def main():
info(' '.join(sys.argv))
info()
parser = OptionParser(
usage='Usage: ' + basename(__file__) +
' --bed BED_file --bam BAM_file -g hg19 -o Output_BEDGRAPH_file '
'--work-dir work_directory --chr chromosome')
parser.add_option('-o', dest='output_dir')
parser.add_option('--samples', dest='sample_names')
parser.add_option('--bams', dest='bams')
parser.add_option('--vcf', dest='vcf_fpath')
parser.add_option('--chr', dest='chrom')
parser.add_option('--bed', dest='bed', help='BED file.')
parser.add_option('-g',
'--genome',
dest='chr_len_fpath',
help='File with chromosomes lengths.')
parser.add_option('--work-dir', dest='work_dir', help='Work directory.')
(opts, args) = parser.parse_args(sys.argv[1:])
cnf = Config(opts.__dict__, determine_sys_cnf(opts), {})
samples = [
BaseSample(sample_name, None, bam=bam)
for (sample_name,
bam) in zip(cnf.sample_names.split(','), cnf.bams.split(','))
]
if not cnf.output_dir or not cnf.bams:
critical(parser.usage)
safe_mkdir(cnf.output_dir)
safe_mkdir(cnf.work_dir)
get_regions_coverage(cnf, samples)
info('Done.')
def main():
info(' '.join(sys.argv))
info()
parser = OptionParser(usage='Usage: ' + basename(__file__) + ' --chr chr --vcf VCF_file --samples Sample1,Sample2 '
'--bams BAM_file1,BAM_file2 -o Output_directory '
'--features BED_file')
add_cnf_t_reuse_prjname_donemarker_workdir_genome_debug(parser)
parser.add_option('-o', dest='output_dir')
parser.add_option('--samples', dest='sample_names')
parser.add_option('--bams', dest='bams')
parser.add_option('--vcf', dest='vcf_fpath')
parser.add_option('--chr', dest='chrom')
parser.add_option('--features', dest='features', help='BED file with real CDS/Exon/Gene/Transcript regions with '
'annotations (default "features" is in system_config)')
(opts, args) = parser.parse_args(sys.argv[1:])
cnf = Config(opts.__dict__, determine_sys_cnf(opts), {})
cnf.verbose = False
if not cnf.output_dir or not cnf.vcf_fpath or not cnf.chrom:
critical(parser.usage)
cnf.features = cnf.features or cnf.genome.features
samples = [BaseSample(sample_name, None, bam=bam) for (sample_name, bam) in zip(cnf.sample_names.split(','), cnf.bams.split(','))]
split_bams(cnf, samples, cnf.vcf_fpath)
info('Done.')
def proc_args(argv):
info(' '.join(sys.argv))
info()
description = 'This script generates target QC reports for each BAM provided as an input. ' \
'Usage: ' + basename(__file__) + ' sample2bam.tsv --bed target.bed --contols sample1:sample2 -o results_dir'
parser = OptionParser(description=description, usage=description)
add_cnf_t_reuse_prjname_donemarker_workdir_genome_debug(parser)
parser.add_option('-o', dest='output_dir', metavar='DIR', default=join(os.getcwd(), 'seq2c'))
parser.add_option('--bed', dest='bed', help='BED file to run Seq2C analysis')
parser.add_option('-c', '--controls', dest='controls', help='Optional control sample names for Seq2C. For multiple controls, separate them using :')
parser.add_option('--seq2c-opts', dest='seq2c_opts', help='Options for the final lr2gene.pl script.')
parser.add_option('--no-prep-bed', dest='prep_bed', help=SUPPRESS_HELP, action='store_false', default=True)
(opts, args) = parser.parse_args()
logger.is_debug = opts.debug
if len(args) == 0:
parser.print_usage()
sys.exit(1)
if len(args) == 1 and not args[0].endswith('.bam'):
sample_names, bam_fpaths = read_samples(verify_file(args[0], is_critical=True, description='Input sample2bam.tsv'))
bam_by_sample = OrderedDict()
for s, b in zip(sample_names, bam_fpaths):
bam_by_sample[s] = b
else:
bam_by_sample = find_bams(args)
run_cnf = determine_run_cnf(opts, is_wgs=not opts.__dict__.get('bed'))
cnf = Config(opts.__dict__, determine_sys_cnf(opts), run_cnf)
check_genome_resources(cnf)
cnf.output_dir = adjust_path(cnf.output_dir)
verify_dir(dirname(cnf.output_dir), is_critical=True)
safe_mkdir(cnf.output_dir)
if not cnf.project_name:
cnf.project_name = basename(cnf.output_dir)
info('Project name: ' + cnf.project_name)
cnf.proc_name = 'Seq2C'
set_up_dirs(cnf)
samples = [
source.TargQC_Sample(name=s_name, dirpath=join(cnf.output_dir, s_name), bam=bam_fpath)
for s_name, bam_fpath in bam_by_sample.items()]
info('Samples: ')
for s in samples:
info(' ' + s.name)
samples.sort(key=lambda _s: _s.key_to_sort())
target_bed = verify_bed(cnf.bed, is_critical=True) if cnf.bed else None
if not cnf.only_summary:
cnf.qsub_runner = adjust_system_path(cnf.qsub_runner)
if not cnf.qsub_runner: critical('Error: qsub-runner is not provided is sys-config.')
verify_file(cnf.qsub_runner, is_critical=True)
return cnf, samples, target_bed, cnf.output_dir
def main():
info(' '.join(sys.argv))
info()
description = 'This script runs preprocessing.'
parser = OptionParser(description=description)
parser.add_option('-1', dest='left_reads_fpath', help='Left reads fpath')
parser.add_option('-2', dest='right_reads_fpath', help='Right reads fpath')
parser.add_option('--sample', dest='sample_name', help='Sample name')
parser.add_option('-o', dest='output_dir', help='Output directory path')
parser.add_option(
'--downsample-to',
dest='downsample_to',
default=None,
type='int',
help=
'Downsample reads to avoid excessive processing times with large files. '
'Default is 1 million. Set to 0 to turn off downsampling.')
add_cnf_t_reuse_prjname_donemarker_workdir_genome_debug(parser, threads=1)
(opts, args) = parser.parse_args()
logger.is_debug = opts.debug
cnf = Config(opts.__dict__, determine_sys_cnf(opts),
determine_run_cnf(opts))
left_reads_fpath = verify_file(opts.left_reads_fpath, is_critical=True)
right_reads_fpath = verify_file(opts.right_reads_fpath, is_critical=True)
output_dirpath = adjust_path(
opts.output_dir) if opts.output_dir else critical(
'Please, specify output directory with -o')
verify_dir(dirname(output_dirpath),
description='output_dir',
is_critical=True)
with workdir(cnf):
sample_name = cnf.sample_name
if not sample_name:
sample_name = _get_sample_name(left_reads_fpath, right_reads_fpath)
results_dirpath = run_fastq(cnf,
sample_name,
left_reads_fpath,
right_reads_fpath,
output_dirpath,
downsample_to=cnf.downsample_to)
verify_dir(results_dirpath, is_critical=True)
info()
info('*' * 70)
info('Fastqc results:')
info(' ' + results_dirpath)
def get_args():
description = (
'Plots a Circos plot given vardict variant file (with all dbSNP SNPs, not the PASS one), '
'Seq2C CNV calls and Manta SVs.')
parser = OptionParser(description=description)
add_cnf_t_reuse_prjname_donemarker_workdir_genome_debug(parser, threads=1)
parser.add_option('--bed', dest='bed_fpath', help='Path to BED file')
parser.add_option('-v', '--mutations', dest='mutations_fpath', help='Path to VarDict.txt file')
parser.add_option('-c', '--seq2c', dest='seq2c_tsv_fpath', help='Path to seq2c copy number file')
parser.add_option('--sv', dest='sv_fpath', help='Path to Manta SV call vcf.gz file')
parser.add_option('-s', '--sample', dest='sample', help='Identifier of sample in VarDict and Seq2c files')
parser.add_option('-o', '--output-dir', dest='output_dir', default="./",
help='Output directory. Defaults to ./')
(opts, args) = parser.parse_args()
run_cnf = determine_run_cnf(opts)
cnf = Config(opts.__dict__, determine_sys_cnf(opts), run_cnf)
return cnf
def main():
parser = OptionParser(usage='Usage: ' + basename(__file__) +
' -o Output_BED_file -g hg19 Input_BED_file')
parser.add_option('-o', '--output-bed', dest='output_fpath')
parser.add_option('-g', '--genome', dest='genome')
(opts, args) = parser.parse_args(sys.argv[1:])
if len(args) < 1:
parser.print_help(file=sys.stderr)
sys.exit(1)
cnf = Config(opts.__dict__, determine_sys_cnf(opts), {})
check_genome_resources(cnf)
if not cnf.output_fpath:
critical(parser.usage)
sort_bed(cnf, verify_bed(args[0], is_critical=True),
adjust_path(cnf.output_fpath))
def _read_args(args_list):
options = [
# (['-k', '--key-genes'], dict(
# dest='key_genes_fpath',
# help='list of key genes (they are at top priority when choosing one of multiple annotations)',
# default='/ngs/reference_data/genomes/Hsapiens/common/az_key_genes.300.txt')
# ),
# (['-a', '--approved-genes'], dict(
# dest='approved_genes_fpath',
# help='list of HGNC approved genes (they are preferable when choosing one of multiple annotations)',
# default='/ngs/reference_data/genomes/Hsapiens/common/HGNC_gene_synonyms.txt')
# ),
# (['-e', '--ensembl-bed'], dict(
# dest='ensembl_bed_fpath',
# help='reference BED file for annotation (Ensembl)')
# ),
# (['-r', '--refseq-bed'], dict(
# dest='refseq_bed_fpath',
# help='reference BED file for annotation (RefSeq)')
# ),
# (['-b', '--bedtools'], dict(
# dest='bedtools',
# help='path to bedtools',
# default='bedtools')
# ),
(['-o', '--output-bed'], dict(dest='output_fpath')),
(['--debug'],
dict(
dest='debug',
help=
'run in a debug more (verbose output, keeping of temporary files)',
default=False,
action='store_true')),
(['--output-hg'],
dict(
dest='output_hg',
help=
'output chromosome names in hg-style (chrM, chr1, .., chr22, chrX, chrY)',
default=False,
action='store_true')),
(['--output-grch'],
dict(
dest='output_grch',
help='output chromosome names in GRCh-style (1, .., 22, X, Y, MT)',
default=False,
action='store_true')),
(['-g', '--genome'], dict(dest='genome', default='hg19')),
]
parser = OptionParser(
usage='usage: %prog [options] Input_BED_file -o Standardized_BED_file',
description='Scripts outputs a standardized version of input BED file. '
'Standardized BED: 1) has 4 or 8 fields (for BEDs with primer info);'
' 2) has HGNC approved symbol in forth column if annotation is '
'possible and not_a_gene_X otherwise;'
' 3) is sorted based on chromosome name -> start -> end;'
' 4) has no duplicated regions (regions with the same chromosome, start and end), '
'the only exception is _CONTROL_ regions.')
for args, kwargs in options:
parser.add_option(*args, **kwargs)
(opts, args) = parser.parse_args(args_list)
if len(args) != 1:
parser.print_help(file=sys.stderr)
sys.exit(1)
cnf = Config(opts.__dict__, determine_sys_cnf(opts), {})
work_dirpath = tempfile.mkdtemp()
info('Creating a temporary working directory ' + work_dirpath)
if not exists(work_dirpath):
os.mkdir(work_dirpath)
input_bed_fpath = abspath(args[0])
info('Input: ' + input_bed_fpath)
output_bed_fpath = adjust_path(cnf.output_fpath)
info('Writing to: ' + output_bed_fpath)
# process configuration
# for k, v in opts.__dict__.iteritems():
# if k.endswith('fpath') and verify_file(v, is_critical=True):
# opts.__dict__[k] = verify_file(v, k)
if cnf.output_grch and cnf.output_hg:
info(
'you cannot specify --output-hg and --output-grch simultaneously!')
# if not which(opts.bedtools):
# info('bedtools executable not found, please specify correct path (current is %s)! '
# 'Did you forget to execute "module load bedtools"?' % opts.bedtools)
# if opts.debug:
# info('Configuration: ')
# for k, v in opts.__dict__.iteritems():
# info('\t' + k + ': ' + str(v))
info()
# opts.ensembl_bed_fpath = verify_file(opts.ensembl_bed_fpath or \
# ('/ngs/reference_data/genomes/Hsapiens/' + opts.genome + '/bed/Exons/Exons.with_genes.bed'))
# opts.refseq_bed_fpath = verify_file(opts.refseq_bed_fpath or \
# ('/ngs/reference_data/genomes/Hsapiens/' + opts.genome + '/bed/Exons/RefSeq/RefSeq_CDS_miRNA.all_features.bed'))
return input_bed_fpath, output_bed_fpath, work_dirpath, cnf
def proc_opts():
parser = OptionParser()
add_cnf_t_reuse_prjname_donemarker_workdir_genome_debug(parser)
parser.add_option('--expose-only',
dest='expose_to_ngs_server_only',
action='store_true',
default=False,
help='Only add project to the webserver')
parser.add_option('--no-expose',
dest='expose',
action='store_false',
default=True,
help='Do not expose the reports')
parser.add_option('-o', dest='output_dir')
parser.add_option('--bed',
dest='bed',
help='BED file to run targetSeq and Seq2C analysis on.')
parser.add_option('--downsample-to', dest='downsample_to', type='int')
(opts, args) = parser.parse_args()
logger.is_debug = opts.debug
if len(args) < 1:
critical('Usage: ' + __file__ + ' *.fq.gz -o output_dir')
# if len(args) < 2:
# info('No dataset path specified, assuming it is the current working directory')
# dataset_dirpath = adjust_path(os.getcwd())
# jira_url = args[0]
fastq_fpaths = [verify_file(fpath) for fpath in args]
fastq_fpaths = [fpath for fpath in fastq_fpaths if fpath]
info(str(len(fastq_fpaths)) + ' fastq files')
run_cnf = determine_run_cnf(opts)
cnf = Config(opts.__dict__, determine_sys_cnf(opts), run_cnf)
cnf.output_dir = adjust_path(cnf.output_dir)
info('Writing to ' + str(cnf.output_dir))
cnf.project_name = cnf.project_name or 'preproc'
if cnf.work_dir:
cnf.debug = True
else:
all_work_dir = join(cnf.output_dir, 'work')
safe_mkdir(all_work_dir)
latest_fpath = join(all_work_dir, 'latest')
if cnf.reuse_intermediate:
cnf.work_dir = latest_fpath
else:
cnf.work_dir = join(
all_work_dir,
datetime.datetime.now().strftime("%Y-%b-%d_%H-%M"))
if islink(latest_fpath):
os.remove(latest_fpath)
if isdir(latest_fpath):
shutil.rmtree(latest_fpath)
if not exists(latest_fpath):
os.symlink(basename(cnf.work_dir), latest_fpath)
cnf.work_dir = adjust_path(cnf.work_dir)
safe_mkdir(cnf.work_dir)
cnf.log_dir = join(cnf.work_dir, 'log')
safe_mkdir(cnf.log_dir)
set_up_log(cnf)
try:
subprocess.call(['chmod', '-R', 'g+w', cnf.work_dir])
except OSError:
err(traceback.format_exc())
pass
if cnf.samplesheet:
cnf.samplesheet = verify_file(cnf.samplesheet, is_critical=True)
info(' '.join(sys.argv))
info()
info('Created a temporary working directory: ' + cnf.work_dir)
if cnf.project_name:
info('Project name: ' + cnf.project_name)
if cnf.samplesheet:
info('Using custom sample sheet ' + cnf.samplesheet)
check_genome_resources(cnf)
check_system_resources(cnf, optional=['fastq'])
return cnf, cnf.output_dir, fastq_fpaths
def _read_args(args_list):
options = [
# (['-k', '--key-genes'], dict(
# dest='key_genes_fpath',
# help='list of key genes (they are at top priority when choosing one of multiple annotations)',
# default='/ngs/reference_data/genomes/Hsapiens/common/az_key_genes.300.txt')
# ),
# (['-a', '--approved-genes'], dict(
# dest='approved_genes_fpath',
# help='list of HGNC approved genes (they are preferable when choosing one of multiple annotations)',
# default='/ngs/reference_data/genomes/Hsapiens/common/HGNC_gene_synonyms.txt')
# ),
# (['-e', '--ensembl-bed'], dict(
# dest='ensembl_bed_fpath',
# help='reference BED file for annotation (Ensembl)')
# ),
# (['-r', '--refseq-bed'], dict(
# dest='refseq_bed_fpath',
# help='reference BED file for annotation (RefSeq)')
# ),
# (['-b', '--bedtools'], dict(
# dest='bedtools',
# help='path to bedtools',
# default='bedtools')
# ),
(['-o', '--output-bed'], dict(
dest='output_fpath')
),
(['--debug'], dict(
dest='debug',
help='run in a debug more (verbose output, keeping of temporary files)',
default=False,
action='store_true')
),
(['--output-hg'], dict(
dest='output_hg',
help='output chromosome names in hg-style (chrM, chr1, .., chr22, chrX, chrY)',
default=False,
action='store_true')
),
(['--output-grch'], dict(
dest='output_grch',
help='output chromosome names in GRCh-style (1, .., 22, X, Y, MT)',
default=False,
action='store_true')
),
(['-g', '--genome'], dict(
dest='genome',
default='hg19')
),
]
parser = OptionParser(usage='usage: %prog [options] Input_BED_file -o Standardized_BED_file',
description='Scripts outputs a standardized version of input BED file. '
'Standardized BED: 1) has 4 or 8 fields (for BEDs with primer info);'
' 2) has HGNC approved symbol in forth column if annotation is '
'possible and not_a_gene_X otherwise;'
' 3) is sorted based on chromosome name -> start -> end;'
' 4) has no duplicated regions (regions with the same chromosome, start and end), '
'the only exception is _CONTROL_ regions.')
for args, kwargs in options:
parser.add_option(*args, **kwargs)
(opts, args) = parser.parse_args(args_list)
if len(args) != 1:
parser.print_help(file=sys.stderr)
sys.exit(1)
cnf = Config(opts.__dict__, determine_sys_cnf(opts), {})
work_dirpath = tempfile.mkdtemp()
info('Creating a temporary working directory ' + work_dirpath)
if not exists(work_dirpath):
os.mkdir(work_dirpath)
input_bed_fpath = abspath(args[0])
info('Input: ' + input_bed_fpath)
output_bed_fpath = adjust_path(cnf.output_fpath)
info('Writing to: ' + output_bed_fpath)
# process configuration
# for k, v in opts.__dict__.items():
# if k.endswith('fpath') and verify_file(v, is_critical=True):
# opts.__dict__[k] = verify_file(v, k)
if cnf.output_grch and cnf.output_hg:
info('you cannot specify --output-hg and --output-grch simultaneously!')
# if not which(opts.bedtools):
# info('bedtools executable not found, please specify correct path (current is %s)! '
# 'Did you forget to execute "module load bedtools"?' % opts.bedtools)
# if opts.debug:
# info('Configuration: ')
# for k, v in opts.__dict__.items():
# info('\t' + k + ': ' + str(v))
info()
# opts.ensembl_bed_fpath = verify_file(opts.ensembl_bed_fpath or \
# ('/ngs/reference_data/genomes/Hsapiens/' + opts.genome + '/bed/Exons/Exons.with_genes.bed'))
# opts.refseq_bed_fpath = verify_file(opts.refseq_bed_fpath or \
# ('/ngs/reference_data/genomes/Hsapiens/' + opts.genome + '/bed/Exons/RefSeq/RefSeq_CDS_miRNA.all_features.bed'))
return input_bed_fpath, output_bed_fpath, work_dirpath, cnf
def get_args():
info(' '.join(sys.argv))
info()
description = (
'The program will filter the VarDict output after vcf2txt.pl to '
'candidate interpretable mutations, somatic or germline.')
parser = OptionParser(description=description)
add_cnf_t_reuse_prjname_donemarker_workdir_genome_debug(parser, threads=1)
parser.add_option('-o', dest='output_file')
parser.add_option('--o-all-transcripts',
dest='all_transcripts_output_file')
parser.add_option('--o-fm', dest='fm_output_file')
parser.add_option('--o-reject', dest='rejected_output_file')
parser.add_option('--cohort-freqs', dest='cohort_freqs_fpath')
parser.add_option('--transcripts', dest='transcripts_fpath')
parser.add_option('-D',
'--min-depth',
dest='filt_depth',
type='int',
help='The minimum total depth')
parser.add_option('-V',
'--min-vd',
dest='min_vd',
type='int',
help='The minimum reads supporting variant')
parser.add_option(
'--gmaf',
dest='min_gmaf',
type='float',
help=
'When the GMAF is greater than specified, it\'s considered common SNP and filtered out.'
)
parser.add_option(
'-f',
'--min-freq',
dest='min_freq',
type='float',
help='The minimum allele frequency for regular variants.')
parser.add_option(
'-F',
'--min-freq-hs',
'--act-min-freq',
dest='act_min_freq',
type='float',
help=
'The minimum allele frequency hotspot somatic mutations, typically lower then -f. '
'Default: 0.01 or half -f, whichever is less')
parser.add_option(
'-N',
'--keep-utr-intronic',
dest='keep_utr_intronic',
action='store_true',
help=
'Keep all intronic and UTR in the output, but will be set as "unknown".'
)
parser.add_option(
'-p',
'--platform',
dest='platform',
help=
'The platform, such as WXS, WGS, RNA-Seq, VALIDATION, etc. No Default. '
'Used for output in FM\'s format')
parser.set_usage('Usage: ' + __file__ +
' vcf2txt_res_fpath [opts] -o output_fpath')
(opts, args) = parser.parse_args()
if len(args) < 1:
critical('Provide the first argument - output from vcf2txt.pl')
logger.is_debug = opts.debug
vcf2txt_res_fpath = verify_file(args[0], is_critical=True)
run_cnf = determine_run_cnf(opts)
cnf = Config(opts.__dict__, determine_sys_cnf(opts), run_cnf)
if not cnf.genome:
critical('Please, specify the --genome option (e.g. --genome hg19)')
check_genome_resources(cnf)
if not cnf.output_file:
critical('Please, specify the output fpath with -o')
info()
return cnf, vcf2txt_res_fpath
def main():
info(' '.join(sys.argv))
info()
description = 'This script generates target QC reports for each BAM provided as an input.'
parser = OptionParser(description=description)
add_cnf_t_reuse_prjname_donemarker_workdir_genome_debug(parser, threads=1)
parser.add_option('--work-dir', dest='work_dir', metavar='DIR')
parser.add_option('--log-dir', dest='log_dir')
parser.add_option('--only-summary',
dest='only_summary',
action='store_true')
parser.add_option('-o',
dest='output_dir',
metavar='DIR',
default=join(os.getcwd(), 'targetqc'))
parser.add_option('--reannotate',
dest='reannotate',
action='store_true',
default=False,
help='re-annotate BED file with gene names')
parser.add_option('--dedup',
dest='dedup',
action='store_true',
default=False,
help='count duplicates in coverage metrics')
parser.add_option('--bed',
dest='bed',
help='BED file to run targetSeq and Seq2C analysis on.')
parser.add_option(
'--exons',
'--exome',
'--features',
dest='features',
help=
'Annotated CDS/Exon/Gene/Transcripts BED file to make targetSeq exon/amplicon regions reports.'
)
(opts, args) = parser.parse_args()
logger.is_debug = opts.debug
if len(args) == 0:
critical('No BAMs provided to input.')
bam_fpaths = list(set([abspath(a) for a in args]))
bad_bam_fpaths = []
for fpath in bam_fpaths:
if not verify_bam(fpath):
bad_bam_fpaths.append(fpath)
if bad_bam_fpaths:
critical('BAM files cannot be found, empty or not BAMs:' +
', '.join(bad_bam_fpaths))
run_cnf = determine_run_cnf(opts, is_wgs=not opts.__dict__.get('bed'))
cnf = Config(opts.__dict__, determine_sys_cnf(opts), run_cnf)
if not cnf.project_name:
cnf.project_name = basename(cnf.output_dir)
info('Project name: ' + cnf.project_name)
cnf.proc_name = 'TargQC'
set_up_dirs(cnf)
# cnf.name = 'TargQC_' + cnf.project_name
check_genome_resources(cnf)
verify_bed(cnf.bed, is_critical=True)
bed_fpath = adjust_path(cnf.bed)
info('Using amplicons/capture panel ' + bed_fpath)
features_bed_fpath = adjust_path(
cnf.features) if cnf.features else adjust_path(cnf.genome.features)
info('Features: ' + features_bed_fpath)
genes_fpath = None
if cnf.genes:
genes_fpath = adjust_path(cnf.genes)
info('Custom genes list: ' + genes_fpath)
if not cnf.only_summary:
cnf.qsub_runner = adjust_system_path(cnf.qsub_runner)
if not cnf.qsub_runner:
critical('Error: qsub-runner is not provided is sys-config.')
verify_file(cnf.qsub_runner, is_critical=True)
info('*' * 70)
info()
targqc_html_fpath = run_targqc(cnf, cnf.output_dir, bam_fpaths, bed_fpath,
features_bed_fpath, genes_fpath)
if targqc_html_fpath:
send_email(
cnf, 'TargQC report for ' + cnf.project_name + ':\n ' +
targqc_html_fpath)
def read_opts_and_cnfs(extra_opts,
key_for_sample_name=None,
required_keys=list(),
file_keys=list(),
dir_keys=list(),
description='',
extra_msg=None,
proc_name=None,
fpath_for_sample_name=None,
main_output_is_file=False,
main_output_is_dir=True):
options = extra_opts
if main_output_is_file:
options += [(['-o', '--output-file'],
dict(dest='output_file',
metavar='FILE',
help='Output file'))]
options += [(
['--output-dir'],
dict(
dest='output_dir',
metavar='DIR',
help=
'Output directory (or directory name in case of bcbio final dir)',
default=os.getcwd()))]
elif main_output_is_dir:
options += [(
['-o', '--output-dir'],
dict(
dest='output_dir',
metavar='DIR',
help=
'Output directory (or directory name in case of bcbio final dir)',
default=os.getcwd()))]
options += [(['--output-file'],
dict(dest='output_file',
metavar='FILE',
help='Output file'))]
options += [
(['-s', '--sample', '--name'],
dict(
dest='sample',
metavar='NAME',
help=
'Sample name (default is part of name of the first parameter prior to the first - or .'
)),
(['-c', '--caller'],
dict(
dest='caller',
metavar='CALLER_NAME',
help=
'Variant caller name (default is part of name of the first parameter between the first - and following .'
)),
(['-t', '--nt', '--threads'],
dict(dest='threads', type='int', help='Number of threads')),
(
['--clean'],
dict( # do not keep work directory
dest='keep_intermediate',
action='store_false',
help=SUPPRESS_HELP)),
(['--debug'],
dict(dest='debug',
action='store_true',
default=False,
help=SUPPRESS_HELP)),
(['--reuse'],
dict(
dest='reuse_intermediate',
help=
'reuse intermediate non-empty files in the work dir from previous run',
action='store_true')),
(['--sys-cnf'],
dict(
dest='sys_cnf',
metavar='SYS_CNF.yaml',
help=
'System configuration file with paths to external tools and genome resources. The default is '
'(see default one %s)' % defaults['sys_cnf'])),
(['--run-cnf'],
dict(
dest='run_cnf',
metavar='RUN_CNF.yaml',
default=defaults['run_cnf_exome_seq'],
help=
'Customised run details: list of annotations/QC metrics/databases/filtering criteria. '
'The default is %s' % defaults['run_cnf_exome_seq'])),
(['--transcripts'], dict(dest='transcripts_fpath')),
(['--work-dir'],
dict(dest='work_dir', metavar='DIR', help=SUPPRESS_HELP)),
(['--log-dir'], dict(dest='log_dir', metavar='DIR',
help=SUPPRESS_HELP)),
(['--proc-name'], dict(dest='proc_name', help=SUPPRESS_HELP)),
(['--project-name'], dict(dest='project_name')),
(['--no-check'],
dict(dest='no_check', action='store_true', help=SUPPRESS_HELP)),
(['-g', '--genome'], dict(dest='genome')),
(['--email'], dict(dest='email', help=SUPPRESS_HELP)),
(['--done-marker'], dict(dest='done_marker', help=SUPPRESS_HELP)),
]
parser = OptionParser(description=description)
for args, kwargs in options:
parser.add_option(*args, **kwargs)
req_keys_usage = ''
if required_keys:
req_keys_usage = '\nRequired options:'
for args, kwargs in options:
try:
if kwargs['dest'] in required_keys:
req_keys_usage += '\n ' + '/'.join(args)
except:
err(format_exc())
pass
parser.set_usage(parser.get_usage() + req_keys_usage)
(opts, args) = parser.parse_args()
logger.is_debug = opts.debug
run_cnf = determine_run_cnf(opts, is_wgs=not opts.__dict__.get('bed'))
cnf = Config(opts.__dict__, determine_sys_cnf(opts), run_cnf)
errors = check_keys_presence(cnf, required_keys)
if errors:
parser.print_help()
critical(errors)
file_keys = [k for k in file_keys if k in required_keys]
dir_keys = [k for k in dir_keys if k in required_keys]
errors = check_dirs_and_files(cnf, file_keys, dir_keys)
if errors:
critical(errors)
if cnf.sample:
cnf.sample = remove_quotes(cnf.sample)
else:
if not fpath_for_sample_name:
if not key_for_sample_name:
critical('Error: --sample must be provided in options.')
fpath_for_sample_name = cnf[key_for_sample_name]
if not fpath_for_sample_name:
critical('Error: --sample or ' + (str(key_for_sample_name)) +
' must be provided in options.')
key_fname = basename(cnf[key_for_sample_name])
cnf.sample = key_fname.split('.')[0]
if cnf.caller:
cnf.caller = remove_quotes(cnf.caller)
# elif key_for_sample_name and cnf[key_for_sample_name]:
# key_fname = basename(cnf[key_for_sample_name])
# try:
# cnf.caller = cnf.caller or key_fname.split('.')[0].split('-')[1]
# except:
# cnf.caller = ''
else:
cnf.caller = None
cnf.proc_name = cnf.proc_name or proc_name
set_up_dirs(cnf)
info(' '.join(sys.argv))
info()
return cnf
def proc_args(argv):
info(' '.join(sys.argv))
info()
description = 'This script generates target QC reports for each BAM provided as an input.'
parser = OptionParser(description=description)
add_cnf_t_reuse_prjname_donemarker_workdir_genome_debug(parser)
parser.add_option('--log-dir', dest='log_dir')
parser.add_option('--is-wgs',
dest='is_wgs',
action='store_true',
default=False,
help='whole genome sequencing')
parser.add_option('--is-deep-seq',
dest='is_deep_seq',
action='store_true',
default=False,
help='deep targeted sequencing')
parser.add_option('--only-summary',
dest='only_summary',
action='store_true')
parser.add_option('-o',
dest='output_dir',
metavar='DIR',
default=join(os.getcwd(), 'targetqc'))
parser.add_option('-c', '--caller', dest='caller')
parser.add_option('--qc', dest='qc', action='store_true', default=False)
parser.add_option('--no-qc',
dest='qc',
action='store_false',
default=False)
parser.add_option('--qc-caption', dest='qc_caption', help=SUPPRESS_HELP)
parser.add_option('--no-tsv',
dest='tsv',
action='store_false',
default=True,
help=SUPPRESS_HELP)
(opts, args) = parser.parse_args()
logger.is_debug = opts.debug
if len(args) == 0:
critical('No vcf files provided to input.')
run_cnf = determine_run_cnf(opts,
is_targetseq=opts.is_deep_seq,
is_wgs=opts.is_wgs)
cnf = Config(opts.__dict__, determine_sys_cnf(opts), run_cnf)
vcf_fpath_by_sample = read_samples(args, cnf.caller)
info()
if not cnf.project_name:
cnf.project_name = basename(cnf.output_dir)
info('Project name: ' + cnf.project_name)
cnf.proc_name = 'Variants'
set_up_dirs(cnf)
# cnf.name = 'TargQC_' + cnf.project_name
info(' '.join(sys.argv))
samples = [
source.VarSample(s_name, join(cnf.output_dir, s_name), vcf=vcf_fpath)
for s_name, vcf_fpath in vcf_fpath_by_sample.items()
]
samples.sort(key=lambda _s: _s.key_to_sort())
check_genome_resources(cnf)
if not cnf.only_summary:
cnf.qsub_runner = adjust_system_path(cnf.qsub_runner)
if not cnf.qsub_runner:
critical('Error: qsub-runner is not provided is sys-config.')
verify_file(cnf.qsub_runner, is_critical=True)
return cnf, samples