comparison mothur/tools/mothur/mothur_wrapper.py @ 5:e2e2071d2c62

Add missing qual params to trim.seqs

4:5265aa9067e0

    cmd_dict['summary.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','all','distance','processors']})
   #cmd_dict['summary.single'] = dict({'required' : [], 'optional' : ['calc','abund','size','label','groupmode']})
    cmd_dict['summary.single'] = dict({'required' : [['list','sabund','rabund','shared']], 'optional' : ['calc','abund','size','label','groupmode']})
   #cmd_dict['tree.shared'] = dict({'required' : [], 'optional' : ['groups','calc','cutoff','precision','label']})
    cmd_dict['tree.shared'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['name','groups','calc','cutoff','precision','label']})
    cmd_dict['trim.seqs'] = dict({'required' : ['fasta'],  'optional' : ['group','oligos','qfile','qaverage','qthreshold','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','allfiles','keepfirst','removelast']})
   #cmd_dict['unifrac.unweighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','root','processors']})
    cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']})
   #cmd_dict['unifrac.weighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','root','processors']})
    cmd_dict['unifrac.weighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']})
   #cmd_dict['unique.seqs'] = dict({'required' : ['fasta'],  'optional' : ['names']})

    parser.add_option( '--fasta', dest='fasta', help='fasta file paths' )
    parser.add_option( '--fastq', dest='fastq', help='fastq file paths' )
    parser.add_option( '--qfile', dest='qfile', help='Sequence read quality file (454 platform)' )
    parser.add_option( '--qaverage', dest='qaverage', type="int", help='Remove sequences that have an average quality below the value' )
    parser.add_option( '--qthreshold', dest='qthreshold', type="int", help='If at any point a base call in a sequence has a quality score below the value provided to the option, the sequence is terminated' )
    parser.add_option( '--qtrim', dest='qtrim', help='For sequence below qthreshold, false to scrap file, true to trimmed and in trim file' )
    parser.add_option( '--flip', dest='flip', help='If true, reverse complement the sequences' )
    parser.add_option( '--maxambig', dest='maxambig', type="int", help='Number of ambiguous base calls to allow' )
    parser.add_option( '--maxhomop', dest='maxhomop', type="int", help='Maximun homopolymer length allowed' )
    parser.add_option( '--minlength', dest='minlength', type="int", help='Minimun sequence length' )

5:e2e2071d2c62

    cmd_dict['summary.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','all','distance','processors']})
   #cmd_dict['summary.single'] = dict({'required' : [], 'optional' : ['calc','abund','size','label','groupmode']})
    cmd_dict['summary.single'] = dict({'required' : [['list','sabund','rabund','shared']], 'optional' : ['calc','abund','size','label','groupmode']})
   #cmd_dict['tree.shared'] = dict({'required' : [], 'optional' : ['groups','calc','cutoff','precision','label']})
    cmd_dict['tree.shared'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['name','groups','calc','cutoff','precision','label']})
    cmd_dict['trim.seqs'] = dict({'required' : ['fasta'],  'optional' : ['group','oligos','qfile','qaverage','qthreshold','qwindowaverage','qwindowsize','rollaverage','qstepsize','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','allfiles','keepfirst','removelast']})
   #cmd_dict['unifrac.unweighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','root','processors']})
    cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']})
   #cmd_dict['unifrac.weighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','root','processors']})
    cmd_dict['unifrac.weighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']})
   #cmd_dict['unique.seqs'] = dict({'required' : ['fasta'],  'optional' : ['names']})

    parser.add_option( '--fasta', dest='fasta', help='fasta file paths' )
    parser.add_option( '--fastq', dest='fastq', help='fastq file paths' )
    parser.add_option( '--qfile', dest='qfile', help='Sequence read quality file (454 platform)' )
    parser.add_option( '--qaverage', dest='qaverage', type="int", help='Remove sequences that have an average quality below the value' )
    parser.add_option( '--qthreshold', dest='qthreshold', type="int", help='If at any point a base call in a sequence has a quality score below the value provided to the option, the sequence is terminated' )
    parser.add_option( '--qwindowaverage', dest='qwindowaverage', type="int", help='Remove sequences that have a window average quality below the value' )
    parser.add_option( '--qwindowsize', dest='qwindowsize', type="int", help='WIndow size for qwindowaverage' )
    parser.add_option( '--rollaverage', dest='rollaverage', type="int", help='Remove sequences that have a average quality below the value in a rolling window' )
    parser.add_option( '--qstepsize', dest='qstepsize', type="int", help='Distance to move a rolling window for each step' )
    parser.add_option( '--qtrim', dest='qtrim', help='For sequence below qthreshold, false to scrap file, true to trimmed and in trim file' )
    parser.add_option( '--flip', dest='flip', help='If true, reverse complement the sequences' )
    parser.add_option( '--maxambig', dest='maxambig', type="int", help='Number of ambiguous base calls to allow' )
    parser.add_option( '--maxhomop', dest='maxhomop', type="int", help='Maximun homopolymer length allowed' )
    parser.add_option( '--minlength', dest='minlength', type="int", help='Minimun sequence length' )