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refactoring argument handling to utils submodule
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,122 @@ | ||
| import textwrap as _textwrap | ||
| from argparse import ArgumentParser, ArgumentTypeError, HelpFormatter | ||
| from nanofilt.version import __version__ | ||
| import sys | ||
| import logging | ||
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| def get_args(): | ||
| epilog = "EXAMPLES:\n" \ | ||
| " gunzip -c reads.fastq.gz | NanoFilt -q 10 -l 500 --headcrop 50 | " \ | ||
| "minimap2 genome.fa - | samtools sort -O BAM -@24 -o alignment.bam -\n" \ | ||
| " gunzip -c reads.fastq.gz | NanoFilt -q 12 --headcrop 75 | " \ | ||
| "gzip > trimmed-reads.fastq.gz\n" \ | ||
| " gunzip -c reads.fastq.gz | NanoFilt -q 10 | gzip > highQuality-reads.fastq.gz\n" | ||
| parser = ArgumentParser( | ||
| description="Perform quality and/or length and/or GC filtering of (long read) fastq data. \ | ||
| Reads on stdin.", | ||
| epilog=epilog, | ||
| formatter_class=custom_formatter, | ||
| add_help=False) | ||
| general = parser.add_argument_group( | ||
| title='General options') | ||
| general.add_argument("-h", "--help", | ||
| action="help", | ||
| help="show the help and exit") | ||
| general.add_argument("-v", "--version", | ||
| help="Print version and exit.", | ||
| action="version", | ||
| version='NanoFilt {}'.format(__version__)) | ||
| general.add_argument("--logfile", | ||
| help="Specify the path and filename for the log file.", | ||
| default="NanoFilt.log") | ||
| general.add_argument("input", | ||
| help="input, uncompressed fastq file", | ||
| default=sys.stdin, | ||
| nargs='?') | ||
| filtering = parser.add_argument_group( | ||
| title='Options for filtering reads on.') | ||
| filtering.add_argument("-l", "--length", | ||
| help="Filter on a minimum read length", | ||
| default=1, | ||
| type=int) | ||
| filtering.add_argument("--maxlength", | ||
| help="Filter on a maximum read length", | ||
| default=1e12, | ||
| type=int) | ||
| filtering.add_argument("-q", "--quality", | ||
| help="Filter on a minimum average read quality score", | ||
| default=0, | ||
| type=int) | ||
| filtering.add_argument("--minGC", | ||
| help="Sequences must have GC content >= to this. Float between 0.0 and 1.0. \ | ||
| Ignored if using summary file.", | ||
| default=0.0, | ||
| type=valid_GC) | ||
| filtering.add_argument("--maxGC", | ||
| help="Sequences must have GC content <= to this. Float between 0.0 and 1.0. \ | ||
| Ignored if using summary file.", | ||
| default=1.0, | ||
| type=valid_GC) | ||
| trimming = parser.add_argument_group( | ||
| title='Options for trimming reads.') | ||
| trimming.add_argument("--headcrop", | ||
| help="Trim n nucleotides from start of read", | ||
| default=None, | ||
| type=int) | ||
| trimming.add_argument("--tailcrop", | ||
| help="Trim n nucleotides from end of read", | ||
| default=None, | ||
| type=int) | ||
| inputoptions = parser.add_argument_group( | ||
| title='Input options.') | ||
| inputoptions.add_argument("-s", "--summary", | ||
| help="Use albacore or guppy summary file for quality scores") | ||
| inputoptions.add_argument("--readtype", | ||
| help="Which read type to extract information about from summary. \ | ||
| Options are 1D, 2D or 1D2", | ||
| default="1D", | ||
| choices=['1D', '2D', "1D2"]) | ||
| args = parser.parse_args() | ||
| if args.minGC > args.maxGC: | ||
| sys.exit("NanoFilt: error: argument --minGC should be smaller than --maxGC") | ||
| if args.minGC == 0.0 and args.maxGC == 1.0: | ||
| args.GC_filter = False | ||
| else: | ||
| args.GC_filter = True | ||
| logging.info('NanoFilt {} started with arguments {}'.format(__version__, args)) | ||
| return args | ||
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| class CustomHelpFormatter(HelpFormatter): | ||
| def _fill_text(self, text, width, indent): | ||
| return ''.join(indent + line for line in text.splitlines(keepends=True)) | ||
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| def _split_lines(self, text, width): | ||
| text = self._whitespace_matcher.sub(' ', text).strip() | ||
| return _textwrap.wrap(text, 80) | ||
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| def custom_formatter(prog): | ||
| return CustomHelpFormatter(prog) | ||
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| def valid_GC(x): | ||
| """type function for argparse to check GC values. | ||
| Check if the supplied value for minGC and maxGC is a valid input, being between 0 and 1 | ||
| """ | ||
| x = float(x) | ||
| if x < 0.0 or x > 1.0: | ||
| raise ArgumentTypeError("{} not in range [0.0, 1.0]".format(x)) | ||
| return x | ||
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| def start_logging(logfile): | ||
| try: | ||
| logging.basicConfig( | ||
| format='%(asctime)s %(message)s', | ||
| filename=logfile, | ||
| level=logging.INFO) | ||
| except PermissionError: | ||
| pass # indicates that user has no write permission in this directory. No logs then |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| __version__ = "2.5.0" | ||
| __version__ = "2.6.0" |