def parallel_blast(contigs_fpath, label, blast_res_fpath, err_fpath, blast_check_fpath, blast_threads):
cmd = blast_fpath('blastn') + (' -query %s -db %s -outfmt 7 -num_threads %s' % (
contigs_fpath, db_fpath, blast_threads))
res_fpath = blast_res_fpath + '_' + label
check_fpath = blast_check_fpath + '_' + label
logger.info(' ' + 'processing ' + label)
qutils.call_subprocess(shlex.split(cmd), stdout=open(res_fpath, 'w'), stderr=open(err_fpath, 'a'), logger=logger)
logger.info(' ' + 'BLAST results for %s are saved to %s...' % (label, res_fpath))
with open(check_fpath, 'w') as check_file:
check_file.writelines('Assembly: %s size: %d\n' % (contigs_fpath, os.path.getsize(contigs_fpath)))
return
def download_blastdb():
if os.path.isfile(db_fpath + '.nsq'):
logger.info()
logger.info('SILVA 16S rRNA database has already been downloaded, unpacked and BLAST database created. '
'If not, please remove %s and rerun MetaQUAST' % db_fpath + '.nsq')
return 0
log_fpath = os.path.join(blastdb_dirpath, 'blastdb.log')
db_gz_fpath = os.path.join(blastdb_dirpath, silva_fname + '.gz')
silva_fpath = os.path.join(blastdb_dirpath, silva_fname)
logger.info()
if os.path.isfile(db_gz_fpath):
logger.info('SILVA 16S ribosomal RNA gene database has already been downloaded.')
else:
logger.info('Downloading SILVA 16S ribosomal RNA gene database...')
if not os.path.isdir(blastdb_dirpath):
os.mkdir(blastdb_dirpath)
silva_download = urllib.URLopener()
silva_remote_fpath = silva_db_path + silva_fname + '.gz'
try:
silva_download.retrieve(silva_remote_fpath, db_gz_fpath + '.download', show_progress)
except Exception:
logger.error(
'Failed downloading SILVA 16S rRNA gene database (%s)! The search for reference genomes cannot be performed. '
'Try to download it manually in %s and restart MetaQUAST.' % (silva_remote_fpath, blastdb_dirpath))
return 1
shutil.move(db_gz_fpath + '.download', db_gz_fpath)
logger.info('Processing downloaded file. Logging to %s...' % log_fpath)
if not os.path.isfile(silva_fpath):
logger.info('Unpacking and replacing " " with "_"...')
unpacked_fpath = silva_fpath + ".unpacked"
cmd = "gunzip -c %s" % db_gz_fpath
qutils.call_subprocess(shlex.split(cmd), stdout=open(unpacked_fpath, 'w'), stderr=open(log_fpath, 'a'), logger=logger)
in_file = open(unpacked_fpath).read()
out_file = open(unpacked_fpath, 'w')
out_file.write(in_file.replace(' ', '_'))
out_file.close()
shutil.move(unpacked_fpath, silva_fpath)
logger.info('Making BLAST database...')
cmd = blast_fpath('makeblastdb') + (' -in %s -dbtype nucl -out %s' % (silva_fpath, db_fpath))
qutils.call_subprocess(shlex.split(cmd), stdout=open(log_fpath, 'a'), stderr=open(log_fpath, 'a'), logger=logger)
if not os.path.exists(db_fpath + '.nsq') or os.path.getsize(db_fpath + '.nsq') < db_nsq_fsize:
logger.error('Failed to make BLAST database ("' + blastdb_dirpath +
'"). See details in log. Try to make it manually: %s' % cmd)
return 1
elif not qconfig.debug:
os.remove(db_gz_fpath)
os.remove(silva_fpath)
return 0
def gmhmm_p_everyGC(tool_dirpath, fasta_fpath, err_fpath, index, tmp_dirpath,
num_threads):
tmp_dirpath = tempfile.mkdtemp(dir=tmp_dirpath)
tool_exec_fpath = os.path.join(tool_dirpath, 'gmsn.pl')
err_file = open(err_fpath, 'w')
fasta_name = qutils.name_from_fpath(fasta_fpath)
return_code = qutils.call_subprocess([
'perl', tool_exec_fpath, '--name', fasta_name, '--clean', '--out',
tmp_dirpath, fasta_fpath
],
stdout=err_file,
stderr=err_file,
indent=' ' +
qutils.index_to_str(index))
if return_code != 0:
return
genes = []
tool_exec_fpath = os.path.join(tool_dirpath, 'gmhmmp')
sub_fasta_fpath = os.path.join(tmp_dirpath, fasta_name)
out_fpath = sub_fasta_fpath + '.gmhmm'
heu_fpath = os.path.join(tmp_dirpath, fasta_name + '_hmm_heuristic.mod')
with open(err_fpath, 'a') as err_file:
ok = gmhmm_p(tool_exec_fpath, fasta_fpath, heu_fpath, out_fpath,
err_file, index)
if ok:
genes.extend(parse_gmhmm_out(out_fpath))
if not qconfig.debug:
shutil.rmtree(tmp_dirpath)
return genes
def gmhmm_p_everyGC(tool_dirpath, fasta_fpath, err_fpath, index, tmp_dirpath, num_threads):
tmp_dirpath = tempfile.mkdtemp(dir=tmp_dirpath)
tool_exec_fpath = os.path.join(tool_dirpath, 'gmsn.pl')
err_file = open(err_fpath, 'w')
fasta_name = qutils.name_from_fpath(fasta_fpath)
return_code = qutils.call_subprocess(
['perl', tool_exec_fpath, '--name', fasta_name, '--clean', '--out', tmp_dirpath,
fasta_fpath],
stdout=err_file,
stderr=err_file,
indent=' ' + qutils.index_to_str(index))
if return_code != 0:
return
genes = []
tool_exec_fpath = os.path.join(tool_dirpath, 'gmhmmp')
sub_fasta_fpath = os.path.join(tmp_dirpath, fasta_name)
out_fpath = sub_fasta_fpath + '.gmhmm'
heu_fpath = os.path.join(tmp_dirpath, fasta_name + '_hmm_heuristic.mod')
with open(err_fpath, 'a') as err_file:
ok = gmhmm_p(tool_exec_fpath, fasta_fpath, heu_fpath,
out_fpath, err_file, index)
if ok:
genes.extend(parse_gmhmm_out(out_fpath))
if not qconfig.debug:
shutil.rmtree(tmp_dirpath)
return genes
def run_gage(i, contigs_fpath, gage_results_dirpath, gage_tool_path, reference, tmp_dir):
assembly_name = qutils.name_from_fpath(contigs_fpath)
assembly_label = qutils.label_from_fpath(contigs_fpath)
logger.info(' ' + qutils.index_to_str(i) + assembly_label + '...')
# run gage tool
log_out_fpath = os.path.join(gage_results_dirpath, 'gage_' + assembly_name + '.stdout')
log_err_fpath = os.path.join(gage_results_dirpath, 'gage_' + assembly_name + '.stderr')
logger.info(' ' + qutils.index_to_str(i) + 'Logging to files ' +
os.path.basename(log_out_fpath) + ' and ' +
os.path.basename(log_err_fpath) + '...')
log_out_f = open(log_out_fpath, 'w')
log_err_f = open(log_err_fpath, 'w')
return_code = qutils.call_subprocess(
['sh', gage_tool_path, reference, contigs_fpath, tmp_dir, str(qconfig.min_contig)],
stdout=log_out_f,
stderr=log_err_f,
indent=' ' + qutils.index_to_str(i),
only_if_debug=False)
if return_code != 0:
logger.info(' ' + qutils.index_to_str(i) + 'Failed.')
else:
logger.info(' ' + qutils.index_to_str(i) + 'Done.')
log_out_f.close()
log_err_f.close()
return return_code
def run_gage(i, contigs_fpath, gage_results_dirpath, gage_tool_path, reference, tmp_dir):
assembly_label = qutils.label_from_fpath_for_fname(contigs_fpath)
logger.info(' ' + qutils.index_to_str(i) + assembly_label + '...')
# run gage tool
log_out_fpath = os.path.join(gage_results_dirpath, 'gage_' + assembly_label + '.stdout')
log_err_fpath = os.path.join(gage_results_dirpath, 'gage_' + assembly_label + '.stderr')
logger.info(' ' + qutils.index_to_str(i) + 'Logging to files ' +
os.path.basename(log_out_fpath) + ' and ' +
os.path.basename(log_err_fpath) + '...')
log_out_f = open(log_out_fpath, 'w')
log_err_f = open(log_err_fpath, 'w')
return_code = qutils.call_subprocess(
['sh', gage_tool_path, reference, contigs_fpath, tmp_dir, str(qconfig.min_contig)],
stdout=log_out_f,
stderr=log_err_f,
indent=' ' + qutils.index_to_str(i),
only_if_debug=False)
if return_code != 0:
logger.info(' ' + qutils.index_to_str(i) + 'Failed.')
else:
logger.info(' ' + qutils.index_to_str(i) + 'Done.')
log_out_f.close()
log_err_f.close()
return return_code
def run(contig_path, tmp_path):
with open(err_path, 'a') as err_file:
return_code = qutils.call_subprocess(
[tool_exec, contig_path, '-d', trained_dir, '-g', '-o', tmp_path],
stdout=err_file,
stderr=err_file,
indent=' ' + qutils.index_to_str(index) + ' ')
return return_code
def parallel_blast(contigs_fpath, label, blast_res_fpath, err_fpath,
blast_check_fpath, blast_threads):
cmd = blast_fpath('blastn') + (
' -query %s -db %s -outfmt 7 -num_threads %s' %
(contigs_fpath, db_fpath, blast_threads))
res_fpath = blast_res_fpath + '_' + label
check_fpath = blast_check_fpath + '_' + label
logger.info(' ' + 'processing ' + label)
qutils.call_subprocess(shlex.split(cmd),
stdout=open(res_fpath, 'w'),
stderr=open(err_fpath, 'a'),
logger=logger)
logger.info(' ' + 'BLAST results for %s are saved to %s...' %
(label, res_fpath))
with open(check_fpath, 'w') as check_file:
check_file.writelines('Assembly: %s size: %d\n' %
(contigs_fpath, os.path.getsize(contigs_fpath)))
return
def do(contigs_fpaths, gene_lengths, out_dirpath):
logger.print_timestamp()
logger.main_info('Running GlimmerHMM...')
tool_dirpath = os.path.join(qconfig.LIBS_LOCATION, 'glimmer')
tool_src_dirpath = os.path.join(tool_dirpath, 'src')
tool_exec_fpath = os.path.join(tool_dirpath, 'glimmerhmm')
tmp_dirpath = os.path.join(out_dirpath, 'tmp')
if not os.path.isfile(tool_exec_fpath):
# making
logger.main_info("Compiling GlimmerHMM...")
return_code = qutils.call_subprocess(
['make', '-C', tool_src_dirpath],
stdout=open(os.path.join(tool_src_dirpath, 'make.log'), 'w'),
stderr=open(os.path.join(tool_src_dirpath, 'make.err'), 'w'),
indent=' ')
if return_code != 0 or not os.path.isfile(tool_exec_fpath):
logger.error(
"Failed to compile GlimmerHMM (" + tool_src_dirpath +
")!\nTry to compile it manually or do not use --gene-finding "
"option with --eukaryote.\nUse --debug option to see the command lines."
)
return
if not os.path.isdir(out_dirpath):
os.makedirs(out_dirpath)
if not os.path.isdir(tmp_dirpath):
os.makedirs(tmp_dirpath)
n_jobs = min(len(contigs_fpaths), qconfig.max_threads)
from joblib import Parallel, delayed
results = Parallel(n_jobs=n_jobs)(
delayed(predict_genes)(index, contigs_fpath, gene_lengths, out_dirpath,
tool_dirpath, tmp_dirpath)
for index, contigs_fpath in enumerate(contigs_fpaths))
# saving results
for i, contigs_fpath in enumerate(contigs_fpaths):
report = reporting.get(contigs_fpath)
unique, cnt = results[i]
if unique is not None:
report.add_field(reporting.Fields.PREDICTED_GENES_UNIQUE, unique)
if cnt is not None:
report.add_field(reporting.Fields.PREDICTED_GENES, cnt)
if unique is None and cnt is None:
logger.error(
'Glimmer failed running Glimmer for %s. ' +
('Run with the --debug option'
' to see the command line.' if not qconfig.debug else '') %
qutils.label_from_fpath(contigs_fpath))
if not qconfig.debug:
shutil.rmtree(tmp_dirpath)
logger.main_info('Done.')
def run(contig_path, tmp_path):
with open(err_path, 'a') as err_file:
return_code = qutils.call_subprocess([
tool_exec, contig_path, '-d', trained_dir, '-g', '-o', tmp_path
],
stdout=err_file,
stderr=err_file,
indent=' ' +
qutils.index_to_str(index) +
' ')
return return_code
def gmhmm_p(tool_exec, fasta_fpath, heu_fpath, out_fpath, err_file, index):
""" Run GeneMark.hmm with this heuristic model (heu_dirpath)
prompt> gmhmmp -m heu_11_45.mod sequence
prompt> gm -m heu_11_45.mat sequence"""
return_code = qutils.call_subprocess(
[tool_exec, '-d', '-p', '0', '-m', heu_fpath, '-o', out_fpath, fasta_fpath],
stdout=err_file,
stderr=err_file,
indent=' ' + qutils.index_to_str(index))
return return_code == 0 and os.path.isfile(out_fpath)
def gmhmm_p(tool_exec, fasta_fpath, heu_fpath, out_fpath, err_file, index):
""" Run GeneMark.hmm with this heuristic model (heu_dirpath)
prompt> gmhmmp -m heu_11_45.mod sequence
prompt> gm -m heu_11_45.mat sequence"""
return_code = qutils.call_subprocess(
[tool_exec, '-d', '-p', '0', '-m', heu_fpath, '-o', out_fpath, fasta_fpath],
stdout=err_file,
stderr=err_file,
indent=' ' + qutils.index_to_str(index))
return return_code == 0 and os.path.isfile(out_fpath)
def do(contigs_fpaths, gene_lengths, out_dirpath):
logger.print_timestamp()
logger.main_info('Running GlimmerHMM...')
tool_dirpath = os.path.join(qconfig.LIBS_LOCATION, 'glimmer')
tool_src_dirpath = os.path.join(tool_dirpath, 'src')
tool_exec_fpath = os.path.join(tool_dirpath, 'glimmerhmm')
tmp_dirpath = os.path.join(out_dirpath, 'tmp')
if not os.path.isfile(tool_exec_fpath):
# making
logger.main_info("Compiling GlimmerHMM...")
return_code = qutils.call_subprocess(
['make', '-C', tool_src_dirpath],
stdout=open(os.path.join(tool_src_dirpath, 'make.log'), 'w'),
stderr=open(os.path.join(tool_src_dirpath, 'make.err'), 'w'),
indent=' ')
if return_code != 0 or not os.path.isfile(tool_exec_fpath):
logger.error("Failed to compile GlimmerHMM (" + tool_src_dirpath +
")!\nTry to compile it manually or do not use --gene-finding "
"option with --eukaryote.\nUse --debug option to see the command lines.")
return
if not os.path.isdir(out_dirpath):
os.makedirs(out_dirpath)
if not os.path.isdir(tmp_dirpath):
os.makedirs(tmp_dirpath)
n_jobs = min(len(contigs_fpaths), qconfig.max_threads)
from joblib import Parallel, delayed
results = Parallel(n_jobs=n_jobs)(delayed(predict_genes)(
index, contigs_fpath, gene_lengths, out_dirpath, tool_dirpath, tmp_dirpath)
for index, contigs_fpath in enumerate(contigs_fpaths))
# saving results
for i, contigs_fpath in enumerate(contigs_fpaths):
report = reporting.get(contigs_fpath)
unique, cnt = results[i]
if unique is not None:
report.add_field(reporting.Fields.PREDICTED_GENES_UNIQUE, unique)
if cnt is not None:
report.add_field(reporting.Fields.PREDICTED_GENES, cnt)
if unique is None and cnt is None:
logger.error(
'Glimmer failed running Glimmer for %s. ' + ('Run with the --debug option'
' to see the command line.' if not qconfig.debug else '') % qutils.label_from_fpath(contigs_fpath))
if not qconfig.debug:
shutil.rmtree(tmp_dirpath)
logger.main_info('Done.')
def gm_es(tool_dirpath, fasta_fpath, err_fpath, index, tmp_dirpath, num_threads):
tool_exec_fpath = os.path.join(tool_dirpath, 'gmes_petap.pl')
libs_dirpath = os.path.join(qconfig.LIBS_LOCATION, 'genemark-es', 'lib')
err_file = open(err_fpath, 'w')
tmp_dirpath += qutils.name_from_fpath(fasta_fpath)
if not os.path.isdir(tmp_dirpath):
os.mkdir(tmp_dirpath)
return_code = qutils.call_subprocess(
['perl', '-I', libs_dirpath, tool_exec_fpath, '--ES', '--cores', str(num_threads), '--sequence', fasta_fpath,
'--out', tmp_dirpath],
stdout=err_file,
stderr=err_file,
indent=' ' + qutils.index_to_str(index))
if return_code != 0:
return
genes = []
_, _, fnames = os.walk(tmp_dirpath).next()
for fname in fnames:
if fname.endswith('gtf'):
genes.extend(parse_gtf_out(os.path.join(tmp_dirpath, fname)))
return genes
def gm_es(tool_dirpath, fasta_fpath, err_fpath, index, tmp_dirpath,
num_threads):
tool_exec_fpath = os.path.join(tool_dirpath, 'gmes_petap.pl')
libs_dirpath = os.path.join(qconfig.LIBS_LOCATION, 'genemark-es', 'lib')
err_file = open(err_fpath, 'w')
tmp_dirpath += qutils.name_from_fpath(fasta_fpath)
if not os.path.isdir(tmp_dirpath):
os.mkdir(tmp_dirpath)
return_code = qutils.call_subprocess([
'perl', '-I', libs_dirpath, tool_exec_fpath, '--ES', '--cores',
str(num_threads), '--sequence', fasta_fpath, '--out', tmp_dirpath
],
stdout=err_file,
stderr=err_file,
indent=' ' +
qutils.index_to_str(index))
if return_code != 0:
return
genes = []
_, _, fnames = os.walk(tmp_dirpath).next()
for fname in fnames:
if fname.endswith('gtf'):
genes.extend(parse_gtf_out(os.path.join(tmp_dirpath, fname)))
return genes
def do(ref_fpath,
contigs_fpaths,
reads_fpaths,
meta_ref_fpaths,
output_dir,
interleaved=False,
external_logger=None):
if external_logger:
global logger
logger = external_logger
logger.print_timestamp()
logger.main_info('Running Structural Variants caller...')
if not os.path.isdir(output_dir):
os.makedirs(output_dir)
if not all_required_binaries_exist(bowtie_dirpath, 'bowtie2-align-l'):
# making
logger.main_info('Compiling Bowtie2 (details are in ' +
os.path.join(bowtie_dirpath, 'make.log') +
' and make.err)')
return_code = qutils.call_subprocess(
['make', '-C', bowtie_dirpath],
stdout=open(os.path.join(bowtie_dirpath, 'make.log'), 'w'),
stderr=open(os.path.join(bowtie_dirpath, 'make.err'), 'w'),
logger=logger)
if return_code != 0 or not all_required_binaries_exist(
bowtie_dirpath, 'bowtie2-align-l'):
logger.error(
'Failed to compile Bowtie2 (' + bowtie_dirpath + ')! '
'Try to compile it manually. ' +
('You can restart QUAST with the --debug flag '
'to see the command line.' if not qconfig.debug else ''))
logger.main_info('Failed searching structural variations')
return None
if not all_required_binaries_exist(samtools_dirpath, 'samtools'):
# making
logger.main_info('Compiling SAMtools (details are in ' +
os.path.join(samtools_dirpath, 'make.log') +
' and make.err)')
return_code = qutils.call_subprocess(
['make', '-C', samtools_dirpath],
stdout=open(os.path.join(samtools_dirpath, 'make.log'), 'w'),
stderr=open(os.path.join(samtools_dirpath, 'make.err'), 'w'),
logger=logger)
if return_code != 0 or not all_required_binaries_exist(
samtools_dirpath, 'samtools'):
logger.error(
'Failed to compile SAMtools (' + samtools_dirpath + ')! '
'Try to compile it manually. ' +
('You can restart QUAST with the --debug flag '
'to see the command line.' if not qconfig.debug else ''))
logger.main_info('Failed searching structural variations')
return None
if not all_required_binaries_exist(manta_bin_dirpath, 'configManta.py'):
# making
if not os.path.exists(manta_build_dirpath):
os.mkdir(manta_build_dirpath)
if qconfig.platform_name == 'linux_64':
logger.main_info(' Downloading binary distribution of Manta...')
manta_downloaded_fpath = os.path.join(manta_build_dirpath,
'manta.tar.bz2')
response = urllib2.urlopen(manta_download_path)
content = response.read()
if content:
logger.main_info(' Manta successfully downloaded!')
f = open(manta_downloaded_fpath + '.download', 'w')
f.write(content)
f.close()
if os.path.exists(manta_downloaded_fpath + '.download'):
logger.info(' Unpacking Manta...')
shutil.move(manta_downloaded_fpath + '.download',
manta_downloaded_fpath)
import tarfile
tar = tarfile.open(manta_downloaded_fpath, "r:bz2")
tar.extractall(manta_build_dirpath)
tar.close()
manta_temp_dirpath = os.path.join(manta_build_dirpath,
tar.members[0].name)
from distutils.dir_util import copy_tree
copy_tree(manta_temp_dirpath, manta_build_dirpath)
shutil.rmtree(manta_temp_dirpath)
os.remove(manta_downloaded_fpath)
logger.main_info(' Done')
else:
logger.main_info(' Failed downloading Manta from %s!' %
manta_download_path)
if not all_required_binaries_exist(manta_bin_dirpath,
'configManta.py'):
logger.main_info('Compiling Manta (details are in ' +
os.path.join(manta_dirpath, 'make.log') +
' and make.err)')
prev_dir = os.getcwd()
os.chdir(manta_build_dirpath)
return_code = qutils.call_subprocess(
[
os.path.join(manta_dirpath, 'source', 'src', 'configure'),
'--prefix=' + os.path.join(manta_dirpath, 'build'),
'--jobs=' + str(qconfig.max_threads)
],
stdout=open(os.path.join(manta_dirpath, 'make.log'), 'w'),
stderr=open(os.path.join(manta_dirpath, 'make.err'), 'w'),
logger=logger)
if return_code == 0:
return_code = qutils.call_subprocess(
['make', '-j' + str(qconfig.max_threads)],
stdout=open(os.path.join(manta_dirpath, 'make.log'), 'a'),
stderr=open(os.path.join(manta_dirpath, 'make.err'), 'a'),
logger=logger)
if return_code == 0:
return_code = qutils.call_subprocess(
['make', 'install'],
stdout=open(os.path.join(manta_dirpath, 'make.log'),
'a'),
stderr=open(os.path.join(manta_dirpath, 'make.err'),
'a'),
logger=logger)
os.chdir(prev_dir)
if return_code != 0 or not all_required_binaries_exist(
manta_bin_dirpath, 'configManta.py'):
logger.error(
'Failed to compile Manta (' + manta_dirpath + ')! '
'Try to compile it manually ' +
('or download binary distribution from https://github.com/Illumina/manta/releases '
'and unpack it into ' +
os.path.join(manta_dirpath, 'build/') if qconfig.
platform_name == 'linux_64' else '') +
('. You can restart QUAST with the --debug flag '
'to see the command line.' if not qconfig.debug else '.'))
logger.main_info(
'Failed searching structural variations. QUAST will search trivial deletions only.'
)
temp_output_dir = os.path.join(output_dir, 'temp_output')
if not os.path.isdir(temp_output_dir):
os.mkdir(temp_output_dir)
log_path = os.path.join(output_dir, 'sv_calling.log')
err_path = os.path.join(output_dir, 'sv_calling.err')
logger.info(' ' + 'Logging to files %s and %s...' % (log_path, err_path))
try:
bed_fpath = run_processing_reads(
ref_fpath, meta_ref_fpaths,
contigs_analyzer.ref_labels_by_chromosomes, reads_fpaths,
temp_output_dir, output_dir, log_path, err_path)
except:
bed_fpath = None
logger.error(
'Failed searching structural variations! This function is experimental and may work improperly. Sorry for the inconvenience.'
)
if not qconfig.debug:
shutil.rmtree(temp_output_dir, ignore_errors=True)
logger.info('Done.')
return bed_fpath
def run_processing_reads(main_ref_fpath, meta_ref_fpaths, ref_labels,
reads_fpaths, output_dirpath, res_path, log_path,
err_path):
ref_name = qutils.name_from_fpath(main_ref_fpath)
sam_fpath = os.path.join(output_dirpath, ref_name + '.sam')
bam_fpath = os.path.join(output_dirpath, ref_name + '.bam')
bam_sorted_fpath = os.path.join(output_dirpath, ref_name + '.sorted')
sam_sorted_fpath = os.path.join(output_dirpath, ref_name + '.sorted.sam')
bed_fpath = os.path.join(res_path, ref_name + '.bed')
if is_non_empty_file(bed_fpath):
logger.info(' Using existing BED-file: ' + bed_fpath)
return bed_fpath
logger.info(' ' + 'Pre-processing for searching structural variations...')
logger.info(' ' + 'Logging to %s...' % err_path)
if is_non_empty_file(sam_fpath):
logger.info(' Using existing SAM-file: ' + sam_fpath)
else:
logger.info(' Running Bowtie2...')
abs_reads_fpaths = [
] # use absolute paths because we will change workdir
for reads_fpath in reads_fpaths:
abs_reads_fpaths.append(os.path.abspath(reads_fpath))
prev_dir = os.getcwd()
os.chdir(output_dirpath)
cmd = [bin_fpath('bowtie2-build'), main_ref_fpath, ref_name]
qutils.call_subprocess(cmd,
stdout=open(log_path, 'a'),
stderr=open(err_path, 'a'),
logger=logger)
cmd = bin_fpath('bowtie2') + ' -x ' + ref_name + ' -1 ' + abs_reads_fpaths[0] + ' -2 ' + abs_reads_fpaths[1] + ' -S ' + \
sam_fpath + ' --no-unal -a -p %s' % str(qconfig.max_threads)
qutils.call_subprocess(shlex.split(cmd),
stdout=open(log_path, 'a'),
stderr=open(err_path, 'a'),
logger=logger)
logger.info(' Done.')
os.chdir(prev_dir)
if not os.path.exists(sam_fpath) or os.path.getsize(sam_fpath) == 0:
logger.error(' Failed running Bowtie2 for the reference. See ' +
log_path + ' for information.')
logger.info(' Failed searching structural variations.')
return None
logger.info(' Sorting SAM-file...')
if is_non_empty_file(sam_sorted_fpath):
logger.info(' Using existing sorted SAM-file: ' + sam_sorted_fpath)
else:
qutils.call_subprocess([
samtools_fpath('samtools'), 'view', '-@',
str(qconfig.max_threads), '-bS', sam_fpath
],
stdout=open(bam_fpath, 'w'),
stderr=open(err_path, 'a'),
logger=logger)
qutils.call_subprocess([
samtools_fpath('samtools'), 'sort', '-@',
str(qconfig.max_threads), bam_fpath, bam_sorted_fpath
],
stderr=open(err_path, 'a'),
logger=logger)
qutils.call_subprocess([
samtools_fpath('samtools'), 'view', '-@',
str(qconfig.max_threads), bam_sorted_fpath + '.bam'
],
stdout=open(sam_sorted_fpath, 'w'),
stderr=open(err_path, 'a'),
logger=logger)
if meta_ref_fpaths:
logger.info(' Splitting SAM-file by references...')
headers = []
seq_name_length = {}
with open(sam_fpath) as sam_file:
for line in sam_file:
if not line.startswith('@'):
break
if line.startswith('@SQ') and 'SN:' in line and 'LN:' in line:
seq_name = line.split('\tSN:')[1].split('\t')[0]
seq_length = int(line.split('\tLN:')[1].split('\t')[0])
seq_name_length[seq_name] = seq_length
headers.append(line.strip())
need_ref_splitting = False
if meta_ref_fpaths:
ref_files = {}
for cur_ref_fpath in meta_ref_fpaths:
ref = qutils.name_from_fpath(cur_ref_fpath)
new_ref_sam_fpath = os.path.join(output_dirpath, ref + '.sam')
if is_non_empty_file(new_ref_sam_fpath):
logger.info(' Using existing split SAM-file for %s: %s' %
(ref, new_ref_sam_fpath))
ref_files[ref] = None
else:
new_ref_sam_file = open(new_ref_sam_fpath, 'w')
new_ref_sam_file.write(headers[0] + '\n')
chrs = []
for h in (h for h in headers
if h.startswith('@SQ') and 'SN:' in h):
seq_name = h.split('\tSN:')[1].split('\t')[0]
if seq_name in ref_labels and ref_labels[seq_name] == ref:
new_ref_sam_file.write(h + '\n')
chrs.append(seq_name)
new_ref_sam_file.write(headers[-1] + '\n')
ref_files[ref] = new_ref_sam_file
need_ref_splitting = True
deletions = []
trivial_deletions_fpath = os.path.join(output_dirpath,
qconfig.trivial_deletions_fname)
logger.info(
' Looking for trivial deletions (long zero-covered fragments)...')
need_trivial_deletions = True
if os.path.exists(trivial_deletions_fpath):
need_trivial_deletions = False
logger.info(' Using existing file: ' + trivial_deletions_fpath)
if need_trivial_deletions or need_ref_splitting:
with open(sam_sorted_fpath) as sam_file:
cur_deletion = None
for line in sam_file:
mapping = Mapping.parse(line)
if mapping:
# common case: continue current deletion (potential) on the same reference
if cur_deletion and cur_deletion.ref == mapping.ref:
if cur_deletion.next_bad is None: # previous mapping was in region BEFORE 0-covered fragment
# just passed 0-covered fragment
if mapping.start - cur_deletion.prev_bad > QuastDeletion.MIN_GAP:
cur_deletion.set_next_bad(mapping)
if mapping.mapq >= Mapping.MIN_MAP_QUALITY:
cur_deletion.set_next_good(mapping)
if cur_deletion.is_valid():
deletions.append(cur_deletion)
cur_deletion = QuastDeletion(
mapping.ref).set_prev_good(mapping)
# continue region BEFORE 0-covered fragment
elif mapping.mapq >= Mapping.MIN_MAP_QUALITY:
cur_deletion.set_prev_good(mapping)
else:
cur_deletion.set_prev_bad(mapping)
else: # previous mapping was in region AFTER 0-covered fragment
# just passed another 0-cov fragment between end of cur_deletion BAD region and this mapping
if mapping.start - cur_deletion.next_bad_end > QuastDeletion.MIN_GAP:
if cur_deletion.is_valid(
): # add previous fragment's deletion if needed
deletions.append(cur_deletion)
cur_deletion = QuastDeletion(
mapping.ref).set_prev_bad(
position=cur_deletion.next_bad_end)
# continue region AFTER 0-covered fragment (old one or new/another one -- see "if" above)
if mapping.mapq >= Mapping.MIN_MAP_QUALITY:
cur_deletion.set_next_good(mapping)
if cur_deletion.is_valid():
deletions.append(cur_deletion)
cur_deletion = QuastDeletion(
mapping.ref).set_prev_good(mapping)
else:
cur_deletion.set_next_bad_end(mapping)
# special case: just started or just switched to the next reference
else:
if cur_deletion and cur_deletion.ref in seq_name_length: # switched to the next ref
cur_deletion.set_next_good(
position=seq_name_length[cur_deletion.ref])
if cur_deletion.is_valid():
deletions.append(cur_deletion)
cur_deletion = QuastDeletion(
mapping.ref).set_prev_good(mapping)
if need_ref_splitting:
cur_ref = ref_labels[mapping.ref]
if mapping.ref_next.strip(
) == '=' or cur_ref == ref_labels[mapping.ref_next]:
if ref_files[cur_ref] is not None:
ref_files[cur_ref].write(line)
if cur_deletion and cur_deletion.ref in seq_name_length: # switched to the next ref
cur_deletion.set_next_good(
position=seq_name_length[cur_deletion.ref])
if cur_deletion.is_valid():
deletions.append(cur_deletion)
if need_ref_splitting:
for ref_handler in ref_files.values():
if ref_handler is not None:
ref_handler.close()
if need_trivial_deletions:
logger.info(' Trivial deletions: %d found' % len(deletions))
logger.info(' Saving to: ' + trivial_deletions_fpath)
with open(trivial_deletions_fpath, 'w') as f:
for deletion in deletions:
f.write(str(deletion) + '\n')
if os.path.exists(config_manta_fpath):
manta_sv_fpath = search_sv_with_manta(main_ref_fpath, meta_ref_fpaths,
output_dirpath, err_path)
qutils.cat_files([manta_sv_fpath, trivial_deletions_fpath], bed_fpath)
elif os.path.exists(trivial_deletions_fpath):
shutil.copy(trivial_deletions_fpath, bed_fpath)
if os.path.exists(bed_fpath):
logger.main_info(' Structural variations saved to ' + bed_fpath)
return bed_fpath
else:
logger.main_info(' Failed searching structural variations.')
return None
def run_processing_reads(main_ref_fpath, meta_ref_fpaths, ref_labels, reads_fpaths, output_dirpath, res_path, log_path, err_path):
ref_name = qutils.name_from_fpath(main_ref_fpath)
sam_fpath = os.path.join(output_dirpath, ref_name + '.sam')
bam_fpath = os.path.join(output_dirpath, ref_name + '.bam')
bam_sorted_fpath = os.path.join(output_dirpath, ref_name + '.sorted')
sam_sorted_fpath = os.path.join(output_dirpath, ref_name + '.sorted.sam')
bed_fpath = os.path.join(res_path, ref_name + '.bed')
if is_non_empty_file(bed_fpath):
logger.info(' Using existing BED-file: ' + bed_fpath)
return bed_fpath
logger.info(' ' + 'Pre-processing for searching structural variations...')
logger.info(' ' + 'Logging to %s...' % err_path)
if is_non_empty_file(sam_fpath):
logger.info(' Using existing SAM-file: ' + sam_fpath)
else:
logger.info(' Running Bowtie2...')
abs_reads_fpaths = [] # use absolute paths because we will change workdir
for reads_fpath in reads_fpaths:
abs_reads_fpaths.append(os.path.abspath(reads_fpath))
prev_dir = os.getcwd()
os.chdir(output_dirpath)
cmd = [bin_fpath('bowtie2-build'), main_ref_fpath, ref_name]
qutils.call_subprocess(cmd, stdout=open(log_path, 'a'), stderr=open(err_path, 'a'), logger=logger)
cmd = bin_fpath('bowtie2') + ' -x ' + ref_name + ' -1 ' + abs_reads_fpaths[0] + ' -2 ' + abs_reads_fpaths[1] + ' -S ' + \
sam_fpath + ' --no-unal -a -p %s' % str(qconfig.max_threads)
qutils.call_subprocess(shlex.split(cmd), stdout=open(log_path, 'a'), stderr=open(err_path, 'a'), logger=logger)
logger.info(' Done.')
os.chdir(prev_dir)
if not os.path.exists(sam_fpath) or os.path.getsize(sam_fpath) == 0:
logger.error(' Failed running Bowtie2 for the reference. See ' + log_path + ' for information.')
logger.info(' Failed searching structural variations.')
return None
logger.info(' Sorting SAM-file...')
if is_non_empty_file(sam_sorted_fpath):
logger.info(' Using existing sorted SAM-file: ' + sam_sorted_fpath)
else:
qutils.call_subprocess([samtools_fpath('samtools'), 'view', '-@', str(qconfig.max_threads), '-bS', sam_fpath], stdout=open(bam_fpath, 'w'),
stderr=open(err_path, 'a'), logger=logger)
qutils.call_subprocess([samtools_fpath('samtools'), 'sort', '-@', str(qconfig.max_threads), bam_fpath, bam_sorted_fpath],
stderr=open(err_path, 'a'), logger=logger)
qutils.call_subprocess([samtools_fpath('samtools'), 'view', '-@', str(qconfig.max_threads), bam_sorted_fpath + '.bam'], stdout=open(sam_sorted_fpath, 'w'),
stderr=open(err_path, 'a'), logger=logger)
if meta_ref_fpaths:
logger.info(' Splitting SAM-file by references...')
headers = []
seq_name_length = {}
with open(sam_fpath) as sam_file:
for line in sam_file:
if not line.startswith('@'):
break
if line.startswith('@SQ') and 'SN:' in line and 'LN:' in line:
seq_name = line.split('\tSN:')[1].split('\t')[0]
seq_length = int(line.split('\tLN:')[1].split('\t')[0])
seq_name_length[seq_name] = seq_length
headers.append(line.strip())
need_ref_splitting = False
if meta_ref_fpaths:
ref_files = {}
for cur_ref_fpath in meta_ref_fpaths:
ref = qutils.name_from_fpath(cur_ref_fpath)
new_ref_sam_fpath = os.path.join(output_dirpath, ref + '.sam')
if is_non_empty_file(new_ref_sam_fpath):
logger.info(' Using existing split SAM-file for %s: %s' % (ref, new_ref_sam_fpath))
ref_files[ref] = None
else:
new_ref_sam_file = open(new_ref_sam_fpath, 'w')
new_ref_sam_file.write(headers[0] + '\n')
chrs = []
for h in (h for h in headers if h.startswith('@SQ') and 'SN:' in h):
seq_name = h.split('\tSN:')[1].split('\t')[0]
if seq_name in ref_labels and ref_labels[seq_name] == ref:
new_ref_sam_file.write(h + '\n')
chrs.append(seq_name)
new_ref_sam_file.write(headers[-1] + '\n')
ref_files[ref] = new_ref_sam_file
need_ref_splitting = True
deletions = []
trivial_deletions_fpath = os.path.join(output_dirpath, qconfig.trivial_deletions_fname)
logger.info(' Looking for trivial deletions (long zero-covered fragments)...')
need_trivial_deletions = True
if os.path.exists(trivial_deletions_fpath):
need_trivial_deletions = False
logger.info(' Using existing file: ' + trivial_deletions_fpath)
if need_trivial_deletions or need_ref_splitting:
with open(sam_sorted_fpath) as sam_file:
cur_deletion = None
for line in sam_file:
mapping = Mapping.parse(line)
if mapping:
# common case: continue current deletion (potential) on the same reference
if cur_deletion and cur_deletion.ref == mapping.ref:
if cur_deletion.next_bad is None: # previous mapping was in region BEFORE 0-covered fragment
# just passed 0-covered fragment
if mapping.start - cur_deletion.prev_bad > QuastDeletion.MIN_GAP:
cur_deletion.set_next_bad(mapping)
if mapping.mapq >= Mapping.MIN_MAP_QUALITY:
cur_deletion.set_next_good(mapping)
if cur_deletion.is_valid():
deletions.append(cur_deletion)
cur_deletion = QuastDeletion(mapping.ref).set_prev_good(mapping)
# continue region BEFORE 0-covered fragment
elif mapping.mapq >= Mapping.MIN_MAP_QUALITY:
cur_deletion.set_prev_good(mapping)
else:
cur_deletion.set_prev_bad(mapping)
else: # previous mapping was in region AFTER 0-covered fragment
# just passed another 0-cov fragment between end of cur_deletion BAD region and this mapping
if mapping.start - cur_deletion.next_bad_end > QuastDeletion.MIN_GAP:
if cur_deletion.is_valid(): # add previous fragment's deletion if needed
deletions.append(cur_deletion)
cur_deletion = QuastDeletion(mapping.ref).set_prev_bad(position=cur_deletion.next_bad_end)
# continue region AFTER 0-covered fragment (old one or new/another one -- see "if" above)
if mapping.mapq >= Mapping.MIN_MAP_QUALITY:
cur_deletion.set_next_good(mapping)
if cur_deletion.is_valid():
deletions.append(cur_deletion)
cur_deletion = QuastDeletion(mapping.ref).set_prev_good(mapping)
else:
cur_deletion.set_next_bad_end(mapping)
# special case: just started or just switched to the next reference
else:
if cur_deletion and cur_deletion.ref in seq_name_length: # switched to the next ref
cur_deletion.set_next_good(position=seq_name_length[cur_deletion.ref])
if cur_deletion.is_valid():
deletions.append(cur_deletion)
cur_deletion = QuastDeletion(mapping.ref).set_prev_good(mapping)
if need_ref_splitting:
cur_ref = ref_labels[mapping.ref]
if mapping.ref_next.strip() == '=' or cur_ref == ref_labels[mapping.ref_next]:
if ref_files[cur_ref] is not None:
ref_files[cur_ref].write(line)
if cur_deletion and cur_deletion.ref in seq_name_length: # switched to the next ref
cur_deletion.set_next_good(position=seq_name_length[cur_deletion.ref])
if cur_deletion.is_valid():
deletions.append(cur_deletion)
if need_ref_splitting:
for ref_handler in ref_files.values():
if ref_handler is not None:
ref_handler.close()
if need_trivial_deletions:
logger.info(' Trivial deletions: %d found' % len(deletions))
logger.info(' Saving to: ' + trivial_deletions_fpath)
with open(trivial_deletions_fpath, 'w') as f:
for deletion in deletions:
f.write(str(deletion) + '\n')
if os.path.exists(config_manta_fpath):
manta_sv_fpath = search_sv_with_manta(main_ref_fpath, meta_ref_fpaths, output_dirpath, err_path)
qutils.cat_files([manta_sv_fpath, trivial_deletions_fpath], bed_fpath)
elif os.path.exists(trivial_deletions_fpath):
shutil.copy(trivial_deletions_fpath, bed_fpath)
if os.path.exists(bed_fpath):
logger.main_info(' Structural variations saved to ' + bed_fpath)
return bed_fpath
else:
logger.main_info(' Failed searching structural variations.')
return None
def process_one_ref(cur_ref_fpath, output_dirpath, err_path, bed_fpath=None):
ref = qutils.name_from_fpath(cur_ref_fpath)
ref_sam_fpath = os.path.join(output_dirpath, ref + '.sam')
ref_bam_fpath = os.path.join(output_dirpath, ref + '.bam')
ref_bamsorted_fpath = os.path.join(output_dirpath, ref + '.sorted')
ref_bed_fpath = bed_fpath if bed_fpath else os.path.join(
output_dirpath, ref + '.bed')
if os.path.getsize(
ref_sam_fpath
) < 1024 * 1024: # TODO: make it better (small files will cause Manta crush -- "not enough reads...")
logger.info(' SAM file is too small for Manta (%d Kb), skipping..' %
(os.path.getsize(ref_sam_fpath) // 1024))
return None
if is_non_empty_file(ref_bed_fpath):
logger.info(' Using existing Manta BED-file: ' + ref_bed_fpath)
return ref_bed_fpath
if not os.path.exists(ref_bamsorted_fpath + '.bam'):
qutils.call_subprocess(
[samtools_fpath('samtools'), 'view', '-bS', ref_sam_fpath],
stdout=open(ref_bam_fpath, 'w'),
stderr=open(err_path, 'a'),
logger=logger)
qutils.call_subprocess([
samtools_fpath('samtools'), 'sort', ref_bam_fpath,
ref_bamsorted_fpath
],
stderr=open(err_path, 'a'),
logger=logger)
if not is_non_empty_file(ref_bamsorted_fpath + '.bam.bai'):
qutils.call_subprocess([
samtools_fpath('samtools'), 'index', ref_bamsorted_fpath + '.bam'
],
stderr=open(err_path, 'a'),
logger=logger)
if not is_non_empty_file(cur_ref_fpath + '.fai'):
qutils.call_subprocess(
[samtools_fpath('samtools'), 'faidx', cur_ref_fpath],
stderr=open(err_path, 'a'),
logger=logger)
vcfoutput_dirpath = os.path.join(output_dirpath, ref + '_manta')
found_SV_fpath = os.path.join(vcfoutput_dirpath,
'results/variants/diploidSV.vcf.gz')
unpacked_SV_fpath = found_SV_fpath + '.unpacked'
if not is_non_empty_file(found_SV_fpath):
if os.path.exists(vcfoutput_dirpath):
shutil.rmtree(vcfoutput_dirpath, ignore_errors=True)
os.makedirs(vcfoutput_dirpath)
qutils.call_subprocess([
config_manta_fpath, '--normalBam', ref_bamsorted_fpath + '.bam',
'--referenceFasta', cur_ref_fpath, '--runDir', vcfoutput_dirpath
],
stdout=open(err_path, 'a'),
stderr=open(err_path, 'a'),
logger=logger)
if not os.path.exists(os.path.join(vcfoutput_dirpath,
'runWorkflow.py')):
return None
qutils.call_subprocess([
os.path.join(vcfoutput_dirpath, 'runWorkflow.py'), '-m', 'local',
'-j',
str(qconfig.max_threads)
],
stderr=open(err_path, 'a'),
logger=logger)
if not is_non_empty_file(unpacked_SV_fpath):
cmd = 'gunzip -c %s' % found_SV_fpath
qutils.call_subprocess(shlex.split(cmd),
stdout=open(unpacked_SV_fpath, 'w'),
stderr=open(err_path, 'a'),
logger=logger)
from manta import vcfToBedpe
vcfToBedpe.vcfToBedpe(open(unpacked_SV_fpath), open(ref_bed_fpath, 'w'))
return ref_bed_fpath
def create_meta_report(results_dirpath, json_texts):
html_fpath = os.path.join(results_dirpath, report_fname)
if not os.path.isfile(html_fpath):
init(html_fpath, is_meta=True)
from libs import search_references_meta
taxons_for_krona = search_references_meta.taxons_for_krona
meta_log = get_logger(qconfig.LOGGER_META_NAME)
if taxons_for_krona:
meta_log.info(' Drawing interactive Krona plots...')
krona_dirpath = os.path.join(qconfig.LIBS_LOCATION, 'kronatools')
krona_res_dirpath = os.path.join(results_dirpath,
qconfig.krona_dirname)
simplejson_error = False
try:
import json
except ImportError:
try:
import simplejson as json
except ImportError:
log.warning(
'Can\'t draw Krona charts - please install python-simplejson'
)
simplejson_error = True
if not simplejson_error:
if not os.path.isdir(krona_res_dirpath):
os.mkdir(krona_res_dirpath)
json_data = json.loads(json_texts[0])
assemblies = json_data['assembliesNames']
krona_txt_ext = '_taxonomy.txt'
krona_common_fpath = os.path.join(krona_res_dirpath,
'overall' + krona_txt_ext)
krona_common_file = open(krona_common_fpath, 'w')
for index, name in enumerate(assemblies):
krona_file = open(
os.path.join(krona_res_dirpath, name + krona_txt_ext), 'w')
krona_file.close()
for json_text in json_texts[1:]:
json_data = json.loads(json_text)
ref = json_data['referenceName']
report = json_data['report'][0]
for metric in report[1]:
if metric['metricName'] == 'Total length':
lengths = metric['values']
break
cur_assemblies = json_data['assembliesNames']
for index, name in enumerate(cur_assemblies):
krona_fpath = os.path.join(krona_res_dirpath,
name + krona_txt_ext)
with open(krona_fpath, 'a') as f_krona:
if ref in taxons_for_krona:
f_krona.write(
str(lengths[index]) + '\t' +
taxons_for_krona[ref] + '\n')
else:
f_krona.write(str(lengths[index]) + '\n')
if ref in taxons_for_krona:
krona_common_file.write(
str(sum(lengths)) + '\t' + taxons_for_krona[ref] +
'\n')
else:
krona_common_file.write(str(sum(lengths)) + '\n')
krona_common_file.close()
krona_fpaths = []
for index, name in enumerate(assemblies):
krona_fpath = os.path.join(krona_res_dirpath,
name + '_taxonomy_chart.html')
krona_txt_fpath = os.path.join(krona_res_dirpath,
name + krona_txt_ext)
qutils.call_subprocess([
'perl', '-I', krona_dirpath + '/lib',
krona_dirpath + '/scripts/ImportText.pl', krona_txt_fpath,
'-o', krona_fpath, '-a'
],
stdout=open(os.devnull, 'w'),
stderr=open(os.devnull, 'w'))
krona_fpaths.append(
os.path.join(qconfig.krona_dirname,
name + '_taxonomy_chart.html'))
meta_log.main_info(' Krona chart for ' + name +
' is saved to ' + krona_fpath)
os.remove(krona_txt_fpath)
if len(assemblies) > 1:
name = 'summary'
krona_fpath = os.path.join(krona_res_dirpath,
name + '_taxonomy_chart.html')
qutils.call_subprocess([
'perl', '-I', krona_dirpath + '/lib',
krona_dirpath + '/scripts/ImportText.pl',
krona_common_fpath, '-o', krona_fpath, '-a'
],
stdout=open(os.devnull, 'w'),
stderr=open(os.devnull, 'w'))
meta_log.main_info(' Summary Krona chart is saved to ' +
krona_fpath)
krona_fpaths.append(
os.path.join(qconfig.krona_dirname, name +
'_taxonomy_chart.html')) # extra fpath!
os.remove(krona_common_fpath)
save_krona_paths(results_dirpath, krona_fpaths, assemblies)
# reading html template file
with open(html_fpath) as f_html:
html_text = f_html.read()
keyword = 'totalReport'
html_text = re.sub('{{ ' + keyword + ' }}',
'[' + ','.join(json_texts) + ']', html_text)
html_text = re.sub(r'{{(\s+\S+\s+)}}', '{}', html_text)
with open(html_fpath, 'w') as f_html:
f_html.write(html_text)
meta_log.main_info(
' Extended version of HTML-report (for all references and assemblies) is saved to '
+ html_fpath)
def do(ref_fpath, contigs_fpaths, reads_fpaths, meta_ref_fpaths, output_dir, interleaved=False, external_logger=None):
if external_logger:
global logger
logger = external_logger
logger.print_timestamp()
logger.main_info('Running Structural Variants caller...')
if not os.path.isdir(output_dir):
os.makedirs(output_dir)
if not all_required_binaries_exist(bowtie_dirpath, 'bowtie2-align-l'):
# making
logger.main_info('Compiling Bowtie2 (details are in ' + os.path.join(bowtie_dirpath, 'make.log') + ' and make.err)')
return_code = qutils.call_subprocess(
['make', '-C', bowtie_dirpath],
stdout=open(os.path.join(bowtie_dirpath, 'make.log'), 'w'),
stderr=open(os.path.join(bowtie_dirpath, 'make.err'), 'w'), logger=logger)
if return_code != 0 or not all_required_binaries_exist(bowtie_dirpath, 'bowtie2-align-l'):
logger.error('Failed to compile Bowtie2 (' + bowtie_dirpath + ')! '
'Try to compile it manually. ' + (
'You can restart QUAST with the --debug flag '
'to see the command line.' if not qconfig.debug else ''))
logger.main_info('Failed searching structural variations')
return None
if not all_required_binaries_exist(samtools_dirpath, 'samtools'):
# making
logger.main_info(
'Compiling SAMtools (details are in ' + os.path.join(samtools_dirpath, 'make.log') + ' and make.err)')
return_code = qutils.call_subprocess(
['make', '-C', samtools_dirpath],
stdout=open(os.path.join(samtools_dirpath, 'make.log'), 'w'),
stderr=open(os.path.join(samtools_dirpath, 'make.err'), 'w'), logger=logger)
if return_code != 0 or not all_required_binaries_exist(samtools_dirpath, 'samtools'):
logger.error('Failed to compile SAMtools (' + samtools_dirpath + ')! '
'Try to compile it manually. ' + (
'You can restart QUAST with the --debug flag '
'to see the command line.' if not qconfig.debug else ''))
logger.main_info('Failed searching structural variations')
return None
if not all_required_binaries_exist(manta_bin_dirpath, 'configManta.py'):
# making
if not os.path.exists(manta_build_dirpath):
os.mkdir(manta_build_dirpath)
if qconfig.platform_name == 'linux_64':
logger.main_info(' Downloading binary distribution of Manta...')
manta_downloaded_fpath = os.path.join(manta_build_dirpath, 'manta.tar.bz2')
response = urllib2.urlopen(manta_download_path)
content = response.read()
if content:
logger.main_info(' Manta successfully downloaded!')
f = open(manta_downloaded_fpath + '.download', 'w' )
f.write(content)
f.close()
if os.path.exists(manta_downloaded_fpath + '.download'):
logger.info(' Unpacking Manta...')
shutil.move(manta_downloaded_fpath + '.download', manta_downloaded_fpath)
import tarfile
tar = tarfile.open(manta_downloaded_fpath, "r:bz2")
tar.extractall(manta_build_dirpath)
tar.close()
manta_temp_dirpath = os.path.join(manta_build_dirpath, tar.members[0].name)
from distutils.dir_util import copy_tree
copy_tree(manta_temp_dirpath, manta_build_dirpath)
shutil.rmtree(manta_temp_dirpath)
os.remove(manta_downloaded_fpath)
logger.main_info(' Done')
else:
logger.main_info(' Failed downloading Manta from %s!' % manta_download_path)
if not all_required_binaries_exist(manta_bin_dirpath, 'configManta.py'):
logger.main_info('Compiling Manta (details are in ' + os.path.join(manta_dirpath, 'make.log') + ' and make.err)')
prev_dir = os.getcwd()
os.chdir(manta_build_dirpath)
return_code = qutils.call_subprocess(
[os.path.join(manta_dirpath, 'source', 'src', 'configure'), '--prefix=' + os.path.join(manta_dirpath, 'build'),
'--jobs=' + str(qconfig.max_threads)],
stdout=open(os.path.join(manta_dirpath, 'make.log'), 'w'),
stderr=open(os.path.join(manta_dirpath, 'make.err'), 'w'), logger=logger)
if return_code == 0:
return_code = qutils.call_subprocess(
['make', '-j' + str(qconfig.max_threads)],
stdout=open(os.path.join(manta_dirpath, 'make.log'), 'a'),
stderr=open(os.path.join(manta_dirpath, 'make.err'), 'a'), logger=logger)
if return_code == 0:
return_code = qutils.call_subprocess(
['make', 'install'],
stdout=open(os.path.join(manta_dirpath, 'make.log'), 'a'),
stderr=open(os.path.join(manta_dirpath, 'make.err'), 'a'), logger=logger)
os.chdir(prev_dir)
if return_code != 0 or not all_required_binaries_exist(manta_bin_dirpath, 'configManta.py'):
logger.error('Failed to compile Manta (' + manta_dirpath + ')! '
'Try to compile it manually ' + (
'or download binary distribution from https://github.com/Illumina/manta/releases '
'and unpack it into ' + os.path.join(manta_dirpath, 'build/') if qconfig.platform_name == 'linux_64' else '') + (
'. You can restart QUAST with the --debug flag '
'to see the command line.' if not qconfig.debug else '.'))
logger.main_info('Failed searching structural variations. QUAST will search trivial deletions only.')
temp_output_dir = os.path.join(output_dir, 'temp_output')
if not os.path.isdir(temp_output_dir):
os.mkdir(temp_output_dir)
log_path = os.path.join(output_dir, 'sv_calling.log')
err_path = os.path.join(output_dir, 'sv_calling.err')
logger.info(' ' + 'Logging to files %s and %s...' % (log_path, err_path))
try:
bed_fpath = run_processing_reads(ref_fpath, meta_ref_fpaths, contigs_analyzer.ref_labels_by_chromosomes, reads_fpaths, temp_output_dir, output_dir, log_path, err_path)
except:
bed_fpath = None
logger.error('Failed searching structural variations! This function is experimental and may work improperly. Sorry for the inconvenience.')
if not qconfig.debug:
shutil.rmtree(temp_output_dir, ignore_errors=True)
logger.info('Done.')
return bed_fpath
def download_blastdb():
if os.path.isfile(db_fpath + '.nsq'):
logger.info()
logger.info(
'SILVA 16S rRNA database has already been downloaded, unpacked and BLAST database created. '
'If not, please remove %s and rerun MetaQUAST' % db_fpath + '.nsq')
return 0
log_fpath = os.path.join(blastdb_dirpath, 'blastdb.log')
db_gz_fpath = os.path.join(blastdb_dirpath, silva_fname + '.gz')
silva_fpath = os.path.join(blastdb_dirpath, silva_fname)
logger.info()
if os.path.isfile(db_gz_fpath):
logger.info(
'SILVA 16S ribosomal RNA gene database has already been downloaded.'
)
else:
logger.info('Downloading SILVA 16S ribosomal RNA gene database...')
if not os.path.isdir(blastdb_dirpath):
os.mkdir(blastdb_dirpath)
silva_download = urllib.URLopener()
silva_remote_fpath = silva_db_path + silva_fname + '.gz'
try:
silva_download.retrieve(silva_remote_fpath,
db_gz_fpath + '.download', show_progress)
except Exception:
logger.error(
'Failed downloading SILVA 16S rRNA gene database (%s)! The search for reference genomes cannot be performed. '
'Try to download it manually in %s and restart MetaQUAST.' %
(silva_remote_fpath, blastdb_dirpath))
return 1
shutil.move(db_gz_fpath + '.download', db_gz_fpath)
logger.info('Processing downloaded file. Logging to %s...' % log_fpath)
if not os.path.isfile(silva_fpath):
logger.info('Unpacking and replacing " " with "_"...')
unpacked_fpath = silva_fpath + ".unpacked"
cmd = "gunzip -c %s" % db_gz_fpath
qutils.call_subprocess(shlex.split(cmd),
stdout=open(unpacked_fpath, 'w'),
stderr=open(log_fpath, 'a'),
logger=logger)
in_file = open(unpacked_fpath).read()
out_file = open(unpacked_fpath, 'w')
out_file.write(in_file.replace(' ', '_'))
out_file.close()
shutil.move(unpacked_fpath, silva_fpath)
logger.info('Making BLAST database...')
cmd = blast_fpath('makeblastdb') + (' -in %s -dbtype nucl -out %s' %
(silva_fpath, db_fpath))
qutils.call_subprocess(shlex.split(cmd),
stdout=open(log_fpath, 'a'),
stderr=open(log_fpath, 'a'),
logger=logger)
if not os.path.exists(db_fpath +
'.nsq') or os.path.getsize(db_fpath +
'.nsq') < db_nsq_fsize:
logger.error('Failed to make BLAST database ("' + blastdb_dirpath +
'"). See details in log. Try to make it manually: %s' %
cmd)
return 1
elif not qconfig.debug:
os.remove(db_gz_fpath)
os.remove(silva_fpath)
return 0
def create_meta_report(results_dirpath, json_texts):
html_fpath = os.path.join(results_dirpath, report_fname)
if not os.path.isfile(html_fpath):
init(html_fpath, is_meta=True)
from libs import search_references_meta
taxons_for_krona = search_references_meta.taxons_for_krona
meta_log = get_logger(qconfig.LOGGER_META_NAME)
if taxons_for_krona:
meta_log.info(" Drawing interactive Krona plots...")
krona_dirpath = os.path.join(qconfig.LIBS_LOCATION, "kronatools")
krona_res_dirpath = os.path.join(results_dirpath, qconfig.krona_dirname)
simplejson_error = False
try:
import json
except ImportError:
try:
import simplejson as json
except ImportError:
log.warning("Can't draw Krona charts - please install python-simplejson")
simplejson_error = True
if not simplejson_error:
if not os.path.isdir(krona_res_dirpath):
os.mkdir(krona_res_dirpath)
json_data = json.loads(json_texts[0])
assemblies = json_data["assembliesNames"]
krona_txt_ext = "_taxonomy.txt"
krona_common_fpath = os.path.join(krona_res_dirpath, "overall" + krona_txt_ext)
krona_common_file = open(krona_common_fpath, "w")
for index, name in enumerate(assemblies):
krona_file = open(os.path.join(krona_res_dirpath, name + krona_txt_ext), "w")
krona_file.close()
for json_text in json_texts[1:]:
json_data = json.loads(json_text)
ref = json_data["referenceName"]
report = json_data["report"][0]
for metric in report[1]:
if metric["metricName"] == "Total length":
lengths = metric["values"]
break
cur_assemblies = json_data["assembliesNames"]
for index, name in enumerate(cur_assemblies):
krona_fpath = os.path.join(krona_res_dirpath, name + krona_txt_ext)
with open(krona_fpath, "a") as f_krona:
if ref in taxons_for_krona:
f_krona.write(str(lengths[index]) + "\t" + taxons_for_krona[ref] + "\n")
else:
f_krona.write(str(lengths[index]) + "\n")
if ref in taxons_for_krona:
krona_common_file.write(str(sum(lengths)) + "\t" + taxons_for_krona[ref] + "\n")
else:
krona_common_file.write(str(sum(lengths)) + "\n")
krona_common_file.close()
krona_fpaths = []
for index, name in enumerate(assemblies):
krona_fpath = os.path.join(krona_res_dirpath, name + "_taxonomy_chart.html")
krona_txt_fpath = os.path.join(krona_res_dirpath, name + krona_txt_ext)
qutils.call_subprocess(
[
"perl",
"-I",
krona_dirpath + "/lib",
krona_dirpath + "/scripts/ImportText.pl",
krona_txt_fpath,
"-o",
krona_fpath,
"-a",
],
stdout=open(os.devnull, "w"),
stderr=open(os.devnull, "w"),
)
krona_fpaths.append(os.path.join(qconfig.krona_dirname, name + "_taxonomy_chart.html"))
meta_log.main_info(" Krona chart for " + name + " is saved to " + krona_fpath)
os.remove(krona_txt_fpath)
if len(assemblies) > 1:
name = "summary"
krona_fpath = os.path.join(krona_res_dirpath, name + "_taxonomy_chart.html")
qutils.call_subprocess(
[
"perl",
"-I",
krona_dirpath + "/lib",
krona_dirpath + "/scripts/ImportText.pl",
krona_common_fpath,
"-o",
krona_fpath,
"-a",
],
stdout=open(os.devnull, "w"),
stderr=open(os.devnull, "w"),
)
meta_log.main_info(" Summary Krona chart is saved to " + krona_fpath)
krona_fpaths.append(os.path.join(qconfig.krona_dirname, name + "_taxonomy_chart.html")) # extra fpath!
os.remove(krona_common_fpath)
save_krona_paths(results_dirpath, krona_fpaths, assemblies)
# reading html template file
with open(html_fpath) as f_html:
html_text = f_html.read()
keyword = "totalReport"
html_text = re.sub("{{ " + keyword + " }}", "[" + ",".join(json_texts) + "]", html_text)
html_text = re.sub(r"{{(\s+\S+\s+)}}", "{}", html_text)
with open(html_fpath, "w") as f_html:
f_html.write(html_text)
meta_log.main_info(
" Extended version of HTML-report (for all references and assemblies) is saved to " + html_fpath
)
def process_one_ref(cur_ref_fpath, output_dirpath, err_path, bed_fpath=None):
ref = qutils.name_from_fpath(cur_ref_fpath)
ref_sam_fpath = os.path.join(output_dirpath, ref + '.sam')
ref_bam_fpath = os.path.join(output_dirpath, ref + '.bam')
ref_bamsorted_fpath = os.path.join(output_dirpath, ref + '.sorted')
ref_bed_fpath = bed_fpath if bed_fpath else os.path.join(output_dirpath, ref + '.bed')
if os.path.getsize(ref_sam_fpath) < 1024 * 1024: # TODO: make it better (small files will cause Manta crush -- "not enough reads...")
logger.info(' SAM file is too small for Manta (%d Kb), skipping..' % (os.path.getsize(ref_sam_fpath) // 1024))
return None
if is_non_empty_file(ref_bed_fpath):
logger.info(' Using existing Manta BED-file: ' + ref_bed_fpath)
return ref_bed_fpath
if not os.path.exists(ref_bamsorted_fpath + '.bam'):
qutils.call_subprocess([samtools_fpath('samtools'), 'view', '-bS', ref_sam_fpath], stdout=open(ref_bam_fpath, 'w'),
stderr=open(err_path, 'a'), logger=logger)
qutils.call_subprocess([samtools_fpath('samtools'), 'sort', ref_bam_fpath, ref_bamsorted_fpath],
stderr=open(err_path, 'a'), logger=logger)
if not is_non_empty_file(ref_bamsorted_fpath + '.bam.bai'):
qutils.call_subprocess([samtools_fpath('samtools'), 'index', ref_bamsorted_fpath + '.bam'],
stderr=open(err_path, 'a'), logger=logger)
if not is_non_empty_file(cur_ref_fpath + '.fai'):
qutils.call_subprocess([samtools_fpath('samtools'), 'faidx', cur_ref_fpath],
stderr=open(err_path, 'a'), logger=logger)
vcfoutput_dirpath = os.path.join(output_dirpath, ref + '_manta')
found_SV_fpath = os.path.join(vcfoutput_dirpath, 'results/variants/diploidSV.vcf.gz')
unpacked_SV_fpath = found_SV_fpath + '.unpacked'
if not is_non_empty_file(found_SV_fpath):
if os.path.exists(vcfoutput_dirpath):
shutil.rmtree(vcfoutput_dirpath, ignore_errors=True)
os.makedirs(vcfoutput_dirpath)
qutils.call_subprocess([config_manta_fpath, '--normalBam', ref_bamsorted_fpath + '.bam',
'--referenceFasta', cur_ref_fpath, '--runDir', vcfoutput_dirpath],
stdout=open(err_path, 'a'), stderr=open(err_path, 'a'), logger=logger)
if not os.path.exists(os.path.join(vcfoutput_dirpath, 'runWorkflow.py')):
return None
qutils.call_subprocess([os.path.join(vcfoutput_dirpath, 'runWorkflow.py'), '-m', 'local', '-j', str(qconfig.max_threads)],
stderr=open(err_path, 'a'), logger=logger)
if not is_non_empty_file(unpacked_SV_fpath):
cmd = 'gunzip -c %s' % found_SV_fpath
qutils.call_subprocess(shlex.split(cmd), stdout=open(unpacked_SV_fpath, 'w'),
stderr=open(err_path, 'a'), logger=logger)
from manta import vcfToBedpe
vcfToBedpe.vcfToBedpe(open(unpacked_SV_fpath), open(ref_bed_fpath, 'w'))
return ref_bed_fpath