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|
#!/usr/bin/env python
import os.path
import sys
import argparse
#logger
import logging
logger = logging.getLogger('poretools')
# poretools imports
import poretools.version
def run_subtool(parser, args):
if args.command == 'combine':
from . import combine as submodule
elif args.command == 'events':
from . import events as submodule
elif args.command == 'fasta':
from . import fasta as submodule
elif args.command == 'fastq':
from . import fastq as submodule
elif args.command == 'hist':
from . import hist as submodule
elif args.command == 'metadata':
from . import metadata as submodule
elif args.command == 'nucdist':
from . import nucdist as submodule
elif args.command == 'occupancy':
from . import occupancy as submodule
elif args.command == 'qualdist':
from . import qualdist as submodule
elif args.command == 'qualpos':
from . import qual_v_pos as submodule
elif args.command == 'readstats':
from . import readstats as submodule
elif args.command == 'stats':
from . import stats as submodule
elif args.command == 'tabular':
from . import tabular as submodule
elif args.command == 'times':
from . import times as submodule
elif args.command == 'squiggle':
from . import squiggle as submodule
elif args.command == 'winner':
from . import winner as submodule
elif args.command == 'yield_plot':
from . import yield_plot as submodule
elif args.command == 'index':
from . import index as submodule
elif args.command == 'organise':
from . import organise as submodule
# run the chosen submodule.
submodule.run(parser, args)
class ArgumentParserWithDefaults(argparse.ArgumentParser):
def __init__(self, *args, **kwargs):
super(ArgumentParserWithDefaults, self).__init__(*args, **kwargs)
self.add_argument("-q", "--quiet", help="Do not output warnings to stderr",
action="store_true",
dest="quiet")
def main():
logging.basicConfig()
#########################################
# create the top-level parser
#########################################
parser = argparse.ArgumentParser(prog='poretools', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("-v", "--version", help="Installed poretools version",
action="version",
version="%(prog)s " + str(poretools.version.__version__))
subparsers = parser.add_subparsers(title='[sub-commands]', dest='command', parser_class=ArgumentParserWithDefaults)
#########################################
# create the individual tool parsers
#########################################
##########
# combine
##########
parser_combine = subparsers.add_parser('combine',
help='Combine a set of FAST5 files in a TAR achive')
parser_combine.add_argument('files', metavar='FILES', nargs='+',
help='The input FAST5 files.')
parser_combine.add_argument('-o',
dest='tar_filename',
metavar='STRING',
required=True,
help='The name of the output TAR archive for the set of FAST5 files.')
parser_combine.set_defaults(func=run_subtool)
##########
# FASTQ
##########
parser_fastq = subparsers.add_parser('fastq',
help='Extract FASTQ sequences from a set of FAST5 files')
parser_fastq.add_argument('files', metavar='FILES', nargs='+',
help='The input FAST5 files.')
parser_fastq.add_argument('--type',
dest='type',
metavar='STRING',
choices=['all', 'fwd', 'rev', '2D', 'fwd,rev', 'best'],
default='all',
help='Which type of FASTQ entries should be reported? Def.=all')
parser_fastq.add_argument('--start',
dest='start_time',
default=None,
type=int,
help='Only report reads from after start timestamp')
parser_fastq.add_argument('--end',
dest='end_time',
default=None,
type=int,
help='Only report reads from before end timestamp')
parser_fastq.add_argument('--min-length',
dest='min_length',
default=0,
type=int,
help=('Minimum read length for FASTQ entry to be reported.'))
parser_fastq.add_argument('--max-length',
dest='max_length',
default=-1,
type=int,
help=('Maximum read length for FASTQ entry to be reported.'))
parser_fastq.add_argument('--high-quality',
dest='high_quality',
default=False,
action='store_true',
help=('Only report reads with more complement events than template.'))
parser_fastq.add_argument('--normal-quality',
dest='normal_quality',
default=False,
action='store_true',
help=('Only report reads with fewer complement events than template.'))
parser_fastq.add_argument('--group',
dest='group',
default=0,
type=int,
help=('Base calling group serial number to extract, default 000'))
parser_fastq.set_defaults(func=run_subtool)
##########
# FASTA
##########
parser_fasta = subparsers.add_parser('fasta',
help='Extract FASTA sequences from a set of FAST5 files')
parser_fasta.add_argument('files', metavar='FILES', nargs='+',
help='The input FAST5 files.')
parser_fasta.add_argument('--type',
dest='type',
metavar='STRING',
choices=['all', 'fwd', 'rev', '2D', 'fwd,rev', 'best'],
default='all',
help='Which type of FASTQ entries should be reported? Def.=all')
parser_fasta.add_argument('--start',
dest='start_time',
default=None,
type=int,
help='Only report reads from after start timestamp')
parser_fasta.add_argument('--end',
dest='end_time',
default=None,
type=int,
help='Only report reads from before end timestamp')
parser_fasta.add_argument('--min-length',
dest='min_length',
default=0,
type=int,
help=('Minimum read length for FASTA entry to be reported.'))
parser_fasta.add_argument('--max-length',
dest='max_length',
default=-1,
type=int,
help=('Maximum read length for FASTA entry to be reported.'))
parser_fasta.add_argument('--high-quality',
dest='high_quality',
default=False,
action='store_true',
help=('Only report reads with more complement events than template.'))
parser_fasta.add_argument('--normal-quality',
dest='normal_quality',
default=False,
action='store_true',
help=('Only report reads with fewer complement events than template.'))
parser_fasta.add_argument('--group',
dest='group',
default=0,
type=int,
help=('Base calling group serial number to extract, default 000'))
parser_fasta.set_defaults(func=run_subtool)
##########
# stats
##########
parser_stats = subparsers.add_parser('stats',
help='Get read size stats for a set of FAST5 files')
parser_stats.add_argument('files', metavar='FILES', nargs='+',
help='The input FAST5 files.')
parser_stats.add_argument('--type',
dest='type',
metavar='STRING',
choices=['all', 'fwd', 'rev', '2D', 'fwd,rev', 'best'],
default='all',
help='Which type of FASTQ entries should be reported? Def.=all')
parser_stats.add_argument('--full-tsv',
dest='full_tsv',
default=False,
action='store_true',
help=('Verbose output in tab-separated format.'))
parser_stats.set_defaults(func=run_subtool)
##########
# hist
##########
parser_hist = subparsers.add_parser('hist',
help='Plot read size histogram for a set of FAST5 files')
parser_hist.add_argument('files', metavar='FILES', nargs='+',
help='The input FAST5 files.')
parser_hist.add_argument('--min-length',
dest='min_length',
default=0,
type=int,
help=('Minimum read length to be included in histogram.'))
parser_hist.add_argument('--max-length',
dest='max_length',
default=1000000000,
type=int,
help=('Maximum read length to be included in histogram.'))
parser_hist.add_argument('--num-bins',
dest='num_bins',
default=50,
type=int,
help=('The number of histogram bins.'))
parser_hist.add_argument('--saveas',
dest='saveas',
metavar='STRING',
help='Save the plot to a file.',
default=None)
parser_hist.add_argument('--theme-bw',
dest='theme_bw',
default=False,
action='store_true',
help="Use a black and white theme.")
parser_hist.add_argument('--watch',
dest='watch',
default=False,
action='store_true',
help="Monitor a directory.")
parser_hist.set_defaults(func=run_subtool)
###########
# events
###########
parser_events = subparsers.add_parser('events',
help='Extract each nanopore event for each read.')
parser_events.add_argument('files', metavar='FILES', nargs='+',
help='The input FAST5 files.')
parser_events.add_argument('--pre-basecalled',
dest='pre_basecalled',
default=False,
action='store_true',
help=('Report pre-basecalled events'))
parser_events.set_defaults(func=run_subtool)
###########
# readstats
###########
parser_readstats = subparsers.add_parser('readstats',
help='Extract signal information for each read over time.')
parser_readstats.add_argument('files', metavar='FILES', nargs='+',
help='The input FAST5 files.')
parser_readstats.set_defaults(func=run_subtool)
##########
# tabular
##########
parser_tabular = subparsers.add_parser('tabular',
help='Extract the lengths and name/seq/quals from a set of FAST5 files in TAB delimited format')
parser_tabular.add_argument('files', metavar='FILES', nargs='+',
help='The input FAST5 files.')
parser_tabular.add_argument('--type',
dest='type',
metavar='STRING',
choices=['all', 'fwd', 'rev', '2D', 'fwd,rev', 'best'],
default='all',
help='Which type of FASTA entries should be reported? Def.=all')
parser_tabular.set_defaults(func=run_subtool)
#########
# nucdist
#########
parser_nucdist = subparsers.add_parser('nucdist',
help='Get the nucl. composition of a set of FAST5 files')
parser_nucdist.add_argument('files', metavar='FILES', nargs='+',
help='The input FAST5 files.')
parser_nucdist.set_defaults(func=run_subtool)
#########
# metadata
#########
parser_metadata = subparsers.add_parser('metadata',
help='Return run metadata such as ASIC ID and temperature from a set of FAST5 files')
parser_metadata.add_argument('files', metavar='FILES', nargs='+',
help='The input FAST5 files.')
parser_metadata.add_argument('--read',
dest='read',
default=False,
action='store_true',
help=('Report read level metadata'))
parser_metadata.set_defaults(func=run_subtool)
#########
# index
#########
parser_index = subparsers.add_parser('index',
help='Tabulate all file location info and metadata such as ASIC ID and temperature from a set of FAST5 files')
parser_index.add_argument('files', metavar='FILES', nargs='+',
help='The input FAST5 files.')
parser_index.set_defaults(func=run_subtool)
##########
# qualdist
##########
parser_qualdist = subparsers.add_parser('qualdist',
help='Get the qual score composition of a set of FAST5 files')
parser_qualdist.add_argument('files', metavar='FILES', nargs='+',
help='The input FAST5 files.')
parser_qualdist.set_defaults(func=run_subtool)
##########
# qual vs. position
##########
parser_qualpos = subparsers.add_parser('qualpos',
help='Get the qual score distribution over positions in reads')
parser_qualpos.add_argument('files', metavar='FILES', nargs='+',
help='The input FAST5 files.')
parser_qualpos.set_defaults(func=run_subtool)
parser_qualpos.add_argument('--min-length',
dest='min_length',
default=0,
type=int,
help=('Minimum read length to be included in analysis.'))
parser_qualpos.add_argument('--max-length',
dest='max_length',
default=1000000000,
type=int,
help=('Maximum read length to be included in analysis.'))
parser_qualpos.add_argument('--bin-width',
dest='bin_width',
default=1000,
type=int,
help=('The width of bins (default: 1000 bp).'))
parser_qualpos.add_argument('--type',
dest='type',
metavar='STRING',
choices=['all', 'fwd', 'rev', '2D', 'fwd,rev', 'best'],
default='all',
help='Which type of reads should be analyzed? Def.=all, choices=[all, fwd, rev, 2D, fwd,rev, best]')
parser_qualpos.add_argument('--start',
dest='start_time',
default=None,
type=int,
help='Only analyze reads from after start timestamp')
parser_qualpos.add_argument('--end',
dest='end_time',
default=None,
type=int,
help='Only analyze reads from before end timestamp')
parser_qualpos.add_argument('--high-quality',
dest='high_quality',
default=False,
action='store_true',
help='Only analyze reads with more complement events than template.')
parser_qualpos.add_argument('--saveas',
dest='saveas',
metavar='STRING',
help='''Save the plot to a file named filename.extension (e.g. pdf, jpg)''',
default=None)
##########
# winner
##########
parser_winner = subparsers.add_parser('winner',
help='Get the longest read from a set of FAST5 files')
parser_winner.add_argument('files', metavar='FILES', nargs='+',
help='The input FAST5 files.')
parser_winner.add_argument('--type',
dest='type',
metavar='STRING',
choices=['all', 'fwd', 'rev', '2D', 'fwd,rev', 'best'],
default='all',
help='Which type of FASTA entries should be reported? Def.=all')
parser_winner.set_defaults(func=run_subtool)
###########
# squiggle
###########
parser_squiggle = subparsers.add_parser('squiggle',
help='Plot the observed signals for FAST5 reads.')
parser_squiggle.add_argument('files', metavar='FILES', nargs='+',
help='The input FAST5 files.')
parser_squiggle.add_argument('--saveas',
dest='saveas',
metavar='STRING',
choices=['pdf', 'png'],
help='Save the squiggle plot to a file.',
default=None)
parser_squiggle.add_argument('--num-facets',
dest='num_facets',
metavar='INTEGER',
default=6,
type=int,
help=('The number of plot facets (sub-plots). More is better for long reads. (def=6)'))
parser_squiggle.add_argument('--theme-bw',
dest='theme_bw',
default=False,
action='store_true',
help="Use a black and white theme.")
parser_squiggle.set_defaults(func=run_subtool)
##########
# times
##########
parser_times = subparsers.add_parser('times',
help='Return the start times from a set of FAST5 files in tabular format')
parser_times.add_argument('files', metavar='FILES', nargs='+',
help='The input FAST5 files.')
parser_times.set_defaults(func=run_subtool)
############
# yield_plot
############
parser_yield_plot = subparsers.add_parser('yield_plot',
help='Plot the yield over time for a set of FAST5 files')
parser_yield_plot.add_argument('files', metavar='FILES', nargs='+',
help='The input FAST5 files.')
parser_yield_plot.add_argument('--saveas',
dest='saveas',
metavar='STRING',
help='Save the plot to a file. Extension (.pdf or .png) drives type.',
default=None)
parser_yield_plot.add_argument('--plot-type',
dest='plot_type',
metavar='STRING',
choices=['reads', 'basepairs'],
help='Save the wiggle plot to a file (def=reads).',
default='reads')
parser_yield_plot.add_argument('--theme-bw',
dest='theme_bw',
default=False,
action='store_true',
help="Use a black and white theme.")
parser_yield_plot.add_argument('--skip',
dest='skip',
metavar='INTEGER',
type=int,
default=1,
help="Only plot every n points to reduce size")
parser_yield_plot.add_argument('--savedf',
dest='savedf',
metavar='STRING',
help='Save the data frame used to construct plot to a file.',
default=None)
parser_yield_plot.set_defaults(func=run_subtool)
############
# yield_plot
############
parser_occupancy = subparsers.add_parser('occupancy',
help='Inspect pore activity over time for a set of FAST5 files')
parser_occupancy.add_argument('files', metavar='FILES', nargs='+',
help='The input FAST5 files.')
parser_occupancy.add_argument('--saveas',
dest='saveas',
metavar='STRING',
help='Save the plot to a file. Extension (.pdf or .png) drives type.',
default=None)
parser_occupancy.add_argument('--plot-type',
dest='plot_type',
metavar='STRING',
choices=['read_count', 'total_bp'],
help='The type of plot to generate',
default='read_count')
parser_occupancy.set_defaults(func=run_subtool)
##########
# organise
##########
parser_organise = subparsers.add_parser('organise',
help='Move FAST5 files into a useful folder hierarchy')
parser_organise.add_argument('files', metavar='FILES', nargs='+',
help='The input FAST5 files.')
parser_organise.add_argument('dest',
metavar='STRING',
help='The destination directory.')
parser_organise.add_argument('--copy',
default=False,
action='store_true',
dest='copy',
help='Make a copy of files instead of moving')
parser_organise.set_defaults(func=run_subtool)
#######################################################
# parse the args and call the selected function
#######################################################
args = parser.parse_args()
if not args.command:
parser.print_help()
sys.exit(0)
if args.quiet:
logger.setLevel(logging.ERROR)
try:
args.func(parser, args)
except IOError as e:
if e.errno != 32: # ignore SIGPIPE
raise
if __name__ == "__main__":
main()
|
