def get_settings():
parser = VerboseParser();
build_help = "Genome build to download tables from. This uses UCSC's " +\
"naming convention, i.e. hg17, hg18, etc. Defaults to the latest human genome build.";
parser.add_option("--build",dest="build",help=build_help);
opts,args = parser.parse_args();
# Check build convention.
if opts.build != None and opts.build[0:2] != 'hg':
print >> sys.stderr, "Error: build must look like \'hg19\', \'hg18\', etc."
sys.exit(1);
return (opts,args);
def getCmdLine(self):
parser = VerboseParser();
# Remember: default action is store, default type is string.
snp_help = "Lookup information for a list of SNPs - these must be separated by commas, surrounded by quotes (whitespace ignored.)\n\n" +\
"Examples:\n" +\
"-s \"rs1002227, rs35712349\"\n" +\
"-s \" rs1002227, rs35712349\"\n" +\
"-s \" rs1002227,rs35712349 \"\n" +\
"-s \"rs1002227,rs35712349\"";
parser.add_option("-s","--snp",dest="snp",help=snp_help);
parser.add_option("-g","--gene",dest="gene",help="Lookup information for a list of gene symbols - these must be separated by commas, surrounded by quotes (whitespace ignored)");
snpfile_help = "Provide a list of SNPs to lookup from a file. The file may have *ANY* format. \
The program will pattern match rs### identifiers from your file.";
parser.add_option("--snpfile",dest="snpfile",help=snpfile_help);
genefile_help = "Provide a list of gene symbols in a file. This option unfortunately is not as lenient as --snpfile: you must put \
each gene symbol on a separate line in the file.";
parser.add_option("--genefile",dest="genefile",help=genefile_help);
regions_help = "Provide a list of chromosomal regions. Genes and other "\
"elements inside these regions will be returned.\n"\
"Example:\n"\
" --regions \"chr4:19141-939393,chrX:9191-939393\"";
parser.add_option("-r","--regions",help=regions_help);
build_help = ("Human genome build to use for SNP positions and genes. "
"Snipper ships with hg19 by default. You can download "
"pre-built databases from our website, or build them "
"yourself using the bin/setup_snipper.py script.");
parser.add_option("-b","--build",dest="build",help=build_help);
dist_help = "Distance away from SNP to search, default is " + str(self.distance) + ". " +\
"If a distance is specified, the program will return *ALL* genes within the distance you specify, not just the default of 1. " +\
"To specify a new distance, but still only return 1 gene (or arbitrary number of genes), use -n <number>. " +\
"Distances can be specified using a kb or mb suffix, or as a raw distance. Examples: 500kb, 0.5MB, 1.4MB, 834141.";
parser.add_option("-d",dest="distance",help=dist_help,type="string");
parser.add_option("-n",dest="num_genes",help="Number of genes to return per SNP, default is " + str(self.num_genes),type="int");
terms_help = "Comma-delimited string of terms, enclosed in quotes, to use in searching the literature. \
This will execute a search, per gene, for any of the search terms. For example:\n\
\n\
Genes: RB1, TCF7L2\n\
Search terms: \"glucose,retinoblastoma\"\n\
What happens: \n\
-- Search literature for RB1 AND (glucose OR retinoblastoma)\n\
-- Search literature for TCF7L2 AND (glucose OR retinoblastoma)";
parser.add_option("--terms",dest="terms",help=terms_help);
parser.add_option("--no-generif",dest="gene_rif",action="store_true",default=False,help="Disable GeneRIFs.");
parser.add_option("--no-scandb",dest="no_scandb",action="store_true",default=False,help="Disable use of ScanDB for eQTL information. Enabled by default.");
parser.add_option("--scandb-pval",dest="scandb_pval",default=self.scandb_pval,help="P-value threshold for ScanDB eQTLs.");
parser.add_option("--no-mimi",dest="mimi",action="store_true",default=False,help="Disable querying of MiMI database for interactions between genes near SNPs.");
parser.add_option("--no-omim",dest="omim",action="store_true",default=False,help="Disable display and search of OMIM text.");
parser.add_option("--no-pubmed",dest="pubmed",action="store_true",default=False,help="Disable searching PubMed.");
parser.add_option("--papernum",dest="pnum",type="int",default=self.pnum,help="Number of papers to display, default is " + str(self.pnum));
each_term_help = "When specified, the program will search each gene x searchterm pair, instead of lumping together search terms. \
For example:\n\
\n\
Genes: RB1, TCF7L2\n\
Search terms: \"glucose,retinoblastoma\"\n\
What happens:\n\
-- Search literature for RB1 AND glucose\n\
-- Search literature for RB1 AND retinoblastoma\n\
-- Search literature for TCF7L2 AND glucose\n\
-- Search literature for TCF7L2 AND retinoblastoma\n\
\n\
This is a much more in-depth search, at the cost of running time - NCIBI limits to 1 query / 3 seconds. \
If you have a very large set of genes and search terms, this can take a VERY long time to run!";
parser.add_option("--each-term",dest="per_term",default=False,action="store_true",help=each_term_help);
parser.add_option("--all",dest="all",action="store_true",default=True,help=SUPPRESS_HELP);
parser.add_option("-o","--out",dest="outdir",default=self.outdir,help="Directory to use for storing output. This should be a directory that does not exist yet.");
parser.add_option("--console",dest="console",action="store_true",default=self.console,help="Write results to console, instead of creating directory with HTML/text results.");
parser.add_option("--debug",dest="debug",action="store_true",default=False,help=SUPPRESS_HELP);
# Parse args.
(options,args) = parser.parse_args();
# Was debug enabled?
if options.debug:
__builtin__._SNIPPER_DEBUG = True;
else:
__builtin__._SNIPPER_DEBUG = False;
# If there are positional arguments, there was an error on the command line.
# Let them know the potential problem.
if len(args) > 0:
print >> sys.stderr, "Error: positional arguments detected: " + str(args);
print >> sys.stderr, "Most likely, you simply forgot to surround the entire argument in quotes."
print >> sys.stderr, "Example: -g \"RB1, TCF7L2\" is correct, whereas -g \"RB1\" \"TCF7L2\" is wrong."
sys.exit(1);
# Console mode?
self.console = options.console;
# Human genome build.
if options.build:
self.build = options.build;
# Get genes from command line (and file, if specified.)
if options.gene != None:
self.genes = set([i.upper() for i in parseTerms(options.gene)]);
if options.genefile != None:
self.genes.update(parseGeneFile(options.genefile));
# Get the set of SNPs.
if options.snp != None:
self.snpset = set(parseTerms(options.snp));
if options.snpfile != None:
self.snpset.update(parseSNPFile(options.snpfile));
# Get regions.
if options.regions != None:
self.regions = parseRegions(options.regions);
# Get list of search terms.
if options.terms != None:
self.terms = parseTerms(options.terms);
# HACK: If distance is specified, but num_genes is not,
# then we want to search for all genes in that distance space.
# Set num_genes to a really really big number. :)
if options.distance != None:
options.distance = convertFlank(options.distance);
if options.num_genes != None:
self.distance = options.distance;
self.num_genes = options.num_genes;
else:
self.distance = options.distance;
self.num_genes = 9999;
else:
if options.num_genes != None:
self.num_genes = options.num_genes;
# OMIM?
self.omim = not options.omim;
# Pubmed?
self.pubmed = not options.pubmed;
self.pnum = options.pnum;
self.per_term = options.per_term;
# GeneRIF?
self.gene_rif = not options.gene_rif;
# ScanDB?
if options.no_scandb:
self.scandb = False;
else:
self.scandb_pval = float(options.scandb_pval);
# MIMI?
self.mimi = not options.mimi;
# Check the output directory specified by the user.
# It should not already exist.
if len(sys.argv) > 1 and not self.console:
self.outdir = options.outdir;
if os.path.exists(self.outdir):
msg = "Error: output directory already exists: %s\n"\
"Please rename or move this directory, or use "\
"--output or -o to change the directory name." % self.outdir;
sys.exit(msg);
else:
mkpath(self.outdir);
def getCmdLine(self):
parser = VerboseParser()
# Remember: default action is store, default type is string.
snp_help = "Lookup information for a list of SNPs - these must be separated by commas, surrounded by quotes (whitespace ignored.)\n\n" +\
"Examples:\n" +\
"-s \"rs1002227, rs35712349\"\n" +\
"-s \" rs1002227, rs35712349\"\n" +\
"-s \" rs1002227,rs35712349 \"\n" +\
"-s \"rs1002227,rs35712349\""
parser.add_option("-s", "--snp", dest="snp", help=snp_help)
parser.add_option(
"-g",
"--gene",
dest="gene",
help=
"Lookup information for a list of gene symbols - these must be separated by commas, surrounded by quotes (whitespace ignored)"
)
snpfile_help = "Provide a list of SNPs to lookup from a file. The file may have *ANY* format. \
The program will pattern match rs### identifiers from your file."
parser.add_option("--snpfile", dest="snpfile", help=snpfile_help)
genefile_help = "Provide a list of gene symbols in a file. This option unfortunately is not as lenient as --snpfile: you must put \
each gene symbol on a separate line in the file."
parser.add_option("--genefile", dest="genefile", help=genefile_help)
regions_help = "Provide a list of chromosomal regions. Genes and other "\
"elements inside these regions will be returned.\n"\
"Example:\n"\
" --regions \"chr4:19141-939393,chrX:9191-939393\""
parser.add_option("-r", "--regions", help=regions_help)
build_help = ("Human genome build to use for SNP positions and genes. "
"Snipper ships with hg19 by default. You can download "
"pre-built databases from our website, or build them "
"yourself using the bin/setup_snipper.py script.")
parser.add_option("-b", "--build", dest="build", help=build_help)
dist_help = "Distance away from SNP to search, default is " + str(self.distance) + ". " +\
"If a distance is specified, the program will return *ALL* genes within the distance you specify, not just the default of 1. " +\
"To specify a new distance, but still only return 1 gene (or arbitrary number of genes), use -n <number>. " +\
"Distances can be specified using a kb or mb suffix, or as a raw distance. Examples: 500kb, 0.5MB, 1.4MB, 834141."
parser.add_option("-d", dest="distance", help=dist_help, type="string")
parser.add_option(
"-n",
dest="num_genes",
help="Number of genes to return per SNP, default is " +
str(self.num_genes),
type="int")
terms_help = "Comma-delimited string of terms, enclosed in quotes, to use in searching the literature. \
This will execute a search, per gene, for any of the search terms. For example:\n\
\n\
Genes: RB1, TCF7L2\n\
Search terms: \"glucose,retinoblastoma\"\n\
What happens: \n\
-- Search literature for RB1 AND (glucose OR retinoblastoma)\n\
-- Search literature for TCF7L2 AND (glucose OR retinoblastoma)"
parser.add_option("--terms", dest="terms", help=terms_help)
parser.add_option("--no-generif",
dest="gene_rif",
action="store_true",
default=False,
help="Disable GeneRIFs.")
parser.add_option(
"--no-scandb",
dest="no_scandb",
action="store_true",
default=False,
help=
"Disable use of ScanDB for eQTL information. Enabled by default.")
parser.add_option("--scandb-pval",
dest="scandb_pval",
default=self.scandb_pval,
help="P-value threshold for ScanDB eQTLs.")
parser.add_option(
"--no-mimi",
dest="mimi",
action="store_true",
default=False,
help=
"Disable querying of MiMI database for interactions between genes near SNPs."
)
parser.add_option("--no-omim",
dest="omim",
action="store_true",
default=False,
help="Disable display and search of OMIM text.")
parser.add_option("--no-pubmed",
dest="pubmed",
action="store_true",
default=False,
help="Disable searching PubMed.")
parser.add_option("--papernum",
dest="pnum",
type="int",
default=self.pnum,
help="Number of papers to display, default is " +
str(self.pnum))
each_term_help = "When specified, the program will search each gene x searchterm pair, instead of lumping together search terms. \
For example:\n\
\n\
Genes: RB1, TCF7L2\n\
Search terms: \"glucose,retinoblastoma\"\n\
What happens:\n\
-- Search literature for RB1 AND glucose\n\
-- Search literature for RB1 AND retinoblastoma\n\
-- Search literature for TCF7L2 AND glucose\n\
-- Search literature for TCF7L2 AND retinoblastoma\n\
\n\
This is a much more in-depth search, at the cost of running time - NCIBI limits to 1 query / 3 seconds. \
If you have a very large set of genes and search terms, this can take a VERY long time to run!"
parser.add_option("--each-term",
dest="per_term",
default=False,
action="store_true",
help=each_term_help)
parser.add_option("--all",
dest="all",
action="store_true",
default=True,
help=SUPPRESS_HELP)
parser.add_option(
"-o",
"--out",
dest="outdir",
default=self.outdir,
help=
"Directory to use for storing output. This should be a directory that does not exist yet."
)
parser.add_option(
"--console",
dest="console",
action="store_true",
default=self.console,
help=
"Write results to console, instead of creating directory with HTML/text results."
)
parser.add_option("--debug",
dest="debug",
action="store_true",
default=False,
help=SUPPRESS_HELP)
# Parse args.
(options, args) = parser.parse_args()
# Was debug enabled?
if options.debug:
__builtin__._SNIPPER_DEBUG = True
else:
__builtin__._SNIPPER_DEBUG = False
# If there are positional arguments, there was an error on the command line.
# Let them know the potential problem.
if len(args) > 0:
print >> sys.stderr, "Error: positional arguments detected: " + str(
args)
print >> sys.stderr, "Most likely, you simply forgot to surround the entire argument in quotes."
print >> sys.stderr, "Example: -g \"RB1, TCF7L2\" is correct, whereas -g \"RB1\" \"TCF7L2\" is wrong."
sys.exit(1)
# Console mode?
self.console = options.console
# Human genome build.
if options.build:
self.build = options.build
# Get genes from command line (and file, if specified.)
if options.gene != None:
self.genes = set([i.upper() for i in parseTerms(options.gene)])
if options.genefile != None:
self.genes.update(parseGeneFile(options.genefile))
# Get the set of SNPs.
if options.snp != None:
self.snpset = set(parseTerms(options.snp))
if options.snpfile != None:
self.snpset.update(parseSNPFile(options.snpfile))
# Get regions.
if options.regions != None:
self.regions = parseRegions(options.regions)
# Get list of search terms.
if options.terms != None:
self.terms = parseTerms(options.terms)
# HACK: If distance is specified, but num_genes is not,
# then we want to search for all genes in that distance space.
# Set num_genes to a really really big number. :)
if options.distance != None:
options.distance = convertFlank(options.distance)
if options.num_genes != None:
self.distance = options.distance
self.num_genes = options.num_genes
else:
self.distance = options.distance
self.num_genes = 9999
else:
if options.num_genes != None:
self.num_genes = options.num_genes
# OMIM?
self.omim = not options.omim
# Pubmed?
self.pubmed = not options.pubmed
self.pnum = options.pnum
self.per_term = options.per_term
# GeneRIF?
self.gene_rif = not options.gene_rif
# ScanDB?
if options.no_scandb:
self.scandb = False
else:
self.scandb_pval = float(options.scandb_pval)
# MIMI?
self.mimi = not options.mimi
# Check the output directory specified by the user.
# It should not already exist.
if len(sys.argv) > 1 and not self.console:
self.outdir = options.outdir
if os.path.exists(self.outdir):
msg = "Error: output directory already exists: %s\n"\
"Please rename or move this directory, or use "\
"--output or -o to change the directory name." % self.outdir
sys.exit(msg)
else:
mkpath(self.outdir)