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')