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
