def main01():
#config = Config(open(os.path.normpath('/Users/ivan/Documents/work/binning/tests/CowRumen/01/config.cfg')), 'pPPS')
#config = Config(open(os.path.normpath('/net/metagenomics/projects/PPSmg/tests/V35/config.cfg')), 'pPPS')
#configMl = Config2(config, 'MLTreeMap')
#configPPS = Config2(config, 'PPS')
#read sequences
#sequences = Sequences(config)
#write ids file
#sequences.writeSequences(config.get('inputIdsFastaFile'))
#taxonomy = Taxonomy(config.get('databaseFile'), config.get('taxonomicRanks').split(','))
taxonomicRanks = 'superkingdom,phylum,class,order,family,genus,species'.split(',')
taxonomy = Taxonomy('/Users/ivan/Documents/work/binning/taxonomy/20120828/ncbitax_sqlite.db', taxonomicRanks)
#ppsOut2ppOut('D:\\VM\\tmp\\simMC_AMD\\AMD.Arachne.genus', 'D:\\VM\\tmp\\simMC_AMD\\AMD.Arachne.genus.PP.out', taxonomy, config.get('taxonomicRanks').split(','))
#ppsOut2ppOut('/Users/ivan/Documents/work/binning/data/CowRumen/cowRumenOrderNcbids.txt',
# '/Users/ivan/Documents/work/binning/data/CowRumen/cowRumenOrderNcbids.PP.txt', taxonomy, config.get('taxonomicRanks').split(','))
#ppsOut2ppOut('/net/metagenomics/projects/PPSmg/data/V35/contigsMappedBlast1000LabelsSpecies.txt',
# '/net/metagenomics/projects/PPSmg/data/V35/contigsMappedBlast1000LabelsSpecies.PP.txt', taxonomy, config.get('taxonomicRanks').split(','))
ppsOut2ppOut('/Users/ivan/Documents/work/binning/data/simMC/fromJohannes/contigs.genus.tax',
'/Users/ivan/Documents/work/binning/data/simMC/fromJohannes/contigs.genus.PP.tax', taxonomy, taxonomicRanks)
#readPPSOutput(sequences, taxonomy, config.get('inputIdsFastaFile'))
#sequences.writePlacements(str(config.get('inputIdsFastaFile') + '.pOUT'), config.get('taxonomicRanks').split(','))
#toRealNames(config, sequences)
taxonomy.close()
def ppsOut2ppOut(inFile, outFile, taxonomicRanks, databaseFile):
"""
Transforms a PPS output file into a file in the PP format.
@param inFile: input file in the PPS format (first column: seq name, last column: ncbi taxon id)
@param outFile: output file in the PP format
@param taxonomicRanks: taxonomic ranks (starting from superkingdom)
@param databaseFile: database file in the sqlite3 format
"""
taxonomy = Taxonomy(databaseFile, taxonomicRanks)
outBuff = csv.OutFileBuffer(outFile)
namesList = csv.getColumnAsList(inFile,
entryModifyFunction=None,
colNum=0,
sep='\t',
comment='#')
valCol = 1
ncbidsList = csv.getColumnAsList(inFile,
entryModifyFunction=None,
colNum=valCol,
sep='\t',
comment='#')
while True: # this is not efficient!
valCol += 1
tmpList = csv.getColumnAsList(inFile,
entryModifyFunction=None,
colNum=valCol,
sep='\t',
comment='#')
if len(tmpList) == len(namesList):
ncbidsList = tmpList
else:
break
header = str('#PPS file transformed to PP format, input file: ' +
str(inFile) + '\n#ID' + '\t' + 'root')
for rank in taxonomicRanks:
header += str('\t' + rank)
outBuff.writeText(str(header + '\n'))
for i in range(len(namesList)):
name = namesList[i]
ncbid = ncbidsList[i]
taxPathDict = taxonomy.getPathToRoot(int(ncbid))
buff = str(name)
if taxPathDict is None:
buff += str('\t')
else:
buff += str('\t' + 'root')
for rank in taxonomicRanks:
if (taxPathDict is not None) and (rank in taxPathDict) and (
not taxPathDict[rank].isCopy()):
buff += str('\t' + taxPathDict[rank].name)
else:
buff += '\t'
outBuff.writeText(str(buff + '\n'))
outBuff.close()
taxonomy.close()
def ppsOut2ppOut(inFile, outFile, taxonomicRanks, databaseFile):
"""
Transforms a PPS output file into a file in the PP format.
@param inFile: input file in the PPS format (first column: seq name, last column: ncbi taxon id)
@param outFile: output file in the PP format
@param taxonomicRanks: taxonomic ranks (starting from superkingdom)
@param databaseFile: database file in the sqlite3 format
"""
taxonomy = Taxonomy(databaseFile, taxonomicRanks)
outBuff = csv.OutFileBuffer(outFile)
namesList = csv.getColumnAsList(inFile, entryModifyFunction=None, colNum=0, sep='\t', comment='#')
valCol = 1
ncbidsList = csv.getColumnAsList(inFile, entryModifyFunction=None, colNum=valCol, sep='\t', comment='#')
while True: # this is not efficient!
valCol += 1
tmpList = csv.getColumnAsList(inFile, entryModifyFunction=None, colNum=valCol, sep='\t', comment='#')
if len(tmpList) == len(namesList):
ncbidsList = tmpList
else:
break
header = str('#PPS file transformed to PP format, input file: ' + str(inFile) + '\n#ID' + '\t' + 'root')
for rank in taxonomicRanks:
header += str('\t' + rank)
outBuff.writeText(str(header + '\n'))
for i in range(len(namesList)):
name = namesList[i]
ncbid = ncbidsList[i]
taxPathDict = taxonomy.getPathToRoot(int(ncbid))
buff = str(name)
if taxPathDict is None:
buff += str('\t')
else:
buff += str('\t' + 'root')
for rank in taxonomicRanks:
if (taxPathDict is not None) and (rank in taxPathDict) and (not taxPathDict[rank].isCopy()):
buff += str('\t' + taxPathDict[rank].name)
else:
buff += '\t'
outBuff.writeText(str(buff + '\n'))
outBuff.close()
taxonomy.close()
def main01():
#config = Config(open(os.path.normpath('/Users/ivan/Documents/work/binning/tests/CowRumen/01/config.cfg')), 'pPPS')
#config = Config(open(os.path.normpath('/net/metagenomics/projects/PPSmg/tests/V35/config.cfg')), 'pPPS')
#configMl = Config2(config, 'MLTreeMap')
#configPPS = Config2(config, 'PPS')
#read sequences
#sequences = Sequences(config)
#write ids file
#sequences.writeSequences(config.get('inputIdsFastaFile'))
#taxonomy = Taxonomy(config.get('databaseFile'), config.get('taxonomicRanks').split(','))
taxonomicRanks = 'superkingdom,phylum,class,order,family,genus,species'.split(
',')
taxonomy = Taxonomy(
'/Users/ivan/Documents/work/binning/taxonomy/20120828/ncbitax_sqlite.db',
taxonomicRanks)
#ppsOut2ppOut('D:\\VM\\tmp\\simMC_AMD\\AMD.Arachne.genus', 'D:\\VM\\tmp\\simMC_AMD\\AMD.Arachne.genus.PP.out', taxonomy, config.get('taxonomicRanks').split(','))
#ppsOut2ppOut('/Users/ivan/Documents/work/binning/data/CowRumen/cowRumenOrderNcbids.txt',
# '/Users/ivan/Documents/work/binning/data/CowRumen/cowRumenOrderNcbids.PP.txt', taxonomy, config.get('taxonomicRanks').split(','))
#ppsOut2ppOut('/net/metagenomics/projects/PPSmg/data/V35/contigsMappedBlast1000LabelsSpecies.txt',
# '/net/metagenomics/projects/PPSmg/data/V35/contigsMappedBlast1000LabelsSpecies.PP.txt', taxonomy, config.get('taxonomicRanks').split(','))
ppsOut2ppOut(
'/Users/ivan/Documents/work/binning/data/simMC/fromJohannes/contigs.genus.tax',
'/Users/ivan/Documents/work/binning/data/simMC/fromJohannes/contigs.genus.PP.tax',
taxonomy, taxonomicRanks)
#readPPSOutput(sequences, taxonomy, config.get('inputIdsFastaFile'))
#sequences.writePlacements(str(config.get('inputIdsFastaFile') + '.pOUT'), config.get('taxonomicRanks').split(','))
#toRealNames(config, sequences)
taxonomy.close()