def __init__(self): CommandLineApp.__init__(self) op = self.option_parser op.set_usage('usage: filter-sam.py') op.add_option('-i', '--infile', dest='infile', type='string', default=None, help='Input .sam file') op.add_option('-o', '--outfile', dest='outfile', type='string', default=None, help='Output .sam file') op.add_option('-a', '--bwa_alg', dest='bwa_alg', type='string', default='', help='Output .sam file') op.add_option('-s', '--use_stampy', dest='use_stampy', type='int', default=0, help='SAM file was mapped with stampy')
def __init__(self): CommandLineApp.__init__(self) #self.force_exit = False #enable this when profiling op = self.option_parser op.set_usage('usage: extract_ref_alleles -i indiv -d samdir -o outdir --parent1 parent1_genome --parent2 parent2_genome --chroms csv_list --verbosity') op.add_option('-i', '--individual', dest='indiv', type='string', default=None, help='Name of individual. E.g. for sam file aln_indivA6_AACGAG_sec.sam.gz, indiv would be "indivA6_AACGAG"') op.add_option('-d', '--samdir', dest='samdir', type='string', default='', help='Directory containing SAM files') op.add_option('-o', '--outdir', dest='outdir', type='string', default='', help='Output directory') op.add_option('--parent1', dest='parent1', type='string', default=None, help='Parent 1 genome file to align against') op.add_option('--parent2', dest='parent2', type='string', default=None, help='Parent 2 genome file to align against') op.add_option('--chroms', dest='chroms', type='string', default=None, help='chromosomes desired') op.add_option('--verbosity', action="store_true", dest='verbosity', default=False, help="make lots of noise")
def __init__(self): CommandLineApp.__init__(self) op = self.option_parser op.set_usage('usage: parse_and_map -[npm] -i reads.fq -b barcodes --parent1 parent1_genome --parent2 parent2_genome') op.add_option('-i', '--raw-data', dest='raw_data_file', type='string', default=None, help='Raw Illumina data file') op.add_option('-b', '--barcodes', dest='barcodes_file', type='string', default=None, help='Barcodes file') op.add_option('--re_cutter', dest='re_cutter', type='string', default=None, help='restriction enzyme') op.add_option('--linker_system', dest='linker_system', type='string', default=None, help='linker system') op.add_option('--parent1', dest='parent1', type='string', default=None, help='Parent 1 genome file to align against') op.add_option('--parent2', dest='parent2', type='string', default=None, help='Parent 2 genome file to align against') op.add_option('-m', '--map-only', dest='map_only', default=False, action='store_true', help='Just map data?') op.add_option('-n', '--num-ind', dest='num_ind', default=None, type='int', help='Number of individuals to map') op.add_option('-p', '--parse-only', dest='parse_only', default=False, action='store_true', help='Just parse data?')
def __init__(self): CommandLineApp.__init__(self) op = self.option_parser op.set_usage('usage: filter-sam.py') op.add_option('-i', '--infile', dest='infile', type='string', default=None, help='Input .sam file') op.add_option('-o', '--outfile', dest='outfile', type='string', default=None, help='Output .sam file')
def __init__(self): CommandLineApp.__init__(self) op = self.option_parser op.set_usage( 'usage: extract_ref_alleles -i indiv -d samdir -o outdir --parent1 parent1_genome --parent2 parent2_genome --chroms csv_list --verbosity' ) op.add_option( '-i', '--individual', dest='indiv', type='string', default=None, help= 'Name of individual. E.g. for sam file aln_indivA6_AACGAG_sec.sam.gz, indiv would be "indivA6_AACGAG"' ) op.add_option('-d', '--samdir', dest='samdir', type='string', default='', help='Directory containing SAM files') op.add_option('-o', '--outdir', dest='outdir', type='string', default='', help='Output directory') op.add_option('--parent1', dest='parent1', type='string', default=None, help='Parent 1 genome file to align against') op.add_option('--parent2', dest='parent2', type='string', default=None, help='Parent 2 genome file to align against') op.add_option('--chroms', dest='chroms', type='string', default=None, help='chromosomes desired') op.add_option('--verbosity', action="store_true", dest='verbosity', default=False, help="make lots of noise [default]")
def __init__(self): CommandLineApp.__init__(self) op = self.option_parser op.set_usage('usage: stitchContigs.py') op.add_option('-c', '--chrom', dest='chrom', type='string', default='X', help='chromosome')
def __init__(self): CommandLineApp.__init__(self) op = self.option_parser op.set_usage('usage: create_stats -i reads.fq -b barcodes') op.add_option('-i', '--raw-data', dest='raw_data_file', type='string', default=None, help='Raw Illumina data file') op.add_option('-b', '--barcodes', dest='barcodes_file', type='string', default=None, help='Barcodes file')
def __init__(self): CommandLineApp.__init__(self) argv = sys.argv op = self.option_parser usage = 'usage: %s tree1 tree2' % os.path.basename(argv[0]) op.set_usage(usage) op.add_option('-n', '--dry-run', dest='dry_run', default=False, action='store_true', help="Just print shell commands; don't actually do anything") op.add_option('-d', '--delete', dest='delete', default=False, action='store_true', help="Delete files from receiver that do not exist in sender") op.add_option('--delete-only', dest='delete_only', default=False, action='store_true', help="Delete files from receiver that do not exist in sender, and do not copy files.")
def __init__(self): CommandLineApp.__init__(self) op = self.option_parser usage = [] usage.append("%s --snptest --controls 58C --cases NBS --chrom '21 22' --local" % __progname__) usage.append('%s --cohorts "58C NBS POBI" --snpfile ~/wtccc2/celine-snps-ill'% __progname__) op.set_usage('\n' + '\n'.join(usage)) op.add_option('--pca', dest='pca', default=False, action='store_true', help='Perform PCA of selected cohorts') op.add_option('', '--make-gen', dest='make_gen', default=False, action='store_true', help="Convert to .gen input data format used by chiamo and related software") op.add_option('--snptest', dest='snptest', default=False, action='store_true', help='Perform association tests of selected cases & controls') op.add_option('--sstat', dest='sstat', default=False, action='store_true', help='Compute summary statistics for selected cohorts') op.add_option('--cohorts', dest='cohorts', type='string', default='', help='Space-separated list of cohorts') op.add_option('--cases', dest='cases', type='string', default='', help='Space-separated list of case cohorts') op.add_option('--controls', dest='controls', type='string', default='', help='Space-separated list of control cohorts') op.add_option('--outfile', dest='outfile', type='string', default=None, help='Name of output file') op.add_option('--local', dest='local', default=False, action='store_true', help='Run PCA / snptest locally, not on the cluster') op.add_option('--chrom', dest='chroms', type='string', default=None, help='Chromosomes to include (space-separated; default is 1-22)') op.add_option('--snpfile', dest='snpfile', type='string', default=None, help='File containing SNPs to use (.map format)') op.add_option('--samplefile', dest='samplefile', type='string', default=None, help='sample file to use (chiamo .sample format; defaults to WTCCC2 cohort sample file)') op.add_option('--snptest-opts', dest='snptest_opts', type='string', default='', help='Options to pass to snptest') op.add_option('--factorfile', dest='factor_file', type='string', default=None, help='File containing integer factor classifying individuals (minimum factor level is 1)') op.add_option('--exclude', dest='excludefile', type='string', default=None, help='File containing IDs of individuals to exclude' + \ 'in addition to project exclusions (one ID per line)') op.add_option('-n', dest='dry_run', default=False, action='store_true', help="Don't actually do anything, just print commands") op.add_option('', '--messy', dest='messy', default=False, action='store_true', help="Do not remove intermediate files") op.add_option('--platform', dest='platform', type='string', default=None)
def __init__(self): CommandLineApp.__init__(self) op = self.option_parser usage = 'usage: %s file [file ...]' % os.path.basename(sys.argv[0]) op.set_usage(usage) op.add_option('-f', '--field', dest='field', default=None, type='int', help='Column index of field on which comparison of lines is to be based') op.add_option('-d', '--delimiter', dest='delim', default=None, type='string', help='Field delimiter (default is <TAB>)') op.add_option('-i', '--inplace', dest='inplace', default=False, action='store_true', help='Overwrite input files') op.add_option('-o', '--out', dest='outdir', default='.', type='string', help='Directory into which output files will be saved.' +\ 'Defaults to current directory.' +\ 'The output files are given the name of the corresponding ' + \ 'input file, with the suffix .insect') op.add_option('-u', '--unique', dest='unique', default=False, action='store_true', help='Restrict keys to unique values before insecting. ' + \ 'Duplicate keys result in an error unless this option is in force.')
def __init__(self): CommandLineApp.__init__(self) #self.force_exit = False #enable this when profiling op = self.option_parser op.set_usage('usage: extract_ref_alleles -i indiv -d samdir -o outdir --parent1 parent1_genome --parent2 parent2_genome --chroms csv_list --repeat_threshold AS-XS --verbosity') op.add_option('-i', '--individual', dest='indiv', type='string', default=None, help='Name of individual. E.g. for sam file aln_indivA6_AACGAG_sec.sam.gz, indiv would be "indivA6_AACGAG"') op.add_option('-d', '--samdir', dest='samdir', type='string', default='', help='Directory containing SAM files') op.add_option('-o', '--outdir', dest='outdir', type='string', default='', help='Output directory') op.add_option('--parent1', dest='parent1', type='string', default=None, help='Parent 1 genome file to align against') op.add_option('--parent2', dest='parent2', type='string', default=None, help='Parent 2 genome file to align against') op.add_option('--chroms', dest='chroms', type='string', default=None, help='chromosomes desired') op.add_option('--verbosity', action="store_true", dest='verbosity', default=False, help="make lots of noise") op.add_option('--bwa_alg', dest='bwa_alg', type='string', default='', help='BWA algorithm used to generate SAM files. It should be "aln" or "bwasw".') op.add_option('--use_stampy', dest='use_stampy', type='int', default=0, help='Was STAMPY used to generate SAM files? Set this to 1.') op.add_option('--repeat_threshold', dest='AS_XS_threshold', type='int', default=6, help='Minimum difference between top alignment and suboptimal alignment scores to keep')
def __init__(self): CommandLineApp.__init__(self) op = self.option_parser usage = 'usage: [options] %s -i %s -o %s' % ( __progname__, os.path.sep.join(['location','of','music', 'library']), os.path.sep.join(['folder','to','receive','output'])) op.set_usage(usage) op.add_option('-i', '--library', dest='libdir', type='string', default=None, help='Location of root of music library') op.add_option('-o', '--outdir', dest='outdir', type='string', default='.', help='Folder to receive output, defaults to current folder.') # op.add_option('-u', '--update', dest='update', default=False, action='store_true', # help='Don\'t re-scan whole library; instead update saved dbm data base.') op.add_option('-f', '--libfile', dest='savefile', type='string', default='library.dbm', help="Saved library file, defaults to 'library.dbm'") op.add_option('-r', '--rockbox', dest='path_to_rockbox', type='string', default=None, help='Location of rockbox digital audio player.') op.add_option('', '--mintracks', dest='minArtistTracks', default=0, type='int', help='Playlists and linkfiles will only be generated for artists with' + \ ' more than this number of tracks in the library.') op.add_option('', '--numtries', dest='numtries', default=3, type='int', help='Number of times to attempt web query for an artist before giving up.') op.add_option('', '--noweb', dest='query_lastfm', default=True, action='store_false', help="Don't query last.fm similar artists.") op.add_option('-n', '', dest='create_files', default=True, action='store_false', help='Don\'t create any playlists or link files') op.add_option('', '--version', dest='show_version', default=False, action='store_true', help='Print out version information and exit') op.add_option('', '--show-library', dest='show_tree', default=False, action='store_true', help='Print sparse representation of library, and exit') op.add_option('', '--show-tracks', dest='show_tracks', default=False, action='store_true', help='Include track information when using --show') op.add_option('', '--show-artists', dest='show_artists', default=False, action='store_true', help='Print information on artists in library, and exit') op.add_option('-s', '--musicspace', dest='music_space_file', type='string', default=None, help='Music space file') op.add_option('', '--show-musicspace', dest='show_musicspace', default=False, action='store_true', help="Print summary of neighbouring artists in musicspace, and exit") op.add_option('', '--dropoff', dest='musicspace_dropoff_param', type='float', default=3.0, help="Parameter controlling rate at which probability of inclusion falls away with distance in music space. When generating playlists for artist X, a value of 0 means that all other artists will be included with equal probability; a value of more than 5 or so means that you'll rarely get anybody but X. Default is 3.0") op.add_option('', '--create-musicspace-skeleton', dest='write_music_space', default=False, action='store_true', help='create skeleton music space spreadsheet file and exit') op.add_option('-t', '--target', dest='target', default='rockbox', type='string', help="Specify target platform: defaults to rockbox; " +\ "in the future you will be able to use --target=native " +\ "to create playlists and links for use on the local machine.")
def __init__(self): CommandLineApp.__init__(self) op = self.option_parser usage = 'usage: [options] %s -i %s -o %s' % ( __progname__, os.path.sep.join(['location', 'of', 'music', 'library']), os.path.sep.join(['folder', 'to', 'receive', 'output'])) op.set_usage(usage) op.add_option('-i', '--library', dest='libdir', type='string', default=None, help='Location of root of music library') op.add_option( '-o', '--outdir', dest='outdir', type='string', default='.', help='Folder to receive output, defaults to current folder.') # op.add_option('-u', '--update', dest='update', default=False, action='store_true', # help='Don\'t re-scan whole library; instead update saved dbm data base.') op.add_option('-f', '--libfile', dest='savefile', type='string', default='library.dbm', help="Saved library file, defaults to 'library.dbm'") op.add_option('-r', '--rockbox', dest='path_to_rockbox', type='string', default=None, help='Location of rockbox digital audio player.') op.add_option('', '--mintracks', dest='minArtistTracks', default=0, type='int', help='Playlists and linkfiles will only be generated for artists with' + \ ' more than this number of tracks in the library.') op.add_option( '', '--numtries', dest='numtries', default=3, type='int', help= 'Number of times to attempt web query for an artist before giving up.' ) op.add_option('', '--noweb', dest='query_lastfm', default=True, action='store_false', help="Don't query last.fm similar artists.") op.add_option('-n', '', dest='create_files', default=True, action='store_false', help='Don\'t create any playlists or link files') op.add_option('', '--version', dest='show_version', default=False, action='store_true', help='Print out version information and exit') op.add_option('', '--show-library', dest='show_tree', default=False, action='store_true', help='Print sparse representation of library, and exit') op.add_option('', '--show-tracks', dest='show_tracks', default=False, action='store_true', help='Include track information when using --show') op.add_option('', '--show-artists', dest='show_artists', default=False, action='store_true', help='Print information on artists in library, and exit') op.add_option('-s', '--musicspace', dest='music_space_file', type='string', default=None, help='Music space file') op.add_option( '', '--show-musicspace', dest='show_musicspace', default=False, action='store_true', help="Print summary of neighbouring artists in musicspace, and exit" ) op.add_option( '', '--dropoff', dest='musicspace_dropoff_param', type='float', default=3.0, help= "Parameter controlling rate at which probability of inclusion falls away with distance in music space. When generating playlists for artist X, a value of 0 means that all other artists will be included with equal probability; a value of more than 5 or so means that you'll rarely get anybody but X. Default is 3.0" ) op.add_option( '', '--create-musicspace-skeleton', dest='write_music_space', default=False, action='store_true', help='create skeleton music space spreadsheet file and exit') op.add_option('-t', '--target', dest='target', default='rockbox', type='string', help="Specify target platform: defaults to rockbox; " +\ "in the future you will be able to use --target=native " +\ "to create playlists and links for use on the local machine.")
def __init__(self): CommandLineApp.__init__(self) op = self.option_parser op.set_usage('usage: parse_and_map -[npm] -i reads.fq -b barcodes --parent1 parent1_genome --parent2 parent2_genome') op.add_option('-i', '--raw-data', dest='raw_data_file', type='string', default=None, help='Raw Illumina data file') op.add_option('-b', '--barcodes', dest='barcodes_file', type='string', default=None, help='Barcodes file') op.add_option('--re_cutter', dest='re_cutter', type='string', default=None, help='restriction enzyme') op.add_option('--linker_system', dest='linker_system', type='string', default=None, help='linker system') op.add_option('--parent1', dest='parent1', type='string', default=None, help='Parent 1 genome file to align against') op.add_option('--parent2', dest='parent2', type='string', default=None, help='Parent 2 genome file to align against') op.add_option('-m', '--map-only', dest='map_only', default=False, action='store_true', help='Just map data?') op.add_option('-n', '--num-ind', dest='num_ind', default=None, type='int', help='Number of individuals to map') op.add_option('-p', '--parse-only', dest='parse_only', default=False, action='store_true', help='Just parse data?') op.add_option('--bwa_alg', dest='bwa_alg', type='string', default="aln", help='Algorithm for BWA mapping. Use aln or bwasw. This is ignored is use_stampy is 1.') op.add_option('--bwa_threads', dest='bwa_threads', type='int', default=1, help='Number of threads in the BWA multi-threading mode') op.add_option('--use_stampy', dest='use_stampy', type='int', default=0, help='Use stampy for mapping') op.add_option('--stampy_premap_w_bwa', dest='stampy_premap_w_bwa', type='int', default=1, help='Use BWA before running stampy for a speed boost.') op.add_option('--stampy_pseudo_threads', dest='stampy_pseudo_threads', type='int', default=0, help='Use qsub commands to split up stampy processes during mapping. NOT currently used.') op.add_option('--dbg', dest='debug', default=False, action='store_true', help='More verbose output and leaves temporary files instead of cleaning up') op.add_option('--quality_trim_reads_thresh', dest='quality_trim_reads_thresh', default=None, type='int', help='Illumina parsing only - what level should split files be quality trimmed at') op.add_option('--quality_trim_reads_consec', dest='quality_trim_reads_consec', default=None, type='int', help='Illumina parsing only - Minimum number of consecutive bases passing threshold values') #Set divergence for mapping to a foreign reference (note: this is #strongly recommended for divergences >3%, as it will automatically #shut down BWA pre-mapping which otherwise cause occasional segfaults) #(stampy default if .001) op.add_option('--indiv_stampy_substitution_rate', dest='stampy_substitution_rate', type='float', default=0.001, help='Set divergence for mapping to a foreign reference') op.add_option('--indiv_mapq_filter', dest='mapq_filter', type='int', default=0, help='Filter out poor alignments. Set this to 0 to skip.') op.add_option('--new_parser', dest='new_parser', type='int', default=0, help='Use a faster, experimental parser') op.add_option('--new_parser_offset', dest='new_parser_offset', type='int', default=0, help='When using new parser, how many base pairs after barcode to omit') op.add_option('--new_parser_filter_out_seq', dest='new_parser_filter_out_seq', type='string', default=None, help='A sequence to remove from parsed reads') #Illumina indexing only op.add_option('--index_file', dest='index_file', type='string', default=None, help='When using Illumina indexes, this is the fastq/fasta file with the indexes.') op.add_option('--index_barcodes', dest='index_barcodes', type='string', default=None, help='When using Illumina indexes, this the the file with a listing of index sequences and labels')
def __init__(self): CommandLineApp.__init__(self) op = self.option_parser op.set_usage( 'usage: parse_and_map -[npm] -i reads.fq -b barcodes --parent1 parent1_genome --parent2 parent2_genome' ) op.add_option('-i', '--raw-data', dest='raw_data_file', type='string', default=None, help='Raw Illumina data file') op.add_option('-b', '--barcodes', dest='barcodes_file', type='string', default=None, help='Barcodes file') op.add_option('--re_cutter', dest='re_cutter', type='string', default=None, help='restriction enzyme') op.add_option('--linker_system', dest='linker_system', type='string', default=None, help='linker system') op.add_option('--parent1', dest='parent1', type='string', default=None, help='Parent 1 genome file to align against') op.add_option('--parent2', dest='parent2', type='string', default=None, help='Parent 2 genome file to align against') op.add_option('-m', '--map-only', dest='map_only', default=False, action='store_true', help='Just map data?') op.add_option('-n', '--num-ind', dest='num_ind', default=None, type='int', help='Number of individuals to map') op.add_option('-p', '--parse-only', dest='parse_only', default=False, action='store_true', help='Just parse data?') op.add_option( '--bwa_alg', dest='bwa_alg', type='string', default='aln', help= 'Algorithm for BWA mapping. Use aln or bwasw. This is ignored is use_stampy is 1.' ) op.add_option('--bwa_threads', dest='bwa_threads', type='int', default=1, help='Number of threads in the BWA multi-threading mode') op.add_option('--use_stampy', dest='use_stampy', type='int', default=0, help='Use stampy for mapping') op.add_option('--stampy_premap_w_bwa', dest='stampy_premap_w_bwa', type='int', default=1, help='Use BWA before running stampy for a speed boost.') op.add_option( '--stampy_pseudo_threads', dest='stampy_pseudo_threads', type='int', default=0, help= 'Use qsub commands to split up stampy processes during mapping. NOT currently used.' ) op.add_option( '--dbg', dest='debug', default=False, action='store_true', help= 'More verbose output and leaves temporary files instead of cleaning up' ) op.add_option( '--quality_trim_reads_thresh', dest='quality_trim_reads_thresh', default=None, type='int', help= 'Illumina parsing only - what level should split files be quality trimmed at' ) op.add_option( '--quality_trim_reads_consec', dest='quality_trim_reads_consec', default=None, type='int', help= 'Illumina parsing only - Minimum number of consecutive bases passing threshold values' ) op.add_option( '-S', '--samtools_path', dest='samtools_path', default='samtools', type='string', help= 'Path to samtools 0.1.9 including the name of the binary at the end of the string' ) #Set divergence for mapping to a foreign reference (note: this is #strongly recommended for divergences >3%, as it will automatically #shut down BWA pre-mapping which otherwise cause occasional segfaults) #(stampy default if .001) op.add_option('--indiv_stampy_substitution_rate', dest='stampy_substitution_rate', type='float', default=0.001, help='Set divergence for mapping to a foreign reference') op.add_option( '--indiv_mapq_filter', dest='mapq_filter', type='int', default=0, help='Filter out poor alignments. Set this to 0 to skip.') op.add_option('--new_parser', dest='new_parser', type='int', default=0, help='Use a faster, experimental parser') op.add_option( '--new_parser_offset', dest='new_parser_offset', type='int', default=0, help= 'When using new parser, how many base pairs after barcode to omit') op.add_option('--new_parser_filter_out_seq', dest='new_parser_filter_out_seq', type='string', default=None, help='A sequence to remove from parsed reads') #Illumina indexing only op.add_option( '--index_file', dest='index_file', type='string', default=None, help= 'When using Illumina indexes, this is the fastq/fasta file with the indexes.' ) op.add_option( '--index_barcodes', dest='index_barcodes', type='string', default=None, help= 'When using Illumina indexes, this the the file with a listing of index sequences and labels' )