Renames the command sub-moduel to commands

python/orgasm/commands/compact.py

+'''
+Created on 28 sept. 2014
+
+@author: coissac
+'''
+
+import orgasm.samples
+
+from orgasm import getIndex, getSeeds,getOutput
+from orgasm.tango import cutLowCoverage, cutSNPs,\
+    estimateDeadBrancheLength, estimateFragmentLength,\
+    genesincontig, scaffold, fillGaps, dumpGraph, restoreGraph
+
+import sys
+
+
+__title__="Recompact the assembling graph"
+ 
+default_config = { 'seeds' : None
+                 }
+
+
+def addOptions(parser):
+    parser.add_argument(dest='orgasm:indexfilename',  metavar='index', 
+                        help='index root filename (produced by the oa index command)')
+    
+    parser.add_argument(dest='orgasm:outputfilename',     metavar='output', 
+                                                          nargs='?', 
+                                                          default=None,
+                        help='output prefix' )
+    
+    
+    
+    parser.add_argument('--back',             dest='orgasm:back', 
+                                              type=int, 
+                                              action='store', 
+                                              default=None, 
+                        help='the number of bases taken at the end of '
+                             'contigs to jump with pared-ends [default: <estimated>]')
+    
+
+
+def run(config):
+    
+    logger=config['orgasm']['logger']
+    output = getOutput(config)
+    
+    r = getIndex(config)
+    coverage,x,newprobes = getSeeds(r,config)  
+    
+    asm = restoreGraph(output+'.oax',r,x)
+    meanlength,sdlength = estimateFragmentLength(asm)
+
+    if config['orgasm']['back'] is not None:
+        back = config['orgasm']['back']
+    elif config['orgasm']['back'] is None and meanlength is not None:
+        back = int(meanlength + 4 * sdlength)
+        if back > 500:
+            back=500
+    else:
+        back = 300
+        
+    if meanlength is not None:
+        logger.info("Fragment length estimated : %f pb (sd: %f)" % (meanlength,sdlength))
+
+        
+    cg = asm.compactAssembling(verbose=False)
+    logger.info("Scaffold the assembly")
+    scaffold(asm,cg,minlink=5,back=int(back),addConnectedLink=False)
+    genesincontig(cg,r,x)
+    with open(output+'.gml','w') as gmlfile:
+        print(cg.gml(),file=gmlfile)

python/orgasm/commands/cutlow.py

+'''
+Created on 28 sept. 2014
+
+@author: coissac
+'''
+from orgasm import getOutput,getIndex, getSeeds
+from orgasm.tango import restoreGraph, estimateFragmentLength, genesincontig,\
+    scaffold, cutLowCoverage, estimateDeadBrancheLength, dumpGraph
+
+__title__="Cut low coverage edge in an assembling graph"
+
+default_config = { 'coverage'      : None,
+                   'smallbranches' : None
+                 }
+
+def addOptions(parser):
+    parser.add_argument(dest='orgasm:indexfilename',  metavar='index', 
+                        help='index root filename (produced by the oa index command)')
+    
+    parser.add_argument(dest='orgasm:outputfilename',     metavar='output', 
+                                                          nargs='?', 
+                                                          default=None,
+                        help='output prefix' )
+    
+    
+    parser.add_argument('--coverage',         dest='cutlow:coverage', 
+                                              required=True,
+                                              type=int, 
+                                              action='store', 
+                                              default=None, 
+                        help='All edges with a coverage below this value will be deleted')
+    
+    parser.add_argument('--smallbranches',    dest='cutlow:smallbranches', 
+                                              type=int, 
+                                              action='store', 
+                                              default=None, 
+                        help='maximum length of the branches to cut during '
+                             'the cleaning process [default: <estimated>]')
+
+    parser.add_argument('--back',             dest='orgasm:back', 
+                                              type=int, 
+                                              action='store', 
+                                              default=None, 
+                        help='the number of bases taken at the end of '
+                             'contigs to jump with pared-ends [default: <estimated>]')
+    
+
+
+def run(config):
+
+    logger=config['orgasm']['logger']
+    output = getOutput(config)
+
+    r = getIndex(config)
+    xxx,x,newprobes = getSeeds(r,config)  
+    
+    asm = restoreGraph(output+'.oax',r,x)
+
+    logger.info("Evaluate fragment length")
+    
+    meanlength,sdlength = estimateFragmentLength(asm)
+    
+    if meanlength is not None:
+        logger.info("Fragment length estimated : %f pb (sd: %f)" % (meanlength,sdlength))
+
+    if config['orgasm']['back'] is not None:
+        back = config['orgasm']['back']
+    elif config['orgasm']['back'] is None and meanlength is not None:
+        back = int(meanlength + 4 * sdlength)
+        if back > 500:
+            back=500
+    else:
+        back = 300
+        
+    logger.info("Cut low coverage")
+
+    cutLowCoverage(asm,config['cutlow']['coverage'],terminal=False)
+    
+    if config['cutlow']['smallbranches'] is not None:
+        smallbranches = config['cutlow']['smallbranches']
+    else:
+        smallbranches = estimateDeadBrancheLength(asm)
+        logger.info("Dead branch length setup to : %d bp" % smallbranches)
+    
+    asm.cleanDeadBranches(maxlength=smallbranches)
+    
+    cg = asm.compactAssembling(verbose=False)
+    genesincontig(cg,r,x)
+
+    scaffold(asm,cg,minlink=5,back=int(back),addConnectedLink=False)
+     
+    with open(output+'.gml','w') as gmlfile:
+        print(cg.gml(),file=gmlfile)
+
+    dumpGraph(output+'.oax',asm)
+
+              

python/orgasm/commands/graphstats.py

+'''
+Created on 28 sept. 2014
+
+@author: coissac
+'''
+from orgasm import getOutput,getIndex, getSeeds
+from orgasm.tango import restoreGraph, estimateFragmentLength, genesincontig,\
+    scaffold, selectGoodComponent
+
+__title__="Print some statistics about the assembling graph"
+
+default_config = { 
+                 }
+
+def addOptions(parser):
+    parser.add_argument(dest='orgasm:indexfilename',  metavar='index', 
+                        help='index root filename (produced by the oa index command)')
+    
+    parser.add_argument(dest='orgasm:outputfilename',     metavar='<output>', 
+                                                          nargs='?', 
+                                                          default=None,
+                        help='output prefix' )
+    
+    parser.add_argument('--back',             dest='orgasm:back', 
+                                              metavar='<insert size>',
+                                              type=int, 
+                                              action='store', 
+                                              default=None, 
+                        help='the number of bases taken at the end of '
+                             'contigs to jump with pared-ends [default: <estimated>]')
+
+    
+
+
+def run(config):
+
+    logger=config['orgasm']['logger']
+    output = getOutput(config)
+
+    r = getIndex(config)
+    ecoverage,x,newprobes = getSeeds(r,config)  
+    
+    asm = restoreGraph(output+'.oax',r,x)
+    
+    logger.info("Evaluate fragment length")
+    
+    meanlength,sdlength = estimateFragmentLength(asm)
+    
+    if config['orgasm']['back'] is not None:
+        back = config['orgasm']['back']
+    elif config['orgasm']['back'] is None and meanlength is not None:
+        back = int(meanlength + 4 * sdlength)
+        if back > 500:
+            back=500
+    else:
+        back = 300
+
+    cg = asm.compactAssembling(verbose=False)
+    
+    genesincontig(cg,r,x)
+
+    scaffold(asm,cg,minlink=5,back=int(back),addConnectedLink=False)
+
+    ccs = list(cg.connectedComponentIterator())
+    gcc = selectGoodComponent(cg)
+    gnode=set()
+    for cc in gcc:
+        for e in cc:
+            gnode.add(e[0])
+            gnode.add(e[1])
+    
+    ucc = set()
+    for cc in ccs:
+        ccc = frozenset([-x for x in cc])
+        if ccc not in ucc:
+            ucc.add(frozenset(cc))
+        
+
+    output = open(output+".stats","w")
+
+    print ("AssembledBasePairs:",len(asm)/2,file=output)
+    print ("TotalConnectedComponents:",len(ccs),file=output)
+    print ("UniqueConnectedComponents:",len(ucc),file=output)
+    print ("GoodConnectedComponents:",len(ucc),file=output)
+    print ("CompactNodes:",len(cg),file=output)
+    print ("GoodCompactNodes:",len(gnode),file=output)
+    print ("CompactEdges:",cg.edgeCount(),file=output)
+    print ("GoodCompactEdges:",sum(len(x) for x in gcc),file=output)
+    print ("FragmentMeanLength:",meanlength,file=output)
+    print ("FragmentSdLength:",sdlength,file=output)
+    
+    
+    
+
+              

python/orgasm/commands/list.py

+'''
+Created on 28 sept. 2014
+
+@author: coissac
+'''
+from orgasm import getIndex
+
+__title__="List information about a read index"
+
+default_config = { 
+                 }
+
+def addOptions(parser):
+    parser.add_argument(dest='orgasm:indexfilename',  metavar='index', 
+                        help='index root filename (produced by the oa index command)')
+    
+
+
+def run(config):
+
+    r = getIndex(config)
+    
+    print(len(r),r.getReadSize())
+
+              

python/orgasm/commands/path.py

+'''
+Created on 28 sept. 2014
+
+@author: coissac
+'''
+from orgasm import getOutput,getIndex, getSeeds
+from orgasm.tango import restoreGraph, estimateFragmentLength, genesincontig,\
+     scaffold, path2fasta
+
+__title__="Build a fasta file from a path across the assembling graph"
+
+default_config = { 
+                 }
+
+def addOptions(parser):
+    parser.add_argument(dest='orgasm:indexfilename',  metavar='<index>', 
+                        help='index root filename (produced by the oa index command)')
+    
+    parser.add_argument(dest='orgasm:outputfilename',     metavar='<output>', 
+                                                          nargs='?', 
+                                                          default=None,
+                        help='output prefix' )
+    
+    
+    parser.add_argument('--path',             dest='path:path', 
+                                              action='store',
+                                              metavar='<edgeid>',
+                                              type=int, 
+                                              nargs='+', 
+                                              required=True,
+                                              default=None, 
+                        help='A list of edge id separated by space add -- at the end of the path')
+
+    
+    parser.add_argument('--back',             dest='orgasm:back', 
+                                              metavar='<insert size>',
+                                              type=int, 
+                                              action='store', 
+                                              default=None, 
+                        help='the number of bases taken at the end of '
+                             'contigs to jump with pared-ends [default: <estimated>]')
+
+
+def run(config):
+
+    logger=config['orgasm']['logger']
+    output = getOutput(config)
+
+    r = getIndex(config)
+    ecoverage,x,newprobes = getSeeds(r,config)  
+    
+    asm = restoreGraph(output+'.oax',r,x)
+
+    logger.info("Evaluate fragment length")
+    
+    meanlength,sdlength = estimateFragmentLength(asm)
+    
+    if meanlength is not None:
+        logger.info("Fragment length estimated : %f pb (sd: %f)" % (meanlength,sdlength))
+
+    if config['orgasm']['back'] is not None:
+        back = config['orgasm']['back']
+    elif config['orgasm']['back'] is None and meanlength is not None:
+        back = int(meanlength + 4 * sdlength)
+        if back > 500:
+            back=500
+    else:
+        back = 300
+
+    cg = asm.compactAssembling(verbose=False)
+    
+    genesincontig(cg,r,x)
+
+    scaffold(asm,cg,minlink=config['orgasm']['minlink'],
+             back=int(back),addConnectedLink=False)
+
+    fastaout = open(output+".fasta","w")
+    pathout  = open(output+".path","w")
+        
+    logger.info("Print the result as a fasta file")
+    
+    c=1
+    
+    path = config['path']['path']
+    
+    logger.info('Built path : %s' % str(path))
+                
+    fa = path2fasta(asm,cg,path,
+         identifier="Seq_%d" % c,
+         back=back,
+         minlink=config['orgasm']['minlink'],
+         logger=logger)
+    print(fa,file=fastaout)
+    print(" ".join([str(x) for x in path]),file=pathout)
+
+    print(cg.gml(),file=open(output +'.path.gml','w'))
+              

python/orgasm/commands/seeds.py

+'''
+Created on 28 sept. 2014
+
+@author: coissac
+'''
+
+import orgasm.samples
+
+from orgasm import getOutput,getIndex, getSeeds, getAdapters
+from orgasm.tango import matchtoseed, cutLowCoverage, cutSNPs,\
+    estimateDeadBrancheLength, estimateFragmentLength,\
+    genesincontig, scaffold, fillGaps, dumpGraph, restoreGraph
+
+from orgasm.assembler import Assembler,tango
+import sys
+
+
+__title__="Build the set of seed reads"
+
+
+default_config = { "reformat" : None
+                 }
+
+def addOptions(parser):
+    parser.add_argument(dest='orgasm:indexfilename',  metavar='index', 
+                        help='index root filename (produced by the oa index command)')
+    
+    parser.add_argument(dest='orgasm:outputfilename',     metavar='output', 
+                                                          nargs='?', 
+                                                          default=None,
+                        help='output prefix' )
+    
+    
+    parser.add_argument('--seeds',            dest ='orgasm:seeds', 
+                                              metavar='seeds', 
+                                              action='append',
+                                              default=[], 
+                                              type=str, 
+                        help='protein or nucleic seeds; either a fasta file containing '
+                        'seed sequences or the name of one of the internal set of seeds '
+                        'among %s' % str(list(filter(lambda s: s.startswith('prot') or 
+                                                s.startswith('nuc'),dir(orgasm.samples)))))
+
+    parser.add_argument('--kup',              dest='orgasm:kup', 
+                                              type=int, 
+                                              action='store', 
+                                              default=None, 
+                        help='The word size used to identify the seed reads '
+                             '[default: protein=4, DNA=12]')
+
+    parser.add_argument("--reformat",
+                        dest="seeds:reformat",
+                        action='store_true',
+                        default=None,
+                        help='Asks for reformatting an old sequence index to the new format'
+                       )
+
+
+def run(config):
+    
+    logger=config['orgasm']['logger']
+    progress = config['orgasm']['progress']
+    output = getOutput(config)
+
+    logger.info("Looking for the seed reads")
+    
+    r = getIndex(config)
+    ecoverage,x,newprobes = getSeeds(r,config)   
+
+    logger.info('Coverage estimated from probe matches at : %d' % ecoverage)
+