def splitFasta(inpFasta,
maxChunkSize,
outBase=None,
sfxSep=None,
openWriter=None,
lineLen=80,
verbose=True):
"""Split input multi-FASTA file into multiple files of fixed size"""
assert (outBase is None and sfxSep is None) or openWriter is None,\
"Incompatible argument combination"
if outBase is None:
outBase = ""
if sfxSep is None:
sfxSep = '_'
inpClose = False
if hasattr(inpFasta,"records"):
records = inpFasta.records()
elif hasattr(inpFasta,"read") or is_string(inpFasta):
inpFasta = FastaReader(inpFasta)
inpClose = True
records = inpFasta.records()
else:
records = inpFasta
try:
iChunk = 0
chunkSize = 0
out = None
if openWriter is None:
def _open_new_out(iChunk):
return FastaWriter(outBase+'%s%04d'%(sfxSep,iChunk,),
lineLen=lineLen,mode="w")
else:
_open_new_out = openWriter
out = _open_new_out(iChunk)
try:
if verbose:
print "Writing chunk %i of target size %i" % (iChunk,maxChunkSize)
for rec in records:
hdr = rec.header()
idSeq = rec.getId()
seq = rec.sequence()
out.record(hdr,seq)
lenSeq = len(seq)
yield (idSeq,lenSeq)
chunkSize += lenSeq
# we approximate the next seq length by the last one
if chunkSize + lenSeq >= maxChunkSize:
out.close()
out = None
iChunk += 1
chunkSize = 0
out = _open_new_out(iChunk)
if verbose:
print "Writing chunk %i of target size %i" % (iChunk,maxChunkSize)
finally:
if out is not None:
out.close()
finally:
if inpClose:
inpFasta.close()
def __init__(self,infile):
"""Ctor.
@param infile It can be either a string with a file name, or it can be an
iterator that returns lines (each line should be terminated with a new line),
e.g. a file object. An iterator can be a filter that reads another FastaReader
object, performs transformations on the records and emits them as lines."""
if is_string(infile):
infile = openCompressed(infile,'r')
self.ownInfile = True
else:
self.ownInfile = False
self.infile = infile
self.freshHdr = False
self.maxLineLen = 0
self.seqTotal = 0
self.symbolsTotal = 0
