def do(ref_fpath,
contigs_fpaths,
reads_fpaths,
meta_ref_fpaths,
output_dir,
external_logger=None,
sam_fpath=None,
bam_fpath=None,
bed_fpath=None):
if external_logger:
global logger
logger = external_logger
logger.print_timestamp()
logger.main_info('Running Reads analyzer...')
if not os.path.isdir(output_dir):
os.makedirs(output_dir)
if not compile_reads_analyzer_tools(logger):
logger.main_info('Failed searching structural variations')
return None, None, None
download_manta(logger, bed_fpath)
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')
open(log_path, 'w').close()
open(err_path, 'w').close()
logger.info(' ' + 'Logging to files %s and %s...' % (log_path, err_path))
try:
bed_fpath, cov_fpath, physical_cov_fpath = run_processing_reads(
ref_fpath,
meta_ref_fpaths,
ref_labels_by_chromosomes,
reads_fpaths,
temp_output_dir,
output_dir,
log_path,
err_path,
bed_fpath=bed_fpath,
sam_fpath=sam_fpath,
bam_fpath=bam_fpath)
except:
bed_fpath, cov_fpath, physical_cov_fpath = None, None, 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, cov_fpath, physical_cov_fpath
def do(ref_fpath, contigs_fpaths, output_dir, meta_ref_fpaths=None, external_logger=None):
if external_logger:
global logger
logger = external_logger
logger.print_timestamp()
logger.main_info('Running Reads analyzer...')
if not compile_reads_analyzer_tools(logger):
logger.main_info('Failed reads analysis')
return None, None, None
if not isdir(output_dir):
os.makedirs(output_dir)
download_gridss(logger, qconfig.bed)
temp_output_dir = join(output_dir, 'temp_output')
if not isdir(temp_output_dir):
os.mkdir(temp_output_dir)
if not qconfig.no_check:
if qconfig.forward_reads and not \
all([paired_reads_names_are_equal([read1, read2], temp_output_dir, logger)
for read1, read2 in zip(qconfig.forward_reads, qconfig.reverse_reads)]):
logger.error(' Read names are discordant, skipping reads analysis!')
return None, None, None
log_path = join(output_dir, 'reads_stats.log')
err_fpath = join(output_dir, 'reads_stats.err')
open(log_path, 'w').close()
open(err_fpath, 'w').close()
logger.info(' ' + 'Logging to files %s and %s...' % (log_path, err_fpath))
bed_fpath, cov_fpath, physical_cov_fpath = run_processing_reads(contigs_fpaths, ref_fpath, meta_ref_fpaths, ref_labels_by_chromosomes,
temp_output_dir, output_dir, log_path, err_fpath)
if not qconfig.debug:
shutil.rmtree(temp_output_dir, ignore_errors=True)
logger.info('Done.')
return bed_fpath, cov_fpath, physical_cov_fpath
def do(ref_fpath, contigs_fpaths, output_dir, meta_ref_fpaths=None, external_logger=None):
if external_logger:
global logger
logger = external_logger
logger.print_timestamp()
logger.main_info('Running Reads analyzer...')
if not compile_reads_analyzer_tools(logger):
logger.main_info('Failed reads analysis')
return None, None, None
if not isdir(output_dir):
os.makedirs(output_dir)
download_gridss(logger, qconfig.bed)
temp_output_dir = join(output_dir, 'temp_output')
if not isdir(temp_output_dir):
os.mkdir(temp_output_dir)
if not qconfig.no_check:
if qconfig.forward_reads and not \
all([paired_reads_names_are_equal([read1, read2], temp_output_dir, logger)
for read1, read2 in zip(qconfig.forward_reads, qconfig.reverse_reads)]):
logger.error(' Read names are discordant, skipping reads analysis!')
return None, None, None
log_path = join(output_dir, 'reads_stats.log')
err_fpath = join(output_dir, 'reads_stats.err')
open(log_path, 'w').close()
open(err_fpath, 'w').close()
logger.info(' ' + 'Logging to files %s and %s...' % (log_path, err_fpath))
bed_fpath, cov_fpath, physical_cov_fpath = run_processing_reads(contigs_fpaths, ref_fpath, meta_ref_fpaths, ref_labels_by_chromosomes,
temp_output_dir, output_dir, log_path, err_fpath)
if not qconfig.debug:
shutil.rmtree(temp_output_dir, ignore_errors=True)
logger.info('Done.')
return bed_fpath, cov_fpath, physical_cov_fpath
logger.info('* Compiling aligner *')
if not compile_aligner(logger):
modules_failed_to_install.append(
'Contigs aligners for reference-based evaluation (affects -R and many other options)'
)
logger.info('* Compiling gnuplot *')
if not compile_gnuplot(logger):
logger.warning(
'Cannot compile gnuplot. MUMmer plots will not be drawn')
logger.info('* Compiling Glimmer *')
if not compile_glimmer(logger):
modules_failed_to_install.append(
'Glimmer gene-finding tool (affects --glimmer option)')
logger.info('* Compiling read analysis tools *')
if not compile_reads_analyzer_tools(logger):
modules_failed_to_install.append(
'Read analysis tools (affects -1/--reads1 and -2/--reads2 options)'
)
if install_full:
logger.info('* Downloading Manta *')
if not download_manta(logger):
modules_failed_to_install.append(
'Manta (affects -1/--reads1 and -2/--reads2 options)')
logger.info('* Downloading SILVA 16S rRNA gene database and BLAST *')
if not download_all_blast_binaries(logger) or not download_blastdb(
logger):
modules_failed_to_install.append(
'SILVA 16S rRNA gene database and BLAST (affects metaquast.py in without references mode)'
)
logger.info('* Compiling GAGE *')
try:
pip.main(['install', 'matplotlib'])
except:
logger.warning('Cannot install matplotlib. Static plots will not be drawn (however, HTML will be)')
logger.info('* Compiling aligner *')
if not compile_aligner(logger):
modules_failed_to_install.append('Contigs aligners for reference-based evaluation (affects -R and many other options)')
logger.info('* Compiling gnuplot *')
if not compile_gnuplot(logger):
logger.warning('Cannot compile gnuplot. MUMmer plots will not be drawn')
logger.info('* Compiling Glimmer *')
if not compile_glimmer(logger):
modules_failed_to_install.append('Glimmer gene-finding tool (affects --glimmer option)')
logger.info('* Compiling read analysis tools *')
if not compile_reads_analyzer_tools(logger):
modules_failed_to_install.append('Read analysis tools (affects -1/--reads1 and -2/--reads2 options)')
if install_full:
logger.info('* Downloading GRIDSS *')
if not download_gridss(logger):
modules_failed_to_install.append('GRIDSS (affects -1/--reads1 and -2/--reads2 options)')
logger.info('* Downloading BLAST *')
if not download_blast_binaries(logger):
modules_failed_to_install.append('BLAST (affects metaquast.py in without references mode and --find-conserved-genes option)')
logger.info('* Downloading SILVA 16S rRNA gene database *')
if not download_blastdb(logger):
modules_failed_to_install.append('SILVA 16S rRNA gene database (affects metaquast.py in without references mode)')
if qconfig.platform_name != 'macosx':
logger.info('* Downloading and compiling Augustus *')
if not download_augustus(logger):
modules_failed_to_install.append('Augustus (affects --find-conserved-genes option)')