Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/mothur_wrapper.py @ 5:e2e2071d2c62
Add missing qual params to trim.seqs
| author | jj@dbw-galaxy-dev.msi.umn.edu |
|---|---|
| date | Thu, 09 Jun 2011 16:24:30 -0500 |
| parents | e990ac8a0f58 |
| children | 7bfe1f843858 |
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#!/usr/bin/env python """ http://www.mothur.org/ Supports mothur version mothur v.1.17.0 Class encapsulating Mothur galaxy tool. Expect each invocation to include: Here is an example call to this script with an explanation before each param : mothur_wrapper.py # name of a mothur command, this is required --cmd='summary.shared' # Galaxy output dataset list, these are output files that can be determined before the command is run # The items in the list are separated by commas # Each item contains a regex to match the output filename and a galaxy dataset filepath in which to copy the data (separated by :) --result='^mothur.\S+\.logfile$:'/home/galaxy/data/database/files/002/dataset_2613.dat,'^\S+\.summary$:'/home/galaxy/data/database/files/002/dataset_2614.dat # Galaxy output dataset extra_files_path direcotry in which to put all output files --outputdir='/home/galaxy/data/database/files/002/dataset_2613_files' # The id of one of the galaxy outputs (e.g. the mothur logfile) used for dynamic dataset generation # http://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput --datasetid='2578' # The galaxy directory in which to copy all output files for dynamic dataset generation --new_file_path='/home/galaxy/data/database/tmp' # specifies files to copy to the new_file_path # The list is separated by commas # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :) # The regex match.groups()[0] is used as the id name of the dataset, and must result in unique name for each output --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist' # Many mothur commands first require data to be read into memory using: read.otu, read.dist, or read.tree # This prequisite command and its params are prefixed with 'READ_' --READ_cmd='read.otu' --READ_list=/home/galaxy/data/database/files/001/dataset_1557.dat --READ_group='/home/galaxy/data/database/files/001/dataset_1545.dat' --READ_label='unique,0.07' """ # import pkg_resources; import logging, os, string, sys, tempfile, glob, shutil, types, urllib, optparse, re import shlex, subprocess from stat import * log = logging.getLogger( __name__ ) assert sys.version_info[:2] >= ( 2, 4 ) debug = False #debug = True max_processors = 2 def stop_err( msg ): sys.stderr.write( "%s\n" % msg ) sys.exit() def __main__(): # tranform the logfile into html # add extra file ouput # add object tags for svg files def logfile_to_html(logfile_path,htmlfile_path,tmp_input_dir_name,tmp_output_dir_name,title="Mothur Logfile"): if debug: print >> sys.stdout, 'logfile_to_html %s -> %s' % (logfile_path, htmlfile_path) if debug: print >> sys.stdout, 'logfile_to_html input_dir: %s' % tmp_input_dir_name if debug: print >> sys.stdout, 'logfile_to_html output_dir: %s' % tmp_output_dir_name txt = open(logfile_path,'r') in_pat = re.sub('[^a-zA-Z0-9_/]','.',tmp_input_dir_name) + '/(.+)' out_pat = re.sub('[^a-zA-Z0-9_/]','.',tmp_output_dir_name) + '/(.+)' html = open(htmlfile_path,'w') html.write("<html><head><title>%s</title></head>\n<body>\n<pre>\n" % title) try: for line in txt: if line.find('set.dir') >= 0: continue elif line.find('put directory to ') >= 0: continue elif line.startswith('Mothur\'s directories:') : continue elif line.startswith('outputDir=') : continue elif line.startswith('Type ') : continue elif line.find(tmp_output_dir_name) >= 0: # if debug: print >> sys.stdout, 'logfile_to_html #%s#' % line if line.strip().endswith('.svg'): line = re.sub(out_pat,' <object id="object" type="image/svg+xml" data="\\1">\\1</object> <br><a href="\\1">\\1</a> <hr/>',line) else: line = re.sub(out_pat,'<a href="\\1">\\1</a>',line) elif line.find(tmp_input_dir_name) >= 0: line = re.sub(in_pat,'\\1',line) html.write(line) except Exception, e: print(str(e)) pass html.write('</pre>\n</body>\n</html>\n') html.close() #Overide the processors option def processors_callback(option, opt, value, parser): val = value if value <= max_processors else max_processors setattr(parser.values, option.dest, val) #Strip out "(xx)" confidence values from a taxonomy list def remove_confidence_callback(option, opt, value, parser): # val = "'" + re.sub('\(\d+\)','',value) + "'" setattr(parser.values, option.dest, re.sub('\(\d+\)','',value)) #Mothur separates items in a list of values with hyphens def multi_val_callback(option, opt, value, parser): setattr(parser.values, option.dest, '-'.join(value.split(','))) #Handle list arguments that may contain dataset files def prepare_input(value,input_dir): """ Mothur requires items in a list of input values to be separated by hyphens Change list separator from comma to hyphen If those items are files, copy them to the input dir. """ if input_dir != None and value != None and isinstance(value, str): vals = [] for val in value.split(','): if val[0] == '/' and os.path.isfile(val): (dir,fname) = os.path.split(val) try: os.symlink(val,os.path.join(input_dir,fname)) except: shutil.copy(val,os.path.join(input_dir,fname)) vals.append(fname) if debug: print >> sys.stderr, "scp %s %s" % (val, os.path.join(input_dir,fname)) else: vals.append(val) return '-'.join(vals) return value #Parse Command Line and get a list of params # Prefix is used to differentiate between prerequisite commands: read.otu, read.dist, read.tree def get_params(cmd, options, input_dir, prefix=''): if debug: print >> sys.stderr, options params = [] for opt in cmd_dict[cmd]['required']: if debug: print >> sys.stderr, opt if isinstance(opt,list): # One of these must be present missing = True for sel in opt: # if debug: print >> sys.stderr, sel try: value = prepare_input(getattr(options,prefix+sel), input_dir) if value != None: params.append('%s=%s' % (sel,value)) missing = False except Exception, e: stop_err('Illegal option for cmd %s : %s %s' % (cmd,sel,e)) if missing: stop_err('Missing a required parameter for %s, need one of %s' % (cmd,opt)) else: # This option is required try: value = prepare_input(getattr(options,prefix+opt), input_dir) # if debug: print >> sys.stderr, value if value != None: params.append('%s=%s' % (opt,value)) else: stop_err('Missing a required parameter for %s : %s' % (cmd,opt)) except Exception, e: stop_err('Illegal option %s %s' % (opt,e)) if 'optional' in cmd_dict[cmd]: for opt in cmd_dict[cmd]['optional']: # if debug: print >> sys.stderr, opt try: value = prepare_input(getattr(options,prefix+opt), input_dir) # if debug: print >> sys.stderr, value if value != None: params.append('%s=%s' % (opt,value)) except Exception, e: # should distinguish between READ_ opts and cmd opts # stop_err('Illegal option for %s : %s' % (cmd,opt)) pass return params """ The command dict has a dict for each mothur command with required and options arguments The top level list of required arguments is interpreted that each value item is required and any list item represents a choice of arguments This covers many, but not all of the argument dependency requirements. For example - read.dist required a phylip or (column and name) argument. The complexity of inputs should be handled by the glaxy tool xml file. """ cmd_dict = dict() cmd_dict['align.check'] = dict({'required' : ['fasta','map']}) #cmd_dict['align.seqs'] = dict({'required' : ['candidate','template'], 'optional' : ['search','ksize','align','match','mismatch','gapopen','gapextend','flip','threshold','processors']}) cmd_dict['align.seqs'] = dict({'required' : ['fasta','reference',], 'optional' : ['search','ksize','align','match','mismatch','gapopen','gapextend','flip','threshold','processors']}) cmd_dict['amova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']}) cmd_dict['anosim'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']}) #cmd_dict['bin.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','label','group']}) cmd_dict['bin.seqs'] = dict({'required' : ['list','fasta'], 'optional' : ['name','label','group']}) #cmd_dict['bootstrap.shared'] = dict({'required' : [], 'optional' : ['calc','groups','iters','label']}) cmd_dict['bootstrap.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','groups','iters','label']}) #catchall cmd_dict['chimera.bellerophon'] = dict({'required' : ['fasta'], 'optional' : ['filter','correction','window','increment','processors']}) #cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','template'], 'optional' : ['filter','mask','window','numwanted','processors']}) cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','reference'], 'optional' : ['filter','mask','window','numwanted','processors']}) #cmd_dict['chimera.check'] = dict({'required' : ['fasta','template'], 'optional' : ['ksize','svg','name','increment','processors']}) cmd_dict['chimera.check'] = dict({'required' : ['fasta','reference'], 'optional' : ['ksize','svg','name','increment','processors']}) #cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','template'], 'optional' : ['conservation','quantile','filter','mask','window','increment','processors']}) cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','reference'], 'optional' : ['conservation','quantile','filter','mask','window','increment','processors']}) #cmd_dict['chimera.slayer'] = dict({'required' : ['fasta','template'], 'optional' : ['name','search','window','increment','match','mismatch','numwanted','parents','minsim','mincov','iters','minbs','minsnp','divergence','realign','split','processors']}) cmd_dict['chimera.slayer'] = dict({'required' : ['fasta','reference'], 'optional' : ['name','search','window','increment','match','mismatch','numwanted','parents','minsim','mincov','iters','minbs','minsnp','divergence','realign','split','processors']}) #cmd_dict['chop.seqs'] = dict({'required' : ['fasta','numbases'], 'optional' : ['keep','short']}) cmd_dict['chop.seqs'] = dict({'required' : ['fasta','numbases'], 'optional' : ['countgaps','keep','short']}) cmd_dict['classify.otu'] = dict({'required' : ['list','taxonomy'],'optional' : ['name','cutoff','label','group','probs','basis','reftaxonomy']}) #cmd_dict['classify.seqs'] = dict({'required' : ['fasta','template','taxonomy'],'optional' : ['name','search','ksize','method','match','mismatch','gapopen','gapextend','numwanted','probs','processors']}) cmd_dict['classify.seqs'] = dict({'required' : ['fasta','reference','taxonomy'],'optional' : ['name','search','ksize','method','match','mismatch','gapopen','gapextend','numwanted','probs','processors']}) cmd_dict['clearcut'] = dict({'required' : [['phylip','fasta']],'optional' : ['seed','norandom','shuffle','neighbor','expblen','expdist','ntrees','matrixout','kimura','jukes','protein','DNA']}) #cmd_dict['cluster'] = dict({'required' : [] , 'optional' : ['method','cutoff','hard','precision']}) cmd_dict['cluster'] = dict({'required' : [['phylip','column']] , 'optional' : ['name','method','cutoff','hard','precision','sim','showabund','timing']}) #cmd_dict['cluster.classic'] = dict({'required' : ['phylip'] , 'optional' : ['method','cutoff','hard','precision']}) cmd_dict['cluster.classic'] = dict({'required' : ['phylip'] , 'optional' : ['name','method','cutoff','hard','sim','precision']}) cmd_dict['cluster.fragments'] = dict({'required' : ['fasta'] , 'optional' : ['name','diffs','percent']}) cmd_dict['cluster.split'] = dict({'required' : [['fasta','phylip','column']] , 'optional' : ['name','method','splitmethod','taxonomy','taxlevel','showabund','cutoff','hard','large','precision','timing','processors']}) #cmd_dict['collect.shared'] = dict({'required' : [], 'optional' : ['calc','label','freq','groups','all']}) cmd_dict['collect.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','freq','groups','all']}) #cmd_dict['collect.single'] = dict({'required' : [], 'optional' : ['calc','abund','size','label','freq']}) 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']}) cmd_dict['corr.axes'] = dict({'required' : [['shared','relabund','metadata'],'axes'], 'optional' : ['label','groups','method','numaxes']}) cmd_dict['degap.seqs'] = dict({'required' : ['fasta']}) cmd_dict['deunique.seqs'] = dict({'required' : ['fasta','name'], 'optional' : []}) #cmd_dict['dist.seqs'] = dict({'required' : ['fasta'], 'optional' : ['calc','countends','output','cutoff','processors']}) cmd_dict['dist.seqs'] = dict({'required' : ['fasta'], 'optional' : ['calc','countends','output','cutoff','oldfasta','column','processors']}) #cmd_dict['dist.shared'] = dict({'required' : [], 'optional' : ['calc','label','groups','output']}) cmd_dict['dist.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','output']}) cmd_dict['fastq.info'] = dict({'required' : ['fastq'], 'optional' : []}) cmd_dict['filter.seqs'] = dict({'required' : ['fasta'], 'optional' : ['vertical','trump','soft','hard','processors']}) #cmd_dict['get.group'] = dict({'required' : [], 'optional' : []}) cmd_dict['get.group'] = dict({'required' : ['shared'], 'optional' : []}) cmd_dict['get.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','taxonomy']}) cmd_dict['get.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']}) ##cmd_dict['get.otulist'] = dict({'required' : [], 'optional' : []}) cmd_dict['get.otulist'] = dict({'required' : ['list'], 'optional' : ['label','sort']}) #cmd_dict['get.oturep'] = dict({'required' : ['fasta','list'], 'optional' : ['phylip','column','name','label','group','groups','sorted','precision','cutoff','large','weighted']}) cmd_dict['get.oturep'] = dict({'required' : ['fasta','list',['phylip','column']], 'optional' : ['name','label','group','groups','sorted','precision','cutoff','large','weighted']}) cmd_dict['get.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']}) ##cmd_dict['get.rabund'] = dict({'required' : [],'optional' : []}) cmd_dict['get.rabund'] = dict({'required' : [['list','sabund']],'optional' : ['sorted','label']}) #cmd_dict['get.relabund'] = dict({'required' : [],'optional' : ['scale','label','groups']}) cmd_dict['get.relabund'] = dict({'required' : ['shared'],'optional' : ['scale','label','groups']}) ##cmd_dict['get.sabund'] = dict({'required' : [],'optional' : []}) cmd_dict['get.sabund'] = dict({'required' : [['list','rabund']],'optional' : ['label']}) cmd_dict['get.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']}) ##cmd_dict['get.sharedseqs'] = dict({'required' : [], 'optional' : []}) cmd_dict['get.sharedseqs'] = dict({'required' : ['list','group'], 'optional' : ['label', 'unique', 'shared', 'output', 'fasta']}) cmd_dict['hcluster'] = dict({'required' : [['column','phylip']] , 'optional' : ['name','method','cutoff','hard','precision','sorted','showabund','timing']}) #cmd_dict['heatmap.bin'] = dict({'required' : [], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']}) cmd_dict['heatmap.bin'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']}) #cmd_dict['heatmap.sim'] = dict({'required' : [], 'optional' : ['calc','phylip','column','name','label','groups']}) cmd_dict['heatmap.sim'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['calc','name','label','groups']}) cmd_dict['homova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']}) cmd_dict['indicator'] = dict({'required' : ['tree',['shared','relabund']], 'optional' : ['groups','label','design']}) #cmd_dict['libshuff'] = dict({'required' : [],'optional' : ['iters','form','step','cutoff']}) 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,fastq'] = dict({'required' : ['fasta','qfile'] , 'optional' : []}) #cmd_dict['make.group'] = dict({'required' : ['fasta','groups'], 'optional' : ['output']}) cmd_dict['make.group'] = dict({'required' : ['fasta','groups'], 'optional' : []}) cmd_dict['make.shared'] = dict({'required' : ['list','group'], 'optional' : ['label','groups','ordergroup']}) 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','design'], 'optional' : ['groups', 'label']}) #cmd_dict['metastats'] = dict({'required' : ['design'], 'optional' : ['groups', 'label','iters','threshold','sets','processors']}) cmd_dict['metastats'] = dict({'required' : ['shared','design'], 'optional' : ['groups', 'label','iters','threshold','sets','processors']}) cmd_dict['nmds'] = dict({'required' : ['phylip'], 'optional' : ['axes','mindim','maxdim','iters','maxiters','epsilon']}) #cmd_dict['normalize.shared'] = dict({'required' : [], 'optional' : ['label','method','norm','groups']}) cmd_dict['normalize.shared'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','method','norm','groups','makerelabund']}) ##cmd_dict['otu.hierarchy'] = dict({'required' : [], 'optional' : []}) cmd_dict['otu.hierarchy'] = dict({'required' : ['list','label'], 'optional' : ['output']}) cmd_dict['pairwise.seqs'] = dict({'required' : ['fasta'], 'optional' : ['align','calc','countends','output','cutoff','match','mismatch','gapopen','gapextend','processors']}) cmd_dict['parse.list'] = dict({'required' : ['list','group'], 'optional' : ['label']}) #cmd_dict['parsimony'] = dict({'required' : [], 'optional' : ['groups','iters','random','processors']}) cmd_dict['parsimony'] = dict({'required' : ['tree'], 'optional' : ['group','groups','name','iters','random','processors']}) #cmd_dict['pca'] = dict({'required' : [], 'optional' : ['label','groups','metric']}) cmd_dict['pca'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','groups','metric']}) #cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : []}) cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : ['metric']}) #cmd_dict['phylo.diversity'] = dict({'required' : [],'optional' : ['groups','iters','freq','scale','rarefy','collect','summary','processors']}) cmd_dict['phylo.diversity'] = dict({'required' : ['tree','group'],'optional' : ['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' : ['names','diffs']}) cmd_dict['pre.cluster'] = dict({'required' : ['fasta'], 'optional' : ['name','diffs']}) #cmd_dict['rarefaction.shared'] = dict({'required' : [], 'optional' : ['label','iters','groups','jumble']}) cmd_dict['rarefaction.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','iters','groups','jumble']}) #cmd_dict['rarefaction.single'] = dict({'required' : [], 'optional' : ['calc','abund','iters','label','freq','processors']}) cmd_dict['rarefaction.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','iters','label','freq','processors']}) #cmd_dict['read.dist'] = dict({'required' : [['phylip','column']], 'optional' : ['name','cutoff','hard','precision','sim','group']}) #cmd_dict['read.otu'] = dict({'required' : [['rabund','sabund','list','shared','relabund']], 'optional' : ['label','group','groups','ordergroup']}) #cmd_dict['read.tree'] = dict({'required' : ['tree'], 'optional' : ['name','group']}) cmd_dict['remove.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','taxonomy']}) cmd_dict['remove.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']}) cmd_dict['remove.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']}) #cmd_dict['remove.rare'] = dict({'required' : [['list','sabund','rabund','shared'],'nseqs'], 'optional' : ['group','groups','label','bygroup']}) cmd_dict['remove.rare'] = dict({'required' : [['list','sabund','rabund','shared'],'nseqs'], 'optional' : ['group','groups','label','bygroup']}) cmd_dict['remove.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']}) cmd_dict['reverse.seqs'] = dict({'required' : ['fasta']}) cmd_dict['screen.seqs'] = dict({'required' : ['fasta'], 'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport','processors']}) cmd_dict['sens.spec'] = dict({'required' : ['list',['column','phylip']] , 'optional' : ['label','cutoff','hard','precision']}) cmd_dict['sffinfo'] = dict({'required' : [['sff','sfftxt']], 'optional' : ['fasta','qfile','trim','sfftxt','flow','accnos']}) cmd_dict['split.abund'] = dict({'required' : ['fasta',['name','list']], 'optional' : ['cutoff','group','groups','label','accnos']}) #cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : []}) cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : ['name','groups']}) cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size','persample']}) #cmd_dict['summary.seqs'] = dict({'required' : ['fasta'],'outputs' : ['names']}) cmd_dict['summary.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','processors']}) #cmd_dict['summary.shared'] = dict({'required' : [], 'optional' : ['calc','label','groups','all','distance']}) 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']}) cmd_dict['unique.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name']}) #cmd_dict['venn'] = dict({'required' : [], 'optional' : ['calc','label','groups','abund','nseqs','permute']}) cmd_dict['venn'] = dict({'required' : [['list','shared']], 'optional' : ['calc','label','groups','abund','nseqs','permute']}) ## """ cmd_dict['merge.files'] = dict({'required' : ['input','output']}) cmd_dict['make.group'] = dict({'required' : ['fasta','groups'], 'optional' : ['output']}) cmd_dict['merge.groups'] = dict({'required' : ['shared','design'], 'optional' : ['groups', 'label']}) cmd_dict['summary.seqs'] = dict({'required' : ['fasta'], 'outputs' : ['.names']}) cmd_dict['reverse.seqs'] = dict({'required' : ['fasta']}) cmd_dict['degap.seqs'] = dict({'required' : ['fasta']}) cmd_dict['unique.seqs'] = dict({'required' : ['fasta'], 'optional' : ['names']}) cmd_dict['deunique.seqs'] = dict({'required' : ['fasta','names'], 'optional' : []}) cmd_dict['chop.seqs'] = dict({'required' : ['fasta','numbases'], 'optional' : ['keep','short']}) cmd_dict['filter.seqs'] = dict({'required' : ['fasta'], 'optional' : ['vertical','trump','soft','hard','processors']}) cmd_dict['screen.seqs'] = dict({'required' : ['fasta'], 'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport','processors']}) 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['list.seqs'] = dict({'required' : [['fasta','name','group','list','alignreport','taxonomy']]}) cmd_dict['get.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']}) cmd_dict['remove.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']}) cmd_dict['align.seqs'] = dict({'required' : ['candidate','template'], 'optional' : ['search','ksize','align','match','mismatch','gapopen','gapextend','flip','threshold','processors']}) cmd_dict['align.check'] = dict({'required' : ['fasta','map']}) cmd_dict['pre.cluster'] = dict({'required' : ['fasta'], 'optional' : ['names','diffs']}) cmd_dict['bin.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','label','group']}) cmd_dict['classify.seqs'] = dict({'required' : ['fasta','template','taxonomy'],'optional' : ['name','search','ksize','method','match','mismatch','gapopen','gapextend','numwanted','probs','processors']}) cmd_dict['classify.otu'] = dict({'required' : ['list','taxonomy'],'optional' : ['name','cutoff','label','group','probs','basis','reftaxonomy']}) # label=0.01-0.02-0.03 from 0.01,0.02,0.03 string.replace(options.label,',','-') cmd_dict['chimera.bellerophon'] = dict({'required' : ['fasta'], 'optional' : ['filter','correction','window','increment','processors']}) cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','template'], 'optional' : ['filter','mask','window','numwanted','processors']}) cmd_dict['chimera.check'] = dict({'required' : ['fasta','template'], 'optional' : ['ksize','svg','name','increment','processors']}) cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','template'], 'optional' : ['conservation','quantile','filter','mask','window','increment','processors']}) cmd_dict['chimera.slayer'] = dict({'required' : ['fasta','template'], 'optional' : ['name','search','window','increment','match','mismatch','numwanted','parents','minsim','mincov','iters','minbs','minsnp','divergence','realign','split','processors']}) cmd_dict['dist.seqs'] = dict({'required' : ['fasta'], 'optional' : ['calc','countends','output','cutoff','processors']}) cmd_dict['pairwise.seqs'] = dict({'required' : ['fasta'], 'optional' : ['align','calc','countends','output','cutoff','match','mismatch','gapopen','gapextend','processors']}) cmd_dict['read.dist'] = dict({'required' : [['phylip','column']], 'optional' : ['name','cutoff','hard','precision','sim','group']}) cmd_dict['read.otu'] = dict({'required' : [['rabund','sabund','list','shared','relabund']], 'optional' : ['label','group','groups','ordergroup']}) cmd_dict['read.tree'] = dict({'required' : ['tree'], 'optional' : ['name','group']}) cmd_dict['cluster'] = dict({'required' : [] , 'optional' : ['method','cutoff','hard','precision']}) cmd_dict['hcluster'] = dict({'required' : [['column','phylip']] , 'optional' : ['name','method','cutoff','hard','precision','sorted','showabund']}) cmd_dict['cluster.fragments'] = dict({'required' : ['fasta'] , 'optional' : ['name','diffs','percent']}) cmd_dict['cluster.split'] = dict({'required' : [['fasta','phylip','column']] , 'optional' : ['name','method','splitmethod','taxonomy','taxlevel','showabund','cutoff','hard','large','precision','timing','processors']}) cmd_dict['metastats'] = dict({'required' : ['design'], 'optional' : ['groups', 'label','iters','threshold','sets','processors']}) cmd_dict['summary.single'] = dict({'required' : [], 'optional' : ['calc','abund','size','label','groupmode']}) cmd_dict['summary.shared'] = dict({'required' : [], 'optional' : ['calc','label','groups','all','distance']}) cmd_dict['collect.single'] = dict({'required' : [], 'optional' : ['calc','abund','size','label','freq']}) cmd_dict['collect.shared'] = dict({'required' : [], 'optional' : ['calc','label','freq','groups','all']}) cmd_dict['rarefaction.single'] = dict({'required' : [], 'optional' : ['calc','abund','iters','label','freq','processors']}) cmd_dict['rarefaction.shared'] = dict({'required' : [], 'optional' : ['label','iters','groups','jumble']}) cmd_dict['normalize.shared'] = dict({'required' : [], 'optional' : ['label','method','norm','groups']}) cmd_dict['dist.shared'] = dict({'required' : [], 'optional' : ['calc','label','groups','output']}) cmd_dict['split.abund'] = dict({'required' : ['fasta',['name','list']], 'optional' : ['cutoff','group','groups','label','accnos']}) cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : []}) cmd_dict['tree.shared'] = dict({'required' : [], 'optional' : ['groups','calc','cutoff','precision','label']}) cmd_dict['unifrac.unweighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','root','processors']}) cmd_dict['unifrac.weighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','root','processors']}) cmd_dict['parsimony'] = dict({'required' : [], 'optional' : ['groups','iters','random','processors']}) cmd_dict['sffinfo'] = dict({'required' : ['sff'], 'optional' : ['fasta','qfile','trim','sfftxt','flow','accnos']}) cmd_dict['fastq.info'] = dict({'required' : ['fastq'], 'optional' : []}) cmd_dict['heatmap.bin'] = dict({'required' : [], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']}) cmd_dict['heatmap.sim'] = dict({'required' : [], 'optional' : ['calc','phylip','column','name','label','groups']}) cmd_dict['venn'] = dict({'required' : [], 'optional' : ['calc','label','groups','abund','nseqs','permute']}) cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : []}) cmd_dict['pca'] = dict({'required' : [], 'optional' : ['label','groups','metric']}) cmd_dict['nmds'] = dict({'required' : ['phylip'], 'optional' : ['axes','mindim','maxdim','iters','maxiters','epsilon']}) cmd_dict['corr.axes'] = dict({'required' : [['shared','relabund','metadata'],'axes'], 'optional' : ['label','groups','method','numaxes']}) cmd_dict['get.group'] = dict({'required' : [], 'optional' : []}) cmd_dict['phylotype'] = dict({'required' : ['taxonomy'],'optional' : ['name','cutoff','label']}) cmd_dict['phylo.diversity'] = dict({'required' : [],'optional' : ['groups','iters','freq','scale','rarefy','collect','summary','processors']}) cmd_dict['get.oturep'] = dict({'required' : ['fasta','list'], 'optional' : ['phylip','column','name','label','group','groups','sorted','precision','cutoff','large','weighted']}) cmd_dict['get.relabund'] = dict({'required' : [],'optional' : ['scale','label','groups']}) cmd_dict['libshuff'] = dict({'required' : [],'optional' : ['iters','form','step','cutoff']}) # clearcut options not needed in galaxy: 'version','verbose','quiet','stdout' cmd_dict['clearcut'] = dict({'required' : [['list','fasta']],'optional' : ['seed','norandom','shuffle','neighbor','expblen','expdist','ntrees','matrixout','kimura','jukes','protein','DNA']}) cmd_dict['get.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']}) cmd_dict['remove.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']}) cmd_dict['bootstrap.shared'] = dict({'required' : [], 'optional' : ['calc','groups','iters','label']}) cmd_dict['cluster.classic'] = dict({'required' : ['phylip'] , 'optional' : ['method','cutoff','hard','precision']}) cmd_dict['get.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','taxonomy']}) cmd_dict['remove.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','taxonomy']}) cmd_dict['get.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']}) cmd_dict['remove.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']}) cmd_dict['remove.rare'] = dict({'required' : [['list','sabund','rabund','shared'],'nseqs'], 'optional' : ['group','groups','label','bygroup']}) cmd_dict['parse.list'] = dict({'required' : ['list','group'], 'optional' : ['label']}) cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size','persample']}) cmd_dict['consensus.seqs'] = dict({'required' : ['fasta'], 'optional' : ['list','name','label']}) cmd_dict['indicator'] = dict({'required' : ['tree',['shared','relabund']], 'optional' : ['groups','label','design']}) cmd_dict['amova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']}) cmd_dict['homova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']}) cmd_dict['anosim'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']}) cmd_dict['mantel'] = dict({'required' : ['phylip','phylip2'] , 'optional' : ['method','iters']}) cmd_dict['make,fastq'] = dict({'required' : ['fasta','qfile'] , 'optional' : []}) """ parser = optparse.OptionParser() # Options for managing galaxy interaction parser.add_option( '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout' ) parser.add_option( '--cmd', dest='cmd', help='The mothur command' ) parser.add_option( '--inputdir', dest='inputdir', help='The directory in which to work' ) parser.add_option( '--outputdir', dest='outputdir', help='The directory in which to work' ) parser.add_option( '--tmpdir', dest='tmpdir', help='The directory in which to work' ) parser.add_option( '--tempdefault', dest='tempdefault', help='The default directory in which to search for input' ) parser.add_option( '--result', dest='result', help='The name pattern and destination for each output file' ) parser.add_option( '--new_file_path', dest='new_file_path', help='The Galaxy new_file_path, dir for extra output datasets' ) parser.add_option( '--datasetid', dest='datasetid', help='The Galaxy new_file_path, dir for extra output datasets' ) parser.add_option( '--new_datasets', dest='new_datasets', help='The name pattern and datatype ext for ouputs' ) # Options for prerequisite Read commands parser.add_option( '--READ_cmd', dest='READ_cmd', help='The mothur command' ) # required arguments for Read.dist parser.add_option( '--READ_phylip', dest='READ_phylip', help='' ) parser.add_option( '--READ_column', dest='READ_column', help='' ) # required arguments for Read.otu parser.add_option( '--READ_rabund', dest='READ_rabund', help='' ) parser.add_option( '--READ_sabund', dest='READ_sabund', help='' ) parser.add_option( '--READ_list', dest='READ_list', help='' ) parser.add_option( '--READ_shared', dest='READ_shared', help='' ) parser.add_option( '--READ_relabund', dest='READ_relabund', help='' ) # required arguments for Read.tree parser.add_option( '--READ_tree', dest='READ_tree', help='' ) # optional arguments for Read cmds parser.add_option( '--READ_name', dest='READ_name', help='' ) parser.add_option( '--READ_cutoff', dest='READ_cutoff', type="float", help='' ) parser.add_option( '--READ_hard', dest='READ_hard', help='' ) parser.add_option( '--READ_precision', dest='READ_precision', type="int", help='' ) parser.add_option( '--READ_sim', dest='READ_sim', help='' ) parser.add_option( '--READ_group', dest='READ_group', help='' ) parser.add_option( '--READ_groups', dest='READ_groups', help='' ) parser.add_option( '--READ_ordergroup', dest='READ_ordergroup', help='') parser.add_option( '--READ_label', dest='READ_label', help='' ) # Parameter specified in mothur parser.add_option( '--numbases', dest='numbases', type="int", help='Number of base to allow' ) 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' ) parser.add_option( '--maxlength', dest='maxlength', type="int", help='Maximun sequence length' ) parser.add_option( '--oligos', dest='oligos', help='The oligos option takes a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier.' ) parser.add_option( '--bdiffs', dest='bdiffs', type="int", help='Number of barcode differences to allow' ) parser.add_option( '--pdiffs', dest='pdiffs', type="int", help='Number of primer differences to allow' ) parser.add_option( '--tdiffs', dest='tdiffs', type="int", help='Total number of barcode and primer differences to allow' ) parser.add_option( '--diffs', dest='diffs', type="int", help='Number of mismatched bases to allow between sequences in a group' ) parser.add_option( '--allfiles', dest='allfiles', help='T - generate fasta and group for each barcode' ) parser.add_option( '--name', dest='name', 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' ) parser.add_option( '--list', dest='list', help='A file containing a list of names' ) parser.add_option( '--alignreport', dest='alignreport', help='A align.report file ' ) parser.add_option( '--taxonomy', dest='taxonomy', help='A Taxonomy file' ) parser.add_option( '--reftaxonomy', dest='reftaxonomy', help='A Taxonomy file' ) 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' ) parser.add_option( '--candidate', dest='candidate', help=' file ' ) parser.add_option( '--template', dest='template', help=' file ' ) parser.add_option( '--reference', dest='reference', help=' file ' ) parser.add_option( '--dups', dest='dups', help='if True also apply to the aliases from the names files' ) parser.add_option( '--keep', dest='keep', help='Either front or back to specify the which end of the sequence to keep' ) parser.add_option( '--search', dest='search', help='Method for finding the template sequence: kmer, blast, suffix' ) parser.add_option( '--ksize', dest='ksize', type="int", help='Size of kmers (5 - 12)' ) parser.add_option( '--align', dest='align', help='Alignment method: needleman, blastn, gotoh' ) parser.add_option( '--match', dest='match', type="float", help='Reward for a match, default is +1.0' ) parser.add_option( '--mismatch', dest='mismatch', type="float", help='Penalty for a mismatch, default is -1.0' ) parser.add_option( '--gapopen', dest='gapopen', type="float", help='Penalty for a opening, default is -2.0' ) parser.add_option( '--gapextend', dest='gapextend', type="float", help='Penalty for extending a gap, default is -1.0' ) parser.add_option( '--precision', dest='precision', type="int", help='' ) parser.add_option( '--threshold', dest='threshold', type="float", help='Cutoff at which an alignment is deemed bad and the reverse complement may be tried, 0.0 - 1.0 default 0.50' ) parser.add_option( '--map', dest='map', help='File containing the secondary structure map.' ) parser.add_option( '--label', dest='label', type='string', action="callback", callback=multi_val_callback, help='Distance levels you would like a output files created for(separated by commas or dashes)' ) parser.add_option( '--filter', dest='filter', help='If true, a 50% soft filter will be applied' ) parser.add_option( '--correction', dest='correction', help='If true, square root of the distances is used instead of the distance value' ) parser.add_option( '--window', dest='window', type="int", help='Window size for searching for chimeras, default is 1/4 sequence length' ) parser.add_option( '--increment', dest='increment', type="int", help='How far you move each window while finding chimeric sequences, default is 25' ) parser.add_option( '--mask', dest='mask', help='A file containing one sequence you wish to use as a mask for the your sequences' ) parser.add_option( '--numwanted', dest='numwanted', type="int", help='How many sequences you would each query sequence compared with' ) parser.add_option( '--start', dest='start', type="int", help='Remove sequences that start after thisposition' ) parser.add_option( '--end', dest='end', type="int", help='Remove sequences that end before this position' ) parser.add_option( '--criteria', dest='criteria', type="int", help='Percentage of sequences to match' ) parser.add_option( '--optimize', dest='optimize', help='List of parameters to optimize' ) parser.add_option( '--vertical', dest='vertical', help='Ignore any column that only contains gap characters, "-" or "."' ) parser.add_option( '--trump', dest='trump', help='Remove a column if the trump character is found at that position in any sequence of the alignment.' ) parser.add_option( '--soft', dest='soft', type='int', help='Soft Mask - percentage required to retain column. (0-100)' ) parser.add_option( '--hard', dest='hard', help='Hard Column Filter - A file should only contain one line consisting of 0 and 1 chars' ) parser.add_option( '--calc', dest='calc', help='Calc Method - Gap Penality' ) parser.add_option( '--countends', dest='countends', help='Penalize terminal gaps' ) # parser.add_option( '--cutoff', dest='cutoff', type="float", help='Distance Cutoff threshold, discard larger distances' ) parser.add_option( '--cutoff', dest='cutoff', help='Distance Cutoff threshold, discard larger distances' ) parser.add_option( '--countgaps', dest='countgaps', help='count gaps as bases' ) parser.add_option( '--output', dest='output', help='Format for output' ) parser.add_option( '--method', dest='method', help='Method to use for analysis - cluster' ) parser.add_option( '--splitmethod', dest='splitmethod', help='Method to split a distance file - cluster.split' ) parser.add_option( '--split', dest='split', help='Chimera split parameter, whether to detect trimeras and quadmeras' ) parser.add_option( '--abund', dest='abund', type='int', help='Threshold for rare to Abundant OTU classification' ) parser.add_option( '--size', dest='size', type='int', help='Size - sample size' ) parser.add_option( '--groupmode', dest='groupmode', help='Collate groups into one result table' ) parser.add_option( '--all', dest='all', help='Calculate for all' ) parser.add_option( '--freq', dest='freq', type="float", help='Frequency of sequences to choose, as fraction is 0.0 - 1.0 or iteration if int > 1' ) parser.add_option( '--iters', dest='iters', type='int', help='Iterations of randomizations' ) parser.add_option( '--maxiters', dest='maxiters', type='int', help='Iterations of randomizations' ) 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' ) parser.add_option( '--parents', dest='parents', type='int', help='Number of Parents to investigate' ) parser.add_option( '--minsim', dest='minsim', type='int', help='Minimum simarity (0-100 percent)' ) parser.add_option( '--mincov', dest='mincov', type='int', help='Minimum coverage (0-100 percent)' ) parser.add_option( '--minbs', dest='minbs', type='int', help='Minimum bootstrap support (0-100 percent)' ) parser.add_option( '--minsnp', dest='minsnp', type='int', help='Minimum SNPs to sample(0-100 percent)' ) parser.add_option( '--mindim', dest='mindim', type='int', help='Minimum dimensions' ) parser.add_option( '--maxdim', dest='maxdim', type='int', help='Maximum dimensions' ) parser.add_option( '--percent', dest='percent', type='int', help='(0-100 percent)' ) parser.add_option( '--divergence', dest='divergence', type='float', help='Divergence cutoff for chimera determination' ) parser.add_option( '--sff', dest='sff', help='Sff file' ) parser.add_option( '--svg', dest='svg', help='SVG' ) parser.add_option( '--sfftxt', dest='sfftxt', help='Generate a sff.txt file' ) parser.add_option( '--flow', dest='flow', help='Generate a flowgram file' ) parser.add_option( '--trim', dest='trim', help='Whether sequences and quality scores are trimmed to the clipQualLeft and clipQualRight values' ) parser.add_option( '--input', dest='input', help='' ) parser.add_option( '--phylip', dest='phylip', help='' ) parser.add_option( '--phylip2', dest='phylip2', help='' ) parser.add_option( '--column', dest='column', help='' ) parser.add_option( '--sort', dest='sort', help='specify sort order' ) parser.add_option( '--sorted', dest='sorted', help='Input is presorted' ) parser.add_option( '--showabund', dest='showabund', help='' ) parser.add_option( '--short', dest='short', help='Keep sequences that are too short to chop' ) parser.add_option( '--distance', dest='distance', help='' ) parser.add_option( '--scale', dest='scale', help='' ) parser.add_option( '--numotu', dest='numotu', help='' ) parser.add_option( '--fontsize', dest='fontsize', help='' ) parser.add_option( '--neqs', dest='neqs', help='' ) parser.add_option( '--random', dest='random', help='' ) parser.add_option( '--permute', dest='permute', help='' ) parser.add_option( '--rarefy', dest='rarefy', help='' ) parser.add_option( '--collect', dest='collect', help='' ) parser.add_option( '--summary', dest='summary', help='' ) parser.add_option( '--large', dest='large', help='' ) parser.add_option( '--shuffle', dest='shuffle', help='' ) parser.add_option( '--neighbor', dest='neighbor', help='' ) parser.add_option( '--expblen', dest='expblen', help='' ) parser.add_option( '--expdist', dest='expdist', help='' ) parser.add_option( '--ntrees', dest='ntrees', help='' ) parser.add_option( '--DNA', dest='DNA', help='' ) parser.add_option( '--protein', dest='protein', help='' ) parser.add_option( '--kimura', dest='kimura', help='' ) parser.add_option( '--jukes', dest='jukes', help='' ) parser.add_option( '--matrixout', dest='matrixout', help='' ) parser.add_option( '--nseqs', dest='nseqs', help='' ) parser.add_option( '--bygroup', dest='bygroup', help='' ) parser.add_option( '--design', dest='design', help='' ) parser.add_option( '--sets', dest='sets', help='' ) parser.add_option( '--metric', dest='metric', help='' ) parser.add_option( '--epsilon', dest='epsilon', help='' ) parser.add_option( '--alpha', dest='alpha', help='' ) parser.add_option( '--root', dest='root', help='' ) parser.add_option( '--axes', dest='axes', help='table of name column followed by columns of axis values' ) parser.add_option( '--numaxes', dest='numaxes', help='the number of axes' ) parser.add_option( '--metadata', dest='metadata', help='data table with columns of floating-point values' ) parser.add_option( '--basis', dest='basis', help='what the summary file represents' ) parser.add_option( '--keepfirst', dest='keepfirst', help='trimming' ) parser.add_option( '--removelast', dest='removelast', help='trimming' ) parser.add_option( '--persample', dest='persample', help='sub sample option' ) parser.add_option( '--timing', dest='timing', help='timing option' ) parser.add_option( '--processors', dest='processors', type='int', action='callback', callback=processors_callback, help='Number of processors to use' ) # include read.otu options parser.add_option( '--rabund', dest='rabund', help='' ) parser.add_option( '--sabund', dest='sabund', help='' ) parser.add_option( '--shared', dest='shared', help='' ) parser.add_option( '--relabund', dest='relabund', help='' ) parser.add_option( '--ordergroup', dest='ordergroup', help='') # include read.tree options parser.add_option( '--tree', dest='tree', help='' ) (options, args) = parser.parse_args() """ """ # print >> sys.stderr, options # so will appear as blurb for file if options.debug != None: debug = options.debug params = [] inputdir = None outputdir = None tmp_dir = None tempdefault = '' # Report exception if no command is given if options.cmd == None: stop_err('No mothur command given') # Read directory options if options.tmpdir != None: if not os.path.isdir(options.tmpdir): os.makedirs(options.tmpdir) tmp_dir = options.tmpdir else: if options.outputdir != None: if not os.path.isdir(options.outputdir): os.makedirs(options.outputdir) tmp_dir = os.path.join(options.outputdir,'tmp') if not os.path.isdir(tmp_dir): os.makedirs(tmp_dir) else: tmp_dir = tempfile.mkdtemp() if options.inputdir != None: if not os.path.isdir(options.inputdir): os.makedirs(options.inputdir) inputdir = options.inputdir if options.outputdir != None: if not os.path.isdir(options.outputdir): os.makedirs(options.outputdir) try: outputdir = os.path.join(tmp_dir,'out') os.symlink(options.outputdir,outputdir) except Exception, e: print >> sys.stderr, e outputdir = options.outputdir # Set directories if inputdir == None or not os.path.isdir(inputdir): inputdir = tmp_dir if outputdir == None or not os.path.isdir(outputdir): outputdir = tempfile.mkdtemp() if options.tempdefault != None and os.path.isdir(options.tempdefault): tempdefault = ', tempdefault=%s' % options.tempdefault # params.append('set.dir(input=%s,output=%s%s)' % (inputdir,outputdir,tempdefault)) params.append('set.dir(output=%s%s)' % (outputdir,tempdefault)) # Check for prerequisite read command if options.READ_cmd != None: read_cmd_opts = ','.join(get_params(options.READ_cmd,options,inputdir,prefix='READ_')) params.append('%s(%s)' % (options.READ_cmd,read_cmd_opts)) # Check for command options cmd_opts = ','.join(get_params(options.cmd,options,inputdir)) # print >> sys.stderr, cmd_opts # print >> sys.stderr, params # so will appear as blurb for file params.append('%s(%s)' % (options.cmd,cmd_opts)) if debug: params.append('get.current()') try: # Generate the mothur commandline # http://www.mothur.org/wiki/Command_line_mode cmdline = 'mothur "#' + '; '.join(params) + '"' if debug: print >> sys.stdout, '%s' % cmdline if tmp_dir == None or not os.path.isdir(tmp_dir): tmp_dir = tempfile.mkdtemp() tmp_stderr_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.err' ).name tmp_stderr = open( tmp_stderr_name, 'wb' ) tmp_stdout_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.out' ).name tmp_stdout = open( tmp_stdout_name, 'wb' ) proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno() ) # proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE, stdout=subprocess.PIPE ) returncode = proc.wait() if debug: print >> sys.stdout, 'returncode %d' % returncode tmp_stderr.close() # get stderr, allowing for case where it's very large tmp_stderr = open( tmp_stderr_name, 'rb' ) stderr = '' buffsize = 1048576 try: while True: stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass tmp_stderr.close() tmp_stdout.close() if debug: print >> sys.stdout, 'parse %s' % tmp_stdout_name if returncode != 0: try: # try to copy stdout to the logfile for output in options.result.split(','): # Each item has a regex pattern and a file path to a galaxy dataset (pattern,path) = output.split(':') if debug: print >> sys.stdout, '%s -> %s' % (pattern,path) if pattern.find('\.logfile') > 0: if path != None and os.path.exists(path): logfile_to_html(tmp_stdout_name,path,inputdir,outputdir,title="Mothur %s Error Logfile" % options.cmd) break except: pass raise Exception, stderr stdout = '' # Parse stdout to provide info tmp_stdout = open( tmp_stdout_name, 'rb' ) # try to find a "little" something interesting to print as info for the galaxy interface info = '' if options.cmd.startswith('chimera') and not options.cmd.endswith('check'): pattern = '^.*$' if options.cmd == 'chimera.slayer': # gi|11093931|MNE12|AF293003 yes pattern = '\S.*\tyes$' elif options.cmd == 'chimera.bellerophon': # gi|11093939|MNB2|AF293011 is a suspected chimera at breakpoint 2195 pattern = '\S.* suspected chimera .*' elif options.cmd == 'chimera.ccode': # gi|11093940|MNF8|AF293012 was found have at least one chimeric window. pattern = '\S.* chimeric window.*' elif options.cmd == 'chimera.pintail': pattern = '\S.*chimera.*Yes' # move new generated template .freq and .quan files to outputdir chimera_count = 0 for line in tmp_stdout: if re.match(pattern,line): chimera_count += 1 info += "Chimeras: %d" % chimera_count else: found_begin = False info_chars = 0 for line in tmp_stdout: if line.find(outputdir) >= 0: continue if line.startswith('**************'): continue if re.match('^Processing.*',line): continue if re.match('^Reading .*',line): continue if re.match('^Merging .*',line): continue if re.match('^DONE.*',line): continue if re.match('.*\.\.\.\s*$',line): continue if re.match('^\d*\s*$',line): continue # if re.match('^(unique|[0-9.]*)(\t\d+)+',line): # abundance from cluster commands if not options.cmd.startswith('unifrac') and re.match('^([0-9.]+)(\t\d+)*',line): # abundance from cluster commands, allow unique line into info continue if re.match('Output .*',line): break if found_begin and info_chars < 200: info += "%s" % line info_chars += len(line) if re.match('mothur > ' + options.cmd + '\(.*\)', line): found_begin = True tmp_stdout.close() print >> sys.stdout, info # Collect output files flist = os.listdir(outputdir) if debug: print >> sys.stdout, '%s' % flist # chimera.check can generate svg files, but they are not listed in the mothur.*.logfile, so we'll added them in here if options.cmd == 'chimera.check': svgs = [] mothurlog = None for fname in flist: if fname.endswith('.svg'): svgs.append(fname) elif fname.endswith('.logfile'): mothurlog = fname # process option result first # These are the known galaxy datasets listed in the --result= param if len(flist) > 0 and options.result: # items in list are separated by commas for output in options.result.split(','): # Each item has a regex pattern and a file path to a galaxy dataset (pattern,path) = output.split(':') if debug: print >> sys.stdout, '%s -> %s' % (pattern,path) if path == None or path == 'None': continue found = False for fname in flist: if debug: print >> sys.stdout, 'outdir %s match: %s' % (fname,re.match(pattern,fname)) if re.match(pattern,fname): found = True flist.remove(fname) fpath = os.path.join(outputdir,fname) if fname.endswith('.logfile'): # Make the logfile into html logfile_to_html(fpath,path,inputdir,outputdir,title="Mothur %s Logfile" % options.cmd) elif outputdir == options.outputdir: # Use a hard link if outputdir is the extra_files_path, allows link from mothur logfile without copying data. try: if debug: print >> sys.stdout, 'link %s %s' % (fpath, path) os.link(fpath, path) except: if debug: print >> sys.stdout, 'copy %s %s' % (fpath, path) shutil.copy2(fpath, path) else: if debug: print >> sys.stdout, 'copy2 %s %s' % (fpath, path) shutil.copy2(fpath, path) break # mothur.*.logfile may be in tmp_dir # chimera.pintail e.g. generates files in the working dir that we might want to save if not found: for fname in os.listdir(tmp_dir): if debug: print >> sys.stdout, 'tmpdir %s match: %s' % (fname,re.match(pattern,fname)) if re.match(pattern,fname): fpath = os.path.join(tmp_dir,fname) if fname.endswith('.logfile'): # Make the logfile into html logfile_to_html(fpath,path,inputdir,outputdir,title="Mothur %s Logfile" % options.cmd) else: shutil.copy2(fpath, path) break # Handle the dynamically generated galaxy datasets # http://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput # --new_datasets= specifies files to copy to the new_file_path # The list items are separated by commas # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :) # The regex match.groups()[0] is used as the id name of the dataset, and must result in unique name for each output if options.new_datasets != None and options.new_file_path != None and options.datasetid != None: datasets = options.new_datasets.split(',') for output in options.new_datasets.split(','): (pattern,ext) = output.split(':'); for fname in flist: m = re.match(pattern,fname) if m: fpath = os.path.join(outputdir,fname) if len(m.groups()) > 0: # remove underscores since galaxy uses that as a field separator for dynamic datasets root = m.groups()[0].replace('_','') else: # remove the ext from the name if it exists, galaxy will add back later # remove underscores since galaxy uses that as a field separator for dynamic datasets root = re.sub('\.?'+ext+'$','',fname).replace('_','').replace('.','') # filename pattern required by galaxy fn = "%s_%s_%s_%s_%s" % ( 'primary', options.datasetid, root, 'visible', ext ) if debug: print >> sys.stdout, '> %s' % fpath if debug: print >> sys.stdout, '< %s' % os.path.join(options.new_file_path,fn) try: os.link(fpath, os.path.join(options.new_file_path,fn)) except: shutil.copy2(fpath, os.path.join(options.new_file_path,fn)) except Exception, e: msg = str(e) + stderr """ if len(msg) < 50 and stdout != None: # include the last line of stdout msg += stdout.splitlines()[-1] """ stop_err( 'Error running ' + msg) finally: # Only remove temporary directories # Enclose in try block, so we don't report error on stale nfs handles try: if outputdir != options.outputdir and os.path.exists(outputdir): if os.path.islink(outputdir): if debug: print >> sys.stdout, 'rm outputdir %s' % outputdir os.remove(outputdir) if debug: print >> sys.stdout, 'rmtree outputdir %s' % outputdir shutil.rmtree(os.path.dirname(outputdir)) else: if debug: print >> sys.stdout, 'rmtree %s' % outputdir shutil.rmtree(outputdir) if inputdir != options.inputdir and os.path.exists(inputdir): if debug: print >> sys.stdout, 'rmtree %s' % inputdir shutil.rmtree(inputdir) except: if debug: print >> sys.stdout, 'rmtree failed' pass if __name__ == "__main__": __main__()