def main(inpfile, outfile, xIdx, yIdx):
inpfile.seek(0)
outfile.seek(0)
lineCount = 0
t0 = time.time()
for line in inpfile:
lineCount += 1
if ((lineCount % 10000) == 0):
print >> sys.stderr, "lineCount=", lineCount, " time=", time.time(
) - t0
if (line[0] == 'M'):
FM = MatchRecord.MatchRecord(line)
if (FM.subtype == 'g'):
parentid = FM.matchid
parent_x_forward = (FM.x_orientation == 1)
parent_y_forward = (FM.y_orientation == 1)
parent_x_start = FM.x_start
parent_y_start = FM.y_start
parent_x_length = FM.x_length
parent_y_length = FM.y_length
# Why two orientations and not just a flipped flag?
# Because we want the resulting matches to come out in
# the same sorted order as the input matches.
x_substring = string.upper(
xIdx.getStringFromFasta(parent_x_forward, FM.x_scaf_uid,
FM.x_start, FM.x_length))
y_substring = string.upper(
yIdx.getStringFromFasta(parent_y_forward, FM.y_scaf_uid,
FM.y_start, FM.y_length))
ii = 0
# Here we call the dedasher.
halign.halignStart(x_substring, y_substring)
for segment in iter(halign.halignDedash, None):
#print >>outfile, segment
(bgn1, bgn2, len1, len2, nmat) = segment
# Filter by a minimum length? say four bp.
ii += 1
FM.subtype = 'u'
FM.matchid = parentid + 'u' + str(ii)
# FM.runid = parentid
FM.x_start = parent_x_start + (
parent_x_length - bgn1 - len1, bgn1)[parent_x_forward]
FM.y_start = parent_y_start + (
parent_y_length - bgn2 - len2, bgn2)[parent_y_forward]
FM.x_length = len1
FM.y_length = len2
assert (len1 == len2)
mismatches = 0
for ic in range(len1):
if (x_seq[bgn1 + ic] != y_seq[bgn2 + ic]):
mismatches += 1
FM.extend['mm'] = str(mismatches)
FM.identifier = "" # BEWARE
print >> outfile, FM
else:
print >> outfile, line,
else:
print >> outfile, line,
def main( inpfile, outfile, xIdx, yIdx):
inpfile.seek(0)
outfile.seek(0)
lineCount = 0
t0 = time.time()
for line in inpfile:
lineCount += 1
if((lineCount % 10000)==0):
print >>sys.stderr, "lineCount=",lineCount," time=",time.time()-t0
if(line[0] == 'M'):
FM = MatchRecord.MatchRecord(line)
if(FM.subtype == 'g'):
parentid = FM.matchid
parent_x_forward = (FM.x_orientation == 1)
parent_y_forward = (FM.y_orientation == 1)
parent_x_start = FM.x_start
parent_y_start = FM.y_start
parent_x_length = FM.x_length
parent_y_length = FM.y_length
# Why two orientations and not just a flipped flag?
# Because we want the resulting matches to come out in
# the same sorted order as the input matches.
x_substring = string.upper(
xIdx.getStringFromFasta( parent_x_forward,
FM.x_scaf_uid, FM.x_start, FM.x_length));
y_substring = string.upper(
yIdx.getStringFromFasta( parent_y_forward,
FM.y_scaf_uid, FM.y_start, FM.y_length));
ii = 0
# Here we call the dedasher.
halign.halignStart(x_substring,
y_substring)
for segment in iter(halign.halignDedash,None):
#print >>outfile, segment
(bgn1,bgn2,len1,len2,nmat) = segment
# Filter by a minimum length? say four bp.
ii += 1
FM.subtype = 'u'
FM.matchid = parentid + 'u' + str(ii)
# FM.runid = parentid
FM.x_start = parent_x_start + (parent_x_length-bgn1-len1,bgn1)[parent_x_forward]
FM.y_start = parent_y_start + (parent_y_length-bgn2-len2,bgn2)[parent_y_forward]
FM.x_length = len1
FM.y_length = len2
assert(len1 == len2)
mismatches = 0
for ic in range(len1):
if(x_seq[bgn1+ic] != y_seq[bgn2+ic]):
mismatches += 1
FM.extend['mm'] = str(mismatches)
FM.identifier = "" # BEWARE
print >>outfile, FM
else:
print >>outfile, line,
else:
print >>outfile, line,
def analyzeGap(x, y, left, right, outfile, maxgap, erate, margin):
inter_run_gap_count = 0
x_pos = 0
x_len = 0
y_pos = 0
y_len = 0
if ((left.x_scaf_uid == right.x_scaf_uid)
and (left.y_scaf_uid == right.y_scaf_uid)
and (left.runid == right.runid)):
# (left.sindex + 1 == right.sindex) ): # This is obsolete in Russell's file format.
# sys.stderr.write("Intra-run gap\n")
left_forward = (left.x_orientation == left.y_orientation)
right_forward = (right.x_orientation == right.y_orientation)
if (left_forward != right_forward):
sys.stderr.write("Bad orientations\n")
assert (left_forward == right_forward)
sorted_by_x = (left.x_start <= right.x_start) and \
(left.x_start+left.x_length <= right.x_start+right.x_length)
sorted_by_y = (left.y_start <= right.y_start) and \
(left.y_start+left.y_length <= right.y_start+right.y_length)
if (not (sorted_by_x or sorted_by_y)):
print >> sys.stderr, "bad sorting in runs"
print >> sys.stderr, left
print >> sys.stderr, right
assert (sorted_by_x or sorted_by_y)
# This concept of sorted allows neggaps but not containmant in both axes.
if (not ((not left_forward) or (sorted_by_x and sorted_by_y))):
print >> sys.stderr, "bad sorting in runs"
print >> sys.stderr, left
print >> sys.stderr, right
if (not ((left_forward) or (not (sorted_by_x and sorted_by_y)))):
print >> sys.stderr, "bad sorting in runs"
print >> sys.stderr, left
print >> sys.stderr, right
assert ((not left_forward) or (sorted_by_x and sorted_by_y))
assert ((left_forward) or (not (sorted_by_x and sorted_by_y)))
if (sorted_by_x): # Sorted by x positions.
x_pos = left.x_start + left.x_length # Start of the intra-run gap.
x_len = right.x_start - x_pos # Length of the intra-run gap.
if (left_forward):
y_pos = left.y_start + left.y_length
y_len = right.y_start - y_pos
else:
y_pos = right.y_start + right.y_length
y_len = left.y_start - y_pos
# end if
else: # Assume sorted by y positions
y_pos = left.y_start + left.y_length
y_len = right.y_start - y_pos
if (left_forward):
x_pos = left.x_start + left.x_length
x_len = right.x_start - x_pos
else:
x_pos = right.x_start + right.x_length
x_len = left.x_start - x_pos
# end if
# end if
# print "Left %d,%d Right %d,%d Width %d,%d" % (x_pos,y_pos,x_pos+x_len,y_pos+y_len,x_len,y_len)
assert (left.x_start >= 0)
assert (left.x_length > 0)
assert (left.y_start >= 0)
assert (left.y_length > 0)
assert (right.x_start >= 0)
assert (right.x_length > 0)
assert (right.y_start >= 0)
assert (right.y_length > 0)
if (1 and 0 < x_len and 0 < y_len and x_len < maxgap
and y_len < maxgap):
if 0:
sys.stderr.write(
"About to call local aligner with %d margins\n" % margin)
sys.stderr.write("# left = %s\n" % str(left))
sys.stderr.write("# right= %s\n" % str(right))
sys.stderr.write("x_len=%d y_len=%d\n" % (x_len, y_len))
# Why two orientation flags? We want the output matches
# to be in the same sorted order as the left and right
# matches.
parent_x_start = x_pos - margin
parent_y_start = y_pos - margin
parent_x_length = x_len + 2 * margin
parent_y_length = y_len + 2 * margin
if 0:
print >> sys.stderr, "parent_x_start=%d" % parent_x_start
print >> sys.stderr, "parent_y_start=%d" % parent_y_start
print >> sys.stderr, "parent_x_length=%d" % parent_x_length
print >> sys.stderr, "parent_y_length=%d" % parent_y_length
x_seq = ""
if (x_len > 0):
x_seq = string.upper(
x.getStringFromFasta(sorted_by_x, left.x_scaf_uid,
parent_x_start, parent_x_length))
# end if
y_seq = ""
if (y_len > 0):
y_seq = string.upper(
y.getStringFromFasta(sorted_by_y, left.y_scaf_uid,
parent_y_start, parent_y_length))
# end if
if 0:
print >> outfile, "# STARTED localAlignerInterface.syntenicSegments"
print >> outfile, "# left = %s" % str(left)
print >> outfile, "# right= %s" % str(right)
print >> sys.stderr, "x_seq=" + x_seq
print >> sys.stderr, "len(x_seq)=", len(x_seq)
print >> sys.stderr, "y_seq=" + y_seq
print >> sys.stderr, "len(y_seq)=", len(y_seq)
outfile.flush()
try:
localAlignerInterface.syntenicSegments(outfile, x_seq, 0,
parent_x_length, y_seq,
0, parent_y_length,
erate)
FM = left
parent_id = FM.matchid
#FM.x_orientation = sorted_by_x
#FM.y_orientation = sorted_by_y
# Why two orientations and not just a flipped flag?
# Because we want the resulting matches to come out in
# the same sorted order as the input matches.
ii = 0
for segment in iter(localAlignerInterface.iterateSegments,
None):
#print >>outfile, segment
(bgn1, bgn2, len1, len2, fid) = segment
assert (len1 >= 0)
assert (len2 >= 0)
assert (bgn1 >= 0)
assert (bgn2 >= 0)
if (not (bgn1 + len1 <= parent_x_length)):
print >> sys.stdout, "# warn(not(bgn1 + len1 <= parent_x_length))"
print >> sys.stdout, "# bgn1=%d len1=%d parent_x_length=%d" % (
bgn1, len1, parent_x_length)
print >> sys.stdout, "# left = %s" % str(left)
print >> sys.stdout, "# right= %s" % str(right)
print >> sys.stdout, "# bgn1,bgn2,len1,len2=", bgn1, bgn2, len1, len2
#print >>sys.stdout,"# xseq=%s" % x_seq[bgn1:bgn1+len1]
#print >>sys.stdout,"# yseq=%s" % y_seq[bgn2:bgn2+len2]
len1 = parent_x_length - bgn1
print >> sys.stdout, "# Change len1 = %d" % len1
if (not (bgn2 + len2 <= parent_y_length)):
print >> sys.stdout, "# warn(not(bgn2 + len2 <= parent_y_length))"
print >> sys.stdout, "# bgn2=%d len2=%d parent_y_length=%d" % (
bgn2, len2, parent_y_length)
print >> sys.stdout, "# left = %s" % str(left)
print >> sys.stdout, "# right= %s" % str(right)
print >> sys.stdout, "# bgn1,bgn2,len1,len2=", bgn1, bgn2, len1, len2
#print >>sys.stdout,"# xseq=%s" % x_seq[bgn1:bgn1+len1]
#print >>sys.stdout,"# yseq=%s" % y_seq[bgn2:bgn2+len2]
len2 = parent_y_length - bgn2
print >> sys.stdout, "# Change len2 = %d" % len2
if (len1 == 0):
print >> sys.stdout, "# warn(len1 == 0)"
print >> sys.stdout, "# bgn1,bgn2,len1,len2=", bgn1, bgn2, len1, len2
print >> sys.stdout, "# bgn1=%d len1=%d parent_x_length=%d" % (
bgn1, len1, parent_x_length)
continue
if (len2 == 0):
print >> sys.stdout, "# warn(len2 == 0)"
print >> sys.stdout, "# bgn1,bgn2,len1,len2=", bgn1, bgn2, len1, len2
print >> sys.stdout, "# bgn2=%d len2=%d parent_y_length=%d" % (
bgn2, len2, parent_y_length)
continue
assert (bgn1 >= 0)
assert (bgn2 >= 0)
assert (len1 > 0)
assert (len2 > 0)
assert (bgn1 + len1 <= parent_x_length)
assert (bgn2 + len2 <= parent_y_length)
# Filter by a minimum length? say four bp.
ii += 1
FM.subtype = 'l'
FM.matchid = parent_id + 'l' + str(ii)
# FM.runid = parent_id
child_x_start = parent_x_start + (parent_x_length - bgn1 -
len1, bgn1)[sorted_by_x]
child_y_start = parent_y_start + (parent_y_length - bgn2 -
len2, bgn2)[sorted_by_y]
child_x_length = len1
child_y_length = len2
#FM.identifier = " %f" % fid # CMM BEWARE
FM.x_start = child_x_start
FM.y_start = child_y_start
FM.x_length = child_x_length
FM.y_length = child_y_length
#FM.extend['fid'] = str(fid)
#print >>outfile, FM
# Here we call the dedasher.
#assert(len1 > 0)
#assert(len2 > 0)
#assert(bgn1 >= 0)
#assert(bgn2 >= 0)
#assert(bgn1+len1 <= parent_x_length)
#assert(bgn2+len2 <= parent_y_length)
if 0:
print >> sys.stderr, "# x_seq=%s" % x_seq
print >> sys.stderr, "# y_seq=%s" % y_seq
print >> sys.stderr, "# bgn1,bgn2,len1,len2=", bgn1, bgn2, len1, len2
print >> sys.stderr, "# xseq=%s" % x_seq[bgn1:bgn1 +
len1]
print >> sys.stderr, "# yseq=%s" % y_seq[bgn2:bgn2 +
len2]
halign.halignStart(x_seq[bgn1:bgn1 + len1],
y_seq[bgn2:bgn2 + len2])
outfile.flush()
for hsegment in iter(halign.halignDedash, None):
#print >>outfile, segment
(bgn1h, bgn2h, len1h, len2h, nmat) = hsegment
# Filter by a minimum length? say four bp.
ii += 1
FM.subtype = 'u'
FM.matchid = parent_id + 'a' + str(ii)
# FM.runid = parent_id
FM.x_start = child_x_start + (
child_x_length - bgn1h - len1h, bgn1h)[sorted_by_x]
FM.y_start = child_y_start + (
child_y_length - bgn2h - len2h, bgn2h)[sorted_by_y]
FM.x_length = len1h
FM.y_length = len2h
assert (len1h == len2h)
mismatches = 0
for ic in range(len1h):
if (x_seq[bgn1 + bgn1h + ic] !=
y_seq[bgn2 + bgn2h + ic]):
mismatches += 1
FM.extend['mm'] = str(mismatches)
#FM.identifier = "" # BEWARE
print >> outfile, FM
# localAlignerInterface.free()
# print >>outfile,"# FINISHED localAlignerInterface.syntenicSegments"
except RuntimeError:
print >> outfile, "# NOTE syntenicSegments failed between these records"
print >> outfile, "# STARTED localAlignerInterface.syntenicSegments"
print >> outfile, "# left = %s" % str(left)
print >> outfile, "# right= %s" % str(right)
print >> sys.stderr, "NOTE syntenicSegments failed in fillIntraRunGaps for:"
print >> sys.stderr, "x_seq=" + x_seq
print >> sys.stderr, "len(x_seq)=", len(x_seq)
print >> sys.stderr, "y_seq=" + y_seq
print >> sys.stderr, "len(y_seq)=", len(y_seq)
# end if
else:
# sys.stderr.write("Inter-run gap\n")
inter_run_gap_count += 1
# sys.stderr.write("done\n")
return (inter_run_gap_count, )
def analyzeGap(x,y,left,right,outfile,maxgap,erate,margin):
inter_run_gap_count = 0
x_pos = 0
x_len = 0
y_pos = 0
y_len = 0
if( (left.x_scaf_uid == right.x_scaf_uid) and
(left.y_scaf_uid == right.y_scaf_uid) and
(left.runid == right.runid) ):
# (left.sindex + 1 == right.sindex) ): # This is obsolete in Russell's file format.
# sys.stderr.write("Intra-run gap\n")
left_forward = (left.x_orientation == left.y_orientation)
right_forward = (right.x_orientation == right.y_orientation)
if( left_forward != right_forward): sys.stderr.write("Bad orientations\n")
assert(left_forward == right_forward)
sorted_by_x = (left.x_start <= right.x_start) and \
(left.x_start+left.x_length <= right.x_start+right.x_length)
sorted_by_y = (left.y_start <= right.y_start) and \
(left.y_start+left.y_length <= right.y_start+right.y_length)
if(not(sorted_by_x or sorted_by_y)):
print >>sys.stderr, "bad sorting in runs"
print >>sys.stderr, left
print >>sys.stderr, right
assert(sorted_by_x or sorted_by_y)
# This concept of sorted allows neggaps but not containmant in both axes.
if(not((not left_forward) or (sorted_by_x and sorted_by_y))):
print >>sys.stderr, "bad sorting in runs"
print >>sys.stderr, left
print >>sys.stderr, right
if(not((left_forward) or (not(sorted_by_x and sorted_by_y)))):
print >>sys.stderr, "bad sorting in runs"
print >>sys.stderr, left
print >>sys.stderr, right
assert((not left_forward) or (sorted_by_x and sorted_by_y))
assert((left_forward) or (not(sorted_by_x and sorted_by_y)))
if(sorted_by_x): # Sorted by x positions.
x_pos = left.x_start + left.x_length # Start of the intra-run gap.
x_len = right.x_start - x_pos # Length of the intra-run gap.
if(left_forward):
y_pos = left.y_start + left.y_length
y_len = right.y_start - y_pos
else:
y_pos = right.y_start + right.y_length
y_len = left.y_start - y_pos
# end if
else: # Assume sorted by y positions
y_pos = left.y_start + left.y_length
y_len = right.y_start - y_pos
if(left_forward):
x_pos = left.x_start + left.x_length
x_len = right.x_start - x_pos
else:
x_pos = right.x_start + right.x_length
x_len = left.x_start - x_pos
# end if
# end if
# print "Left %d,%d Right %d,%d Width %d,%d" % (x_pos,y_pos,x_pos+x_len,y_pos+y_len,x_len,y_len)
assert(left.x_start >= 0)
assert(left.x_length > 0)
assert(left.y_start >= 0)
assert(left.y_length > 0)
assert(right.x_start >= 0)
assert(right.x_length > 0)
assert(right.y_start >= 0)
assert(right.y_length > 0)
if( 1
and 0 < x_len and 0 < y_len
and x_len < maxgap and y_len < maxgap
):
if 0:
sys.stderr.write("About to call local aligner with %d margins\n" % margin);
sys.stderr.write("# left = %s\n" % str(left))
sys.stderr.write("# right= %s\n" % str(right))
sys.stderr.write("x_len=%d y_len=%d\n" % (x_len, y_len) );
# Why two orientation flags? We want the output matches
# to be in the same sorted order as the left and right
# matches.
parent_x_start = x_pos - margin
parent_y_start = y_pos - margin
parent_x_length = x_len + 2*margin
parent_y_length = y_len + 2*margin
if 0:
print >>sys.stderr, "parent_x_start=%d" % parent_x_start
print >>sys.stderr, "parent_y_start=%d" % parent_y_start
print >>sys.stderr, "parent_x_length=%d" % parent_x_length
print >>sys.stderr, "parent_y_length=%d" % parent_y_length
x_seq = ""
if(x_len > 0):
x_seq = string.upper(
x.getStringFromFasta( sorted_by_x, left.x_scaf_uid,
parent_x_start, parent_x_length));
# end if
y_seq = ""
if(y_len > 0):
y_seq = string.upper(
y.getStringFromFasta( sorted_by_y, left.y_scaf_uid,
parent_y_start, parent_y_length));
# end if
if 0:
print >>outfile, "# STARTED localAlignerInterface.syntenicSegments"
print >>outfile, "# left = %s" % str(left)
print >>outfile, "# right= %s" % str(right)
print >>sys.stderr, "x_seq="+x_seq
print >>sys.stderr, "len(x_seq)=",len(x_seq)
print >>sys.stderr, "y_seq="+y_seq
print >>sys.stderr, "len(y_seq)=",len(y_seq)
outfile.flush()
try:
localAlignerInterface.syntenicSegments(outfile,
x_seq, 0, parent_x_length,
y_seq, 0, parent_y_length,
erate)
FM = left
parent_id = FM.matchid
#FM.x_orientation = sorted_by_x
#FM.y_orientation = sorted_by_y
# Why two orientations and not just a flipped flag?
# Because we want the resulting matches to come out in
# the same sorted order as the input matches.
ii = 0
for segment in iter(localAlignerInterface.iterateSegments,None):
#print >>outfile, segment
(bgn1,bgn2,len1,len2,fid) = segment
assert(len1 >= 0)
assert(len2 >= 0)
assert(bgn1 >= 0)
assert(bgn2 >= 0)
if(not(bgn1 + len1 <= parent_x_length)):
print >>sys.stdout,"# warn(not(bgn1 + len1 <= parent_x_length))"
print >>sys.stdout,"# bgn1=%d len1=%d parent_x_length=%d" % (bgn1,len1,parent_x_length)
print >>sys.stdout,"# left = %s" % str(left)
print >>sys.stdout,"# right= %s" % str(right)
print >>sys.stdout,"# bgn1,bgn2,len1,len2=", bgn1,bgn2,len1,len2
#print >>sys.stdout,"# xseq=%s" % x_seq[bgn1:bgn1+len1]
#print >>sys.stdout,"# yseq=%s" % y_seq[bgn2:bgn2+len2]
len1 = parent_x_length - bgn1
print >>sys.stdout, "# Change len1 = %d" % len1
if(not(bgn2 + len2 <= parent_y_length)):
print >>sys.stdout,"# warn(not(bgn2 + len2 <= parent_y_length))"
print >>sys.stdout,"# bgn2=%d len2=%d parent_y_length=%d" % (bgn2,len2,parent_y_length)
print >>sys.stdout,"# left = %s" % str(left)
print >>sys.stdout,"# right= %s" % str(right)
print >>sys.stdout,"# bgn1,bgn2,len1,len2=", bgn1,bgn2,len1,len2
#print >>sys.stdout,"# xseq=%s" % x_seq[bgn1:bgn1+len1]
#print >>sys.stdout,"# yseq=%s" % y_seq[bgn2:bgn2+len2]
len2 = parent_y_length - bgn2
print >>sys.stdout,"# Change len2 = %d" % len2
if (len1 == 0):
print >>sys.stdout,"# warn(len1 == 0)"
print >>sys.stdout,"# bgn1,bgn2,len1,len2=", bgn1,bgn2,len1,len2
print >>sys.stdout,"# bgn1=%d len1=%d parent_x_length=%d" % (bgn1,len1,parent_x_length)
continue
if (len2 == 0):
print >>sys.stdout,"# warn(len2 == 0)"
print >>sys.stdout,"# bgn1,bgn2,len1,len2=", bgn1,bgn2,len1,len2
print >>sys.stdout,"# bgn2=%d len2=%d parent_y_length=%d" % (bgn2,len2,parent_y_length)
continue
assert(bgn1 >= 0)
assert(bgn2 >= 0)
assert(len1 > 0)
assert(len2 > 0)
assert(bgn1 + len1 <= parent_x_length);
assert(bgn2 + len2 <= parent_y_length);
# Filter by a minimum length? say four bp.
ii += 1
FM.subtype = 'l'
FM.matchid = parent_id + 'l' + str(ii)
# FM.runid = parent_id
child_x_start = parent_x_start + (parent_x_length-bgn1-len1,bgn1)[sorted_by_x]
child_y_start = parent_y_start + (parent_y_length-bgn2-len2,bgn2)[sorted_by_y]
child_x_length = len1
child_y_length = len2
#FM.identifier = " %f" % fid # CMM BEWARE
FM.x_start = child_x_start
FM.y_start = child_y_start
FM.x_length = child_x_length
FM.y_length = child_y_length
#FM.extend['fid'] = str(fid)
#print >>outfile, FM
# Here we call the dedasher.
#assert(len1 > 0)
#assert(len2 > 0)
#assert(bgn1 >= 0)
#assert(bgn2 >= 0)
#assert(bgn1+len1 <= parent_x_length)
#assert(bgn2+len2 <= parent_y_length)
if 0:
print >>sys.stderr, "# x_seq=%s" % x_seq
print >>sys.stderr, "# y_seq=%s" % y_seq
print >>sys.stderr, "# bgn1,bgn2,len1,len2=", bgn1,bgn2,len1,len2
print >>sys.stderr, "# xseq=%s" % x_seq[bgn1:bgn1+len1]
print >>sys.stderr, "# yseq=%s" % y_seq[bgn2:bgn2+len2]
halign.halignStart(x_seq[bgn1:bgn1+len1], y_seq[bgn2:bgn2+len2])
outfile.flush()
for hsegment in iter(halign.halignDedash,None):
#print >>outfile, segment
(bgn1h,bgn2h,len1h,len2h,nmat) = hsegment
# Filter by a minimum length? say four bp.
ii += 1
FM.subtype = 'u'
FM.matchid = parent_id + 'a' + str(ii)
# FM.runid = parent_id
FM.x_start = child_x_start + (child_x_length-bgn1h-len1h,bgn1h)[sorted_by_x]
FM.y_start = child_y_start + (child_y_length-bgn2h-len2h,bgn2h)[sorted_by_y]
FM.x_length = len1h
FM.y_length = len2h
assert(len1h == len2h)
mismatches = 0
for ic in range(len1h):
if(x_seq[bgn1+bgn1h+ic] != y_seq[bgn2+bgn2h+ic]):
mismatches += 1
FM.extend['mm'] = str(mismatches)
#FM.identifier = "" # BEWARE
print >>outfile, FM
# localAlignerInterface.free()
# print >>outfile,"# FINISHED localAlignerInterface.syntenicSegments"
except RuntimeError:
print >>outfile, "# NOTE syntenicSegments failed between these records"
print >>outfile, "# STARTED localAlignerInterface.syntenicSegments"
print >>outfile, "# left = %s" % str(left)
print >>outfile, "# right= %s" % str(right)
print >>sys.stderr, "NOTE syntenicSegments failed in fillIntraRunGaps for:"
print >>sys.stderr, "x_seq="+x_seq
print >>sys.stderr, "len(x_seq)=",len(x_seq)
print >>sys.stderr, "y_seq="+y_seq
print >>sys.stderr, "len(y_seq)=",len(y_seq)
# end if
else:
# sys.stderr.write("Inter-run gap\n")
inter_run_gap_count += 1
# sys.stderr.write("done\n")
return (inter_run_gap_count,)
