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, bed_fpath):
logger.main_info('Failed searching structural variations')
return None, None, None
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,
ca_utils.misc.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, 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, bed_fpath):
logger.main_info('Failed searching structural variations')
return None, None, None
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
if a_ == 'install_full':
args2.append('install')
else:
args2.append(a_)
args = args2
if cmd_in(['install', 'develop', 'build', 'build_ext']):
logger.info('* Compiling aligner *')
compile_aligner(logger)
logger.info('* Compiling Glimmer *')
compile_glimmer()
logger.info('* Compiling GAGE *')
compile_gage()
if install_full:
logger.info('* Compiling read analisis tools *')
compile_reads_analyzer_tools(logger)
logger.info('* Downloading SILVA 16S rRNA gene database and BLAST *')
download_all_blast_binaries(logger)
download_blastdb(logger)
logger.info('')
if qconfig.platform_name == 'macosx':
nucmer_files = find_package_files('E-MEM-osx')
sambamba_files = [join('sambamba', 'sambamba_osx')]
else:
nucmer_files = find_package_files('MUMmer3.23-linux') + find_package_files(
'E-MEM-linux')
sambamba_files = [join('sambamba', 'sambamba_linux')]
bwa_files = [
import matplotlib
except ImportError:
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, compile_all_aligners=True):
modules_failed_to_install.append('Contigs aligners for reference-based evaluation (affects -R and many other options)')
logger.info('* Compiling Glimmer *')
if not compile_glimmer(logger):
modules_failed_to_install.append('Glimmer gene-finding tool (affects --glimmer option)')
if install_full:
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)')
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 *')
if not compile_gage():
modules_failed_to_install.append('GAGE scripts (affects --gage option [will be deprecated soon])')
logger.info('')
if qconfig.platform_name == 'macosx':
nucmer_files = find_package_files('E-MEM-osx')
sambamba_files = [join('sambamba', 'sambamba_osx')]
else:
nucmer_files = find_package_files('MUMmer3.23-linux') + find_package_files('E-MEM-linux')