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()
