Mercurial > repos > jjohnson > mothur_toolsuite
diff mothur/tools/mothur/mothur_wrapper.py @ 26:5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Wed, 16 May 2012 13:12:05 -0500 |
parents | 09740be2bc9c |
children | 49058b1f8d3f |
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--- a/mothur/tools/mothur/mothur_wrapper.py Wed May 16 12:28:44 2012 -0500 +++ b/mothur/tools/mothur/mothur_wrapper.py Wed May 16 13:12:05 2012 -0500 @@ -202,14 +202,20 @@ cmd_dict['collect.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','freq','groups','all']}) cmd_dict['collect.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','size','label','freq']}) cmd_dict['consensus.seqs'] = dict({'required' : ['fasta'], 'optional' : ['list','name','label','cutoff']}) + + cmd_dict['cooccurrence'] = dict({'required' : ['shared'], 'optional' : ['iters','metric','matrixmodel','groups','label']}) + cmd_dict['corr.axes'] = dict({'required' : [['shared','relabund','metadata'],'axes'], 'optional' : ['label','groups','method','numaxes']}) cmd_dict['count.groups'] = dict({'required' : ['group','shared'], 'optional' : ['accnos','groups']}) cmd_dict['count.seqs'] = dict({'required' : ['name'], 'optional' : ['group','groups']}) + + cmd_dict['create.database'] = dict({'required' : ['list, repfasta','repname','contaxonomy'], 'optional' : ['group','label']}) + cmd_dict['degap.seqs'] = dict({'required' : ['fasta']}) cmd_dict['deunique.seqs'] = dict({'required' : ['fasta','name'], 'optional' : []}) cmd_dict['deunique.tree'] = dict({'required' : ['tree','name'], 'optional' : []}) cmd_dict['dist.seqs'] = dict({'required' : ['fasta'], 'optional' : ['calc','countends','output','cutoff','oldfasta','column','processors']}) - cmd_dict['dist.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','output','processors']}) + cmd_dict['dist.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','output','subsample','iters','processors']}) cmd_dict['fastq.info'] = dict({'required' : ['fastq'], 'optional' : ['fasta','qfile']}) cmd_dict['filter.seqs'] = dict({'required' : ['fasta'], 'optional' : ['vertical','trump','soft','hard','processors']}) cmd_dict['get.group'] = dict({'required' : ['shared'], 'optional' : []}) @@ -230,9 +236,12 @@ cmd_dict['indicator'] = dict({'required' : [['tree','design'],['shared','relabund']], 'optional' : ['groups','label','processors']}) cmd_dict['libshuff'] = dict({'required' : ['phylip','group'],'optional' : ['groups','iters','form','sim','step','cutoff']}) cmd_dict['list.seqs'] = dict({'required' : [['fasta','name','group','list','alignreport','taxonomy']]}) + + cmd_dict['make.biom'] = dict({'required' : ['shared'] , 'optional' : ['contaxonomy','matrixtype','groups','label']}) + cmd_dict['make.fastq'] = dict({'required' : ['fasta','qfile'] , 'optional' : []}) cmd_dict['make.group'] = dict({'required' : ['fasta','groups'], 'optional' : []}) - cmd_dict['make.shared'] = dict({'required' : ['list','group'], 'optional' : ['label','groups']}) + cmd_dict['make.shared'] = dict({'required' : [['list','group','biom']], 'optional' : ['label','groups']}) cmd_dict['mantel'] = dict({'required' : ['phylip','phylip2'] , 'optional' : ['method','iters']}) cmd_dict['merge.files'] = dict({'required' : ['input','output']}) cmd_dict['merge.groups'] = dict({'required' : [['shared','group'],'design'], 'optional' : ['groups', 'label']}) @@ -246,6 +255,9 @@ cmd_dict['parsimony'] = dict({'required' : ['tree'], 'optional' : ['group','groups','name','iters','random','processors']}) cmd_dict['pca'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','groups','metric']}) cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : ['metric']}) + + cmd_dict['pcr.seqs'] = dict({'required' : ['fasta'], 'optional' : ['oligos','name','group','taxonomy','ecoli','start','end','nomatch','keepprimer','keepdots','processors']}) + cmd_dict['phylo.diversity'] = dict({'required' : ['tree'],'optional' : ['group','name','groups','iters','freq','scale','rarefy','collect','summary','processors']}) cmd_dict['phylotype'] = dict({'required' : ['taxonomy'],'optional' : ['name','cutoff','label']}) cmd_dict['pre.cluster'] = dict({'required' : ['fasta'], 'optional' : ['name','diffs','group','processors']}) @@ -272,11 +284,11 @@ cmd_dict['summary.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','all','distance','processors']}) cmd_dict['summary.single'] = dict({'required' : [['list','sabund','rabund','shared']], 'optional' : ['calc','abund','size','label','groupmode']}) cmd_dict['summary.tax'] = dict({'required' : ['taxonomy'], 'optional' : ['name','group','reftaxonomy']}) - cmd_dict['tree.shared'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['name','groups','calc','cutoff','precision','label']}) + cmd_dict['tree.shared'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['name','groups','calc','cutoff','precision','label','subsample','iters','processors']}) cmd_dict['trim.flows'] = dict({'required' : ['flow'], 'optional' : ['oligos','bdiffs','pdiffs','tdiffs','ldiffs','sdiffs','minflows','maxflows','fasta','signal','noise','maxhomop','order','processors']}) cmd_dict['trim.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','group','oligos','qfile','qaverage','qthreshold','qwindowaverage','qwindowsize','rollaverage','qstepsize','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','ldiffs','sdiffs','keepforward','allfiles','keepfirst','removelast','processors']}) - cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']}) - cmd_dict['unifrac.weighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']}) + cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','subsample','consensus','processors']}) + cmd_dict['unifrac.weighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','subsample','consensus','processors']}) cmd_dict['unique.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name']}) cmd_dict['venn'] = dict({'required' : [['list','shared']], 'optional' : ['calc','label','groups','abund','nseqs','permute','fontsize']}) @@ -320,6 +332,7 @@ 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( '--repfasta', dest='repfasta', help='fasta file paths' ) 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' ) @@ -343,6 +356,7 @@ parser.add_option( '--allfiles', dest='allfiles', help='T - generate fasta and group for each barcode' ) parser.add_option( '--keepforward', dest='keepforward', help='T - keep primer' ) parser.add_option( '--name', dest='name', help='A file containing a 2 column table: name, and comma separated list of represetatives' ) + parser.add_option( '--repname', dest='repname', help='A file containing a 2 column table: name, and comma separated list of represetatives' ) parser.add_option( '--accnos', dest='accnos', help='A file containing a list of names' ) parser.add_option( '--groups', dest='groups', help='pairwise group labels' ) parser.add_option( '--group', dest='group', help='A file containing a list of names' ) @@ -351,6 +365,7 @@ parser.add_option( '--report', dest='report', help='' ) parser.add_option( '--taxonomy', dest='taxonomy', help='A Taxonomy file' ) parser.add_option( '--reftaxonomy', dest='reftaxonomy', help='A Taxonomy file' ) + parser.add_option( '--contaxonomy', dest='contaxonomy', help='The Taxonomy file output by classify.otu' ) parser.add_option( '--taxon', dest='taxon', help='A Taxon' ) parser.add_option( '--taxlevel', dest='taxlevel', type="int", help='A Taxonomy level' ) # parser.add_option( '--taxon', dest='taxon', action="callback", callback=remove_confidence_callback, help='A Taxon' ) @@ -401,6 +416,7 @@ parser.add_option( '--iters', dest='iters', type='int', help='Iterations of randomizations' ) parser.add_option( '--maxiter', dest='maxiter', type='int', help='Iterations' ) parser.add_option( '--maxiters', dest='maxiters', type='int', help='Iterations of randomizations' ) + parser.add_option( '--subsample', dest='subsample', help='Number of subsample, or T to default to smallest group size' ) parser.add_option( '--jumble', dest='jumble', help='If false, just a collector curve across the samples' ) parser.add_option( '--conservation', dest='conservation', help='Template frequency information' ) parser.add_option( '--quantile', dest='quantile', help='Template quantile information' ) @@ -461,6 +477,7 @@ parser.add_option( '--design', dest='design', help='' ) parser.add_option( '--sets', dest='sets', help='' ) parser.add_option( '--metric', dest='metric', help='' ) + parser.add_option( '--matrixmodel', dest='matrixmodel', help='' ) parser.add_option( '--epsilon', dest='epsilon', help='' ) parser.add_option( '--alpha', dest='alpha', help='' ) parser.add_option( '--root', dest='root', help='' ) @@ -491,6 +508,13 @@ parser.add_option( '--queryfract', dest='queryfract', type="float", help='') parser.add_option( '--minlen', dest='minlen', type="int", help='Minimun sequence length' ) parser.add_option( '--maxlen', dest='maxlen', type="int", help='Maximun sequence length' ) + parser.add_option( '--ecoli', dest='ecoli', help='ecoli referance fasta' ) + parser.add_option( '--nomatch', dest='nomatch', help='What to with non matching items' ) + parser.add_option( '--keepprimer', dest='keepprimer', help='Whether to retain the primer' ) + parser.add_option( '--keepdots', dest='keepdots', help='Whether to retain dots in the sequence' ) + parser.add_option( '--matrixtype', dest='matrixtype', help='' ) + parser.add_option( '--consensus', dest='consensus', help='boolean' ) + parser.add_option( '--biom', dest='biom', help='biom file' ) # include read.otu options parser.add_option( '--rabund', dest='rabund', help='' ) parser.add_option( '--sabund', dest='sabund', help='' )