty print taxon status
text = " Processing {} ".format(sample)
log.info(text.center(65, "-"))
# ensure that assembly exists
assembly_pth = os.path.join(args.assemblies, sample)
assembly = os.path.join(assembly_pth, "contigs.fasta")
if not os.path.exists(assembly):
raise IOError("Assembly for {} does not appear to exist.".format(sample))
if args.clean:
cleanup_trinity_assembly_folder(log, assembly_pth)
# determine the types of raw read data that we have
fastq = get_input_files(reads, args.subfolder, log)
# create the bwa index
bwa_create_index_files(log, assembly)
samtools_create_faidx(log, sample, assembly_pth, assembly)
picard_create_reference_dict(log, sample, assembly_pth, assembly)
bam = False
bam_se = False
if args.bwa_mem and fastq.r1 and fastq.r2:
bam = bwa_mem_pe_align(log, sample, assembly_pth, assembly, args.cores, fastq.r1, fastq.r2)
bam = picard_clean_up_bam(log, sample, assembly_pth, bam, "pe")
bam = picard_add_rg_header_info(log, sample, assembly_pth, "Generic", bam, "pe")
elif not args.bwa_mem and fastq.r1 and fastq.r2:
bam = bwa_pe_align(log, sample, assembly_pth, assembly, args.cores, fastq.r1, fastq.r2)
bam = picard_clean_up_bam(log, sample, assembly_pth, bam, "pe")
bam = picard_add_rg_header_info(log, sample, assembly_pth, "Generic", bam, "pe")
# get singleton reads for alignment
if args.bwa_mem and fastq.singleton:
bam_se = bwa_mem_se_align(log, sample, assembly_pth, assembly, args.cores, fastq.singleton)
bam_se = picard_clean_up_bam(log, sample, assembly_pth, bam_se, 'se')
bam_se = picard_add_rg_header_info(log, sample, assembly_pth, "Generic", bam_se, "se")
# if we only have se reads, those will be in fastq.r1 only
elif args.bwa_mem and not fastq.r2 and fastq.r1:
bam_se = bwa_mem_se_align(log, sample, assembly_pth, assembly, args.cores, fastq.r1)
bam_se = picard_clean_up_bam(log, sample, assembly_pth, bam_se, 'se')
bam_se = picard_add_rg_header_info(log, sample, assembly_pth, "Generic", bam_se, "se")
elif not args.bwa_mem and fastq.singleton:
bam_se = bwa_se_align(log, sample, assembly_pth, assembly, args.cores, fastq.singleton)
bam_se = picard_clean_up_bam(log, sample, assembly_pth, bam_se, 'se')
bam_se = picard_add_rg_header_info(log, sample, assembly_pth, "Generic", bam_se, "se")
elif not args.bwa_mem and not fastq.r2 and fastq.r1:
bam_se = bwa_se_align(log, sample, assembly_pth, assembly, args.cores, fastq.r1)
bam_se = picard_clean_up_bam(log, sample, assembly_pth, bam_se, 'se')
bam_se = picard_add_rg_header_info(log, sample, assembly_pth, "Generic", bam_se, "se")
if bam and bam_se:
bam = picard_merge_two_bams(log, sample, assembly_pth, bam, bam_se)
elif bam_se and not bam:
bam = bam_se
if not bam:
raise IOError("There is no BAM file. Check bwa log files for problems.")
samtools_index(log, sample, assembly_pth, bam)
coverage = gatk_coverage(log, sample, assembly_pth, assembly, args.cores, bam)
overall_contigs = get_coverage_from_gatk(log, sample, assembly_pth, coverage, args.velvet)
remove_gatk_coverage_files(log, assembly_pth, coverage)
trimmed_fasta_path = filter_screened_contigs_from_assembly(log, sample, assembly_pth, assembly, overall_contigs)
symlink_trimmed_contigs(log, sample, contig_dir, trimmed_fasta_path)
# end
text = " Completed {} ".format(my_name)
log.info(text.center(65, "="))