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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,37 +1,69 @@ | ||
| #!/opt/common/CentOS_6-dev/python/python-2.7.10/bin/python | ||
|
|
||
| import argparse, os, sys, re, subprocess, itertools, glob | ||
| from operator import attrgetter | ||
| import textwrap as _textwrap | ||
| import cmo | ||
|
|
||
| # Custom help formatter to display args in alphabetical order, and fitted line wrap for sphinx | ||
| class SortingHelpFormatter(argparse.ArgumentDefaultsHelpFormatter): | ||
| def add_arguments(self, actions): | ||
| actions = sorted(actions, key=attrgetter('option_strings')) | ||
| super(SortingHelpFormatter, self).add_arguments(actions) | ||
| def _split_lines(self, text, width): | ||
| text = self._whitespace_matcher.sub(' ', text).strip() | ||
| return _textwrap.wrap(text, 78) | ||
|
|
||
| # Function that runs --help on the tool we've wrapped, and extracts documentation | ||
| def parse_script_help(script_path): | ||
| perl = cmo.util.programs['perl']['default'] | ||
| help_text = subprocess.Popen(" ".join([perl, script_path, "-h"]),stdout=subprocess.PIPE,shell=True).communicate()[0] | ||
| valid_args = re.findall(r"\s+(--[\S_]+)\s+([\S \t]+)\n?", help_text, re.M) | ||
| return dict(valid_args) | ||
| help_text = subprocess.Popen(" ".join([perl, script_path, "-h"]), stdout=subprocess.PIPE, shell=True).communicate()[0] | ||
| valid_args = re.findall(r"^\s*(--\S+)\s+([^\[\n]+)", help_text, re.M) | ||
| defaults = re.findall(r"^\s*(--\S+)\s+[\S ]+\[([\S ]+)\]$", help_text, re.M) | ||
| return dict(valid_args), dict(defaults) | ||
|
|
||
| if __name__ =='__main__': | ||
| # We'll first need to figure out which version to run with "-h" to parse the help text | ||
| preparser = argparse.ArgumentParser(description="run maf2vcf", add_help=False) | ||
| preparser.add_argument("--version", choices=cmo.util.programs['vcf2maf'].keys(), default="default") | ||
| preparser = argparse.ArgumentParser(description="Run maf2vcf", add_help=False, formatter_class=SortingHelpFormatter) | ||
| preparser.add_argument("--version", help="Version of tool to run", choices=cmo.util.programs['vcf2maf'].keys(), default="default") | ||
| preparser.add_argument("--ncbi-build", help="Genome build of variants in input", choices=["GRCh37","GRCh38","GRCm38"], default="GRCh37") | ||
| options, _ = preparser.parse_known_args() | ||
|
|
||
| # Figure out the path to the actual Perl script that this Python wrapper will run | ||
| script_path = cmo.util.programs['vcf2maf'][options.version] + "maf2vcf.pl" | ||
| args_dict = parse_script_help(script_path) | ||
| parser = argparse.ArgumentParser(parents = [preparser], add_help=True) | ||
| # Extract arguments and their defaults, by parsing the --help output | ||
| args_dict, defaults_dict = parse_script_help(script_path) | ||
|
|
||
| # With arguments and defaults set, let's construct an argparse instance | ||
| parser = argparse.ArgumentParser(parents = [preparser], add_help=True, formatter_class=SortingHelpFormatter) | ||
| for arg, description in args_dict.items(): | ||
| if arg == "--help": | ||
| # Hide a few arguments from the user, because we'll determine them ourselves | ||
| if arg in ["--help","--man","--ref-fasta"]: | ||
| continue | ||
| parser.add_argument(arg,action="store", metavar='', help=description) | ||
| cmo.util.add_logging_options(parser) | ||
| if arg in defaults_dict and arg not in ["--output-maf"]: | ||
| parser.add_argument(arg, action="store", metavar='', help=description, default=defaults_dict[arg]) | ||
| else: | ||
| parser.add_argument(arg, action="store", metavar='', help=description) | ||
|
|
||
| # Now run the argparse instance, which will parse and execute, or print help text if requested | ||
| args = parser.parse_args() | ||
| args_dict = vars(args) | ||
|
|
||
| # Locate the reference for this genome build | ||
| args_dict['ref_fasta'] = cmo.util.genomes[args.ncbi_build]['fasta'] | ||
|
|
||
| # Remove arguments that the actual wrapped tool won't recognize | ||
| for key in ["version"]: | ||
| del args_dict[key] | ||
|
|
||
| # Build the command we're going to run | ||
| cmd = [cmo.util.programs['perl']['default'], script_path] | ||
| stderr = args.stderr | ||
| stdout = args.stdout | ||
| # Trim out arguments without values | ||
| args_dict = dict((k, v) for k, v in args_dict.iteritems() if v) | ||
| cmo.util.remove_logging_options_from_dict(args_dict) | ||
|
|
||
| # Make sure the arguments are in a format that the script will accept, and kick it off | ||
| for arg, value in args_dict.items(): | ||
| arg = arg.replace("_","-") | ||
| cmd = cmd + ["--"+arg, value] | ||
| cmo.util.call_cmd(" ".join(cmd), stdout=stdout, stderr=stderr) | ||
| sys.stderr.write( "RUNNING: " + " ".join( cmd ) + "\n" ) | ||
| cmo.util.call_cmd( " ".join( cmd )) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| #!/opt/common/CentOS_6-dev/python/python-2.7.10/bin/python | ||
|
|
||
| import argparse, os, sys, re, subprocess, itertools, glob | ||
| from operator import attrgetter | ||
| import textwrap as _textwrap | ||
| import cmo | ||
|
|
||
| # Custom help formatter to display args in alphabetical order, and fitted line wrap for sphinx | ||
| class SortingHelpFormatter(argparse.ArgumentDefaultsHelpFormatter): | ||
| def add_arguments(self, actions): | ||
| actions = sorted(actions, key=attrgetter('option_strings')) | ||
| super(SortingHelpFormatter, self).add_arguments(actions) | ||
| def _split_lines(self, text, width): | ||
| text = self._whitespace_matcher.sub(' ', text).strip() | ||
| return _textwrap.wrap(text, 78) | ||
|
|
||
| # Function that runs --help on the tool we've wrapped, and extracts documentation | ||
| def parse_script_help(script_path): | ||
| perl = cmo.util.programs['perl']['default'] | ||
| help_text = subprocess.Popen(" ".join([perl, script_path, "-h"]), stdout=subprocess.PIPE, shell=True).communicate()[0] | ||
| valid_args = re.findall(r"^\s*(--\S+)\s+([^\[\n]+)", help_text, re.M) | ||
| defaults = re.findall(r"^\s*(--\S+)\s+[\S ]+\[([\S ]+)\]$", help_text, re.M) | ||
| return dict(valid_args), dict(defaults) | ||
|
|
||
| if __name__ =='__main__': | ||
| # We'll first need to figure out which version to run with "-h" to parse the help text | ||
| preparser = argparse.ArgumentParser(description="Run vcf2vcf", add_help=False, formatter_class=SortingHelpFormatter) | ||
| preparser.add_argument("--version", help="Version of tool to run", choices=cmo.util.programs['vcf2maf'].keys(), default="default") | ||
| preparser.add_argument("--ncbi-build", help="Genome build of variants in input", choices=["GRCh37","GRCh38","GRCm38"], default="GRCh37") | ||
| options, _ = preparser.parse_known_args() | ||
|
|
||
| # Figure out the path to the actual Perl script that this Python wrapper will run | ||
| script_path = cmo.util.programs['vcf2maf'][options.version] + "vcf2vcf.pl" | ||
| # Extract arguments and their defaults, by parsing the --help output | ||
| args_dict, defaults_dict = parse_script_help(script_path) | ||
|
|
||
| # With arguments and defaults set, let's construct an argparse instance | ||
| parser = argparse.ArgumentParser(parents = [preparser], add_help=True, formatter_class=SortingHelpFormatter) | ||
| for arg, description in args_dict.items(): | ||
| # Hide a few arguments from the user, because we'll determine them ourselves | ||
| if arg in ["--help","--man","--ref-fasta"]: | ||
| continue | ||
| if arg in defaults_dict and arg not in ["--output-maf"]: | ||
| parser.add_argument(arg, action="store", metavar='', help=description, default=defaults_dict[arg]) | ||
| else: | ||
| parser.add_argument(arg, action="store", metavar='', help=description) | ||
|
|
||
| # Now run the argparse instance, which will parse and execute, or print help text if requested | ||
| args = parser.parse_args() | ||
| args_dict = vars(args) | ||
|
|
||
| # Locate the reference for this genome build | ||
| args_dict['ref_fasta'] = cmo.util.genomes[args.ncbi_build]['fasta'] | ||
|
|
||
| # Remove arguments that the actual wrapped tool won't recognize | ||
| for key in ["version"]: | ||
| del args_dict[key] | ||
|
|
||
| # Build the command we're going to run | ||
| cmd = [cmo.util.programs['perl']['default'], script_path] | ||
| # Trim out arguments without values | ||
| args_dict = dict((k, v) for k, v in args_dict.iteritems() if v) | ||
|
|
||
| # Make sure the arguments are in a format that the script will accept, and kick it off | ||
| for arg, value in args_dict.items(): | ||
| arg = arg.replace("_","-") | ||
| cmd = cmd + ["--"+arg, value] | ||
| sys.stderr.write( "RUNNING: " + " ".join( cmd ) + "\n" ) | ||
| cmo.util.call_cmd( " ".join( cmd )) |