Mercurial > repos > weilong-guo > bs_seeker2
diff BSseeker2/bs_seeker2-build.py @ 1:8b26adf64adc draft default tip
V2.0.5
author | weilong-guo |
---|---|
date | Tue, 05 Nov 2013 01:55:39 -0500 |
parents | e6df770c0e58 |
children |
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--- a/BSseeker2/bs_seeker2-build.py Fri Jul 12 18:47:28 2013 -0400 +++ b/BSseeker2/bs_seeker2-build.py Tue Nov 05 01:55:39 2013 -0500 @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/env python import os from optparse import OptionParser, OptionGroup @@ -12,8 +12,8 @@ parser = OptionParser() parser.add_option("-f", "--file", dest="filename", help="Input your reference genome file (fasta)", metavar="FILE") - parser.add_option("--aligner", dest="aligner", help="Aligner program to perform the analysis: " + ', '.join(supported_aligners) + " [Default: %default]", metavar="ALIGNER", default = BOWTIE2) - parser.add_option("-p", "--path", dest="aligner_path", help="Path to the aligner program. Defaults: " +' '*70+ '\t'.join(('%s: %s '+' '*70) % (al, aligner_path[al]) for al in sorted(supported_aligners)), + parser.add_option("--aligner", dest="aligner", help="Aligner program to perform the analysis: " + ', '.join(supported_aligners) + " [Default: %default]", metavar="ALIGNER", default = BOWTIE) + parser.add_option("-p", "--path", dest="aligner_path", help="Path to the aligner program. Detected: " +' '*70+ '\t'.join(('%s: %s '+' '*70) % (al, aligner_path[al]) for al in sorted(supported_aligners)), metavar="PATH") parser.add_option("-d", "--db", type="string", dest="dbpath", help="Path to the reference genome library (generated in preprocessing genome) [Default: %default]", metavar="DBPATH", default = reference_genome_path) @@ -23,7 +23,7 @@ rrbs_opts = OptionGroup(parser, "Reduced Representation Bisulfite Sequencing Options", "Use this options with conjuction of -r [--rrbs]") rrbs_opts.add_option("-r", "--rrbs", action="store_true", dest="rrbs", help = 'Build index specially for Reduced Representation Bisulfite Sequencing experiments. Genome other than certain fragments will be masked. [Default: %default]', default = False) - rrbs_opts.add_option("-l", "--low",type= "int", dest="low_bound", help="lower bound of fragment length (excluding recognition sequence such as C-CGG) [Default: %default]", default = 40) + rrbs_opts.add_option("-l", "--low",type= "int", dest="low_bound", help="lower bound of fragment length (excluding recognition sequence such as C-CGG) [Default: %default]", default = 20) rrbs_opts.add_option("-u", "--up", type= "int", dest="up_bound", help="upper bound of fragment length (excluding recognition sequence such as C-CGG ends) [Default: %default]", default = 500) rrbs_opts.add_option("-c", "--cut-site", type= "string", dest="cut_format", help="Cut sites of restriction enzyme. Ex: MspI(C-CGG), Mael:(C-TAG), double-enzyme MspI&Mael:(C-CGG,C-TAG). [Default: %default]", default = "C-CGG") parser.add_option_group(rrbs_opts) @@ -33,7 +33,7 @@ # if no options were given by the user, print help and exit if len(sys.argv) == 1: - print parser.print_help() + parser.print_help() exit(0) if options.version : @@ -44,7 +44,11 @@ rrbs = options.rrbs - fasta_file=os.path.expanduser(options.filename) + if options.filename is not None : + fasta_file=os.path.expanduser(options.filename) + else : + error("Please specify the genome file (Fasta) using \"-f\"") + if fasta_file is None: error('Fasta file for the reference genome must be supported') @@ -69,9 +73,14 @@ print "Reference genome file: %s" % fasta_file print "Reduced Representation Bisulfite Sequencing: %s" % rrbs + print "Short reads aligner you are using: %s" % options.aligner print "Builder path: %s" % builder_exec + #--------------------------------------------------------------- + if not os.path.isfile( builder_exec ) : + error("Cannot file program %s for execution." % builder_exec) + ref_path = options.dbpath if os.path.exists(ref_path):