def parseRm4( file ):
"""Parses readmatcher -printFormat 4 output into AlignmentHit objects"""
for line in open(file):
fields = line.rstrip("\n").split(" ")
hit = AlignmentHit()
hit.query_id = fields[0]
hit.target_id = fields[1]
hit.score = - int(fields[2])
hit.pctidentity = float(fields[3])
hit.query_strand = "+" if fields[4] == "0" else "-"
hit.query_start = int(fields[5])
hit.query_end = int(fields[6])
hit.query_length = int(fields[7])
# for negative strand readMatcher query coords are reported on reverse
# complement of the sequence. For the alignmenthit they need to be
# reported on the forward strand
if hit.query_strand == "-":
hit.query_end, hit.query_start = hit.query_length - hit.query_start, hit.query_length - hit.query_end
hit.target_strand = "+" if fields[8] == "0" else "-"
hit.target_start = int(fields[9])
hit.target_end = int(fields[10])
hit.target_length = int(fields[11])
if hit.target_strand == "-":
hit.target_end, hit.target_start = hit.target_length - hit.target_start, hit.target_length - hit.target_end
#if hit.target_strand == hit.query_strand: # always report strand for query
# hit.target_strand = hit.query_strand = "+"
#else:
# hit.query_strand = "-"
# hit.target_strand = "+"
hit.alignedLength = abs(hit.target_end-hit.target_start)
yield hit
def parseRm5( file ):
"""Parses readmatcher -printFormat 5 output into AlignmentHit objects"""
for line in open(file):
#print line
values = line.rstrip("\n").split(" ")
hit = AlignmentHit()
hit.query_id, hit.query_length, hit.query_start, hit.query_end, hit.query_strand = values[0], int(values[1]), int(values[2]), int(values[3]), values[4]
hit.target_id, hit.target_length, hit.target_start, hit.target_end, hit.target_strand = values[6], int(values[7]), int(values[8]), int(values[9]), values[10]
hit.score = -1*int(values[11])
#target_id = values[6] because there is white space in the m5 file before target_id
hit.query_id = "/".join(hit.query_id.split("/")[0:3])
hit.alignedQuery = values[17]
hit.QueryStrOrg = hit.alignedQuery
tempQList = []
tempQList = list(hit.alignedQuery)
for i in range(0, len(tempQList)):
if tempQList[i] == 'A' or tempQList[i] == 'C' or tempQList[i] == 'G' or tempQList[i] == 'T':
hit.QuerySeq.append(tempQList[i])
hit.QueryStr = ''.join(hit.QuerySeq)
hit.alignedTarget = values[19]
hit.TargetStrOrg = hit.alignedTarget
tempTList = []
tempTList = list(hit.alignedTarget)
for i in range(0, len(tempTList)):
if tempTList[i] == 'A' or tempTList[i] == 'C' or tempTList[i] == 'G' or tempTList[i] == 'T':
hit.TargetSeq.append(tempTList[i])
hit.TargetStr = ''.join(hit.TargetSeq)
hit.aligned = values[18]
hit.line = line
#print hit.target_strand
if hit.target_strand == "+":
hit.target_strand = 0
else:
hit.target_strand = 1
if hit.query_strand == "+":
hit.query_strand = 0
else:
hit.query_strand = 1
hit.revcomp()
tempRevQList = []
tempRevQList = list(hit.alignedQuery)
for i in range(0, len(tempRevQList)):
if tempRevQList[i] == 'A' or tempRevQList[i] == 'C' or tempRevQList[i] == 'G' or tempRevQList[i] == 'T':
hit.RevQuerySeq.append(tempRevQList[i])
hit.RevQueryStr = ''.join(hit.RevQuerySeq)
tempRevTList = []
tempRevTList = list(hit.alignedTarget)
for i in range(0, len(tempRevTList)):
if tempRevTList[i] == 'A' or tempRevTList[i] == 'C' or tempRevTList[i] == 'G' or tempRevTList[i] == 'T':
hit.RevTargetSeq.append(tempRevTList[i])
hit.RevTargetStr = ''.join(hit.RevTargetSeq)
yield hit