def ppsOut2Placements(ppsOutFile, scafContigFile=None):
"""
Transforms a PPS assignments to a list of pairs <contigName, assigned_ncbid>
@param ppsOutFile: PPS output file where the first column is the contig/scaffold name and the last column is ncbid
@param scafContigFile: scaffold contig mapping (tab separated) if None then all sequences are considered as contigs
@return: list of pairs <contigName, assigned_ncbid>
"""
#print 'ppsOut2Placements ppsOutFile:', ppsOutFile
#print 'ppsOut2Placements scafContigFile:', scafContigFile
if scafContigFile != None:
scafToContigs = toScafContigMap(scafContigFile)
else:
scafToContigs = dict([])
outList = []
try:
f = open(os.path.normpath(ppsOutFile),'r')
except Exception:
print "Cannot open file:", ppsOutFile
raise
else:
lineCounter = 0
for line in f:
lineCounter += 1
line = common.noNewLine(line)
name = re.sub(r'^([^ \t]+)[ \t]+.*[0-9]+[ \t]*$',r'\1' ,line)
try:
ncbid = int(re.sub(r'^[^ \t]+.*[ \t]+([0-9]+)[ \t]*$',r'\1' ,line))
except Exception:
try:
ncbid = abs(int(re.sub(r'^[^ \t]+.*[ \t]+(-1)[ \t]*$',r'\1' ,line)))
except Exception:
print 'ppsOut2Placements: cannot parse placement for line nr:', lineCounter, 'line:', line
raise
if name in scafToContigs:
contigsList = scafToContigs[name]
for contig in contigsList:
outList.append([contig, ncbid])
#print ':',contig,ncbid
else:
outList.append([name, ncbid])
#print '',name,ncbid
return outList
def ssd2Placements(ssdDir, scafContigFile=None):
"""
Transforms sample specific data to placements. Sequences` names are not allowed to have gaps ' '
@param ssdDir: directory that contains sample specific data
@param scafContigFile: scaffold contig mapping (tab separated) if None then all sequences are considered as contigs
@return: list of pairs <contigName, assigned_ncbid>
"""
#collect map: scaffold -> list of contigs
if scafContigFile != None:
scafToContigs = toScafContigMap(scafContigFile)
else:
scafToContigs = dict([])
outList = []
placedContigs = set([])
for filePath in glob.glob(os.path.join(os.path.normpath(ssdDir),r'*.f[an][sa]')):
ncbid = int(re.sub(r'^.*[^0-9]([0-9]+)\.[0-9]+\.f[an][sa]$',r'\1' ,filePath)) #int
try:
f = open(os.path.normpath(filePath),'r')
except Exception:
print "Cannot open file:", filePath
raise
else:
for line in f:
line = common.noNewLine(line)
if re.match('>', line):
name = re.sub(r'^([^ \t]+)[ \t]*.*$',r'\1',line.replace('>',''))
if name in scafToContigs:
contigsList = scafToContigs[name]
else:
contigsList = [name]
for contig in contigsList:
if contig in placedContigs:
print str('contig "' + contig + '" has already been placed')
else:
placedContigs.add(contig)
outList.append([contig, ncbid])
#count also BP for each contig!!!
return outList
