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Merge pull request #139 from c-zhou/master
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fix bugs
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@ghuryejay
ghuryejay authored May 13, 2021
2 parents 8b1e2dc + e407e61 commit 4c80ac1
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Showing 3 changed files with 69 additions and 26 deletions.
16 changes: 12 additions & 4 deletions alignments2txt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -94,17 +94,25 @@ def update_bed(expanded_scaffold):
prev_info = contig2info[prev_contig]
prev_start = int(prev_attrs[1])
prev_end = int(prev_attrs[2])
new_prev_start = prev_start + prev_info[0]
new_prev_end = prev_end + prev_info[0]
if prev_info[2] == 'FOW':
new_prev_start = prev_info[0] + prev_start
new_prev_end = prev_info[0] + prev_end
else:
new_prev_start = prev_info[0] + unitig_length[prev_contig] - prev_end
new_prev_end = prev_info[0] + unitig_length[prev_contig] - prev_start
olines += "0\t"+prev_scaffold+'\t'+str(new_prev_start)+"\t0\t"
#o_lines += prev_scaffold+'\t'+str(new_prev_start)+'\t'+str(new_prev_end)+'\t'+prev_attrs[3]+'\n'
count += 1

curr_info = contig2info[curr_contig]
curr_start = int(curr_attrs[1])
curr_end = int(curr_attrs[2])
new_curr_start = curr_start + curr_info[0]
new_curr_end = curr_end + curr_info[0]
if curr_info[2] == 'FOW':
new_curr_start = curr_info[0] + curr_start
new_curr_end = curr_info[0] + curr_end
else:
new_curr_start = curr_info[0] + unitig_length[curr_contig] - curr_end
new_curr_end = curr_info[0] + unitig_length[curr_contig] - curr_start
olines += "1\t"+curr_scaffold+'\t'+str(new_curr_start)+"\t1\n"
#o_lines += curr_scaffold+'\t'+str(new_curr_start)+'\t'+str(new_curr_end)+'\t'+curr_attrs[3]+'\n'
count += 1
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37 changes: 27 additions & 10 deletions layout_unitigs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -743,30 +743,38 @@ def update_bed(expanded_scaffold):
s_right = 0
if len(path) == 2:
contig = path[0].split(':')[0]
scaffold_re[key] = re_counts[contig]
ori = path[0].split(':')[1]
left,right = re_counts[contig]
if ori == 'B':
scaffold_re[key] = (left,right)
else:
scaffold_re[key] = (right,left)
else:
midpoint = length/2
for i in xrange(0,len(path),2):
contig = path[i].split(':')[0]
contig2scaffold[contig] = key
left,right = re_counts[contig]
midpoint = length/2
curr_contig_start = contig2info[contig][0]
curr_contig_end = contig2info[contig][1]
curr_contig_ori = contig2info[contig][2]
#curr_contig_ori = contig2info[contig][2]
#print contig
#print curr_contig_start
#print curr_contig_end
#print curr_contig_ori
if curr_contig_end <= midpoint:
if curr_contig_end < midpoint:
s_left += (left+right)
if curr_contig_start >= midpoint:
if curr_contig_start > midpoint:
s_right += (left+right)

if curr_contig_start <= midpoint and curr_contig_end >= midpoint:
left_part = midpoint - curr_contig_start
right_part = curr_contig_end - midpoint
#print "Left part = " + str(left_part)
#print "Right part = " + str(right_part)
s_left += float(left+right)/contig_length[contig]*left_part
s_right += float(left+right)/contig_length[contig]*right_part
'''
if curr_contig_ori == "FOW":
s_left += (left+right)*left_part/contig_length[contig]
s_right += (left+right)*right_part/contig_length[contig]
Expand All @@ -777,6 +785,7 @@ def update_bed(expanded_scaffold):
s_right += (right+left)*left_part/contig_length[contig]
#print "Right RE = " + str(left_part/contig_length[contig])
#print "Left RE = " + str(right*right_part/contig_length[contig])
'''

'''
if offset <= length/2 and i+2 < len(path):
Expand All @@ -802,7 +811,7 @@ def update_bed(expanded_scaffold):
#scaffold_length[key] += contig_length[contig]
'''
#print key+"\t"+str(s_left)+"\t"+str(s_right)
scaffold_re[key] = (s_left,s_right)
scaffold_re[key] = (int(s_left),int(s_right))
#print "=============================="

o_lines = ""
Expand Down Expand Up @@ -835,16 +844,24 @@ def update_bed(expanded_scaffold):
prev_info = contig2info[prev_contig]
prev_start = int(prev_attrs[1])
prev_end = int(prev_attrs[2])
new_prev_start = prev_start + prev_info[0]
new_prev_end = prev_end + prev_info[0]
if prev_info[2] == 'FOW':
new_prev_start = prev_info[0] + prev_start
new_prev_end = prev_info[0] + prev_end
else:
new_prev_start = prev_info[0] + contig_length[prev_contig] - prev_end
new_prev_end = prev_info[0] + contig_length[prev_contig] - prev_start
o_lines += prev_scaffold+'\t'+str(new_prev_start)+'\t'+str(new_prev_end)+'\t'+prev_attrs[3]+'\n'
count += 1

curr_info = contig2info[curr_contig]
curr_start = int(curr_attrs[1])
curr_end = int(curr_attrs[2])
new_curr_start = curr_start + curr_info[0]
new_curr_end = curr_end + curr_info[0]
if curr_info[2] == 'FOW':
new_curr_start = curr_info[0] + curr_start
new_curr_end = curr_info[0] + curr_end
else:
new_curr_start = curr_info[0] + contig_length[curr_contig] - curr_end
new_curr_end = curr_info[0] + contig_length[curr_contig] - curr_start
o_lines += curr_scaffold+'\t'+str(new_curr_start)+'\t'+str(new_curr_end)+'\t'+curr_attrs[3]+'\n'
count += 1
if count == 1000000:
Expand Down
42 changes: 30 additions & 12 deletions refactor_breaks.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -69,31 +69,41 @@ def update_bed(expanded_scaffold):
s_right = 0
if len(path) == 2:
contig = path[0].split(':')[0]
scaffold_re[key] = re_counts[contig]
ori = path[0].split(':')[1]
left,right = re_counts[contig]
if ori == 'B':
scaffold_re[key] = (left,right)
else:
scaffold_re[key] = (right,left)
else:
midpoint = length/2
for i in xrange(0,len(path),2):
contig = path[i].split(':')[0]
contig2scaffold[contig] = key
left,right = re_counts[contig]
midpoint = length/2
curr_contig_start = contig2info[contig][0]
curr_contig_end = contig2info[contig][1]
curr_contig_ori = contig2info[contig][2]
if curr_contig_end <= midpoint:
# curr_contig_ori = contig2info[contig][2]
if curr_contig_end < midpoint:
s_left += (left+right)
if curr_contig_start >= midpoint:
if curr_contig_start > midpoint:
s_right += (left+right)

if curr_contig_start <= midpoint and curr_contig_end >= midpoint:
left_part = midpoint - curr_contig_start
right_part = curr_contig_end - midpoint
s_left += float(left+right)/unitig_length[contig]*left_part
s_right += float(left+right)/unitig_length[contig]*right_part

## do NOT consider forward or reverse orientation here
## left is always left, right is always right
'''
if curr_contig_ori == "FOW":
s_left += (right+left)*left_part/unitig_length[contig]
s_right += (right+left)*right_part/unitig_length[contig]
else:
s_left += (right+left)*right_part/unitig_length[contig]
s_right += (right+left)*left_part/unitig_length[contig]

'''

'''
if offset <= length/2 and i+2 < len(path):
Expand All @@ -118,7 +128,7 @@ def update_bed(expanded_scaffold):
offset += unitig_length[contig]
#scaffold_length[key] += contig_length[contig]
'''
scaffold_re[key] = (s_left,s_right)
scaffold_re[key] = (int(s_left),int(s_right))

o_lines = ""
count = 0
Expand Down Expand Up @@ -151,16 +161,24 @@ def update_bed(expanded_scaffold):
prev_info = contig2info[prev_contig]
prev_start = int(prev_attrs[1])
prev_end = int(prev_attrs[2])
new_prev_start = prev_start + prev_info[0]
new_prev_end = prev_end + prev_info[0]
if prev_info[2] == 'FOW':
new_prev_start = prev_info[0] + prev_start
new_prev_end = prev_info[0] + prev_end
else:
new_prev_start = prev_info[0] + unitig_length[prev_contig] - prev_end
new_prev_end = prev_info[0] + unitig_length[prev_contig] - prev_start
o_lines += prev_scaffold+'\t'+str(new_prev_start)+'\t'+str(new_prev_end)+'\t'+prev_attrs[3]+'\n'
count += 1

curr_info = contig2info[curr_contig]
curr_start = int(curr_attrs[1])
curr_end = int(curr_attrs[2])
new_curr_start = curr_start + curr_info[0]
new_curr_end = curr_end + curr_info[0]
if curr_info[2] == 'FOW':
new_curr_start = curr_info[0] + curr_start
new_curr_end = curr_info[0] + curr_end
else:
new_curr_start = curr_info[0] + unitig_length[curr_contig] - curr_end
new_curr_end = curr_info[0] + unitig_length[curr_contig] - curr_start
o_lines += curr_scaffold+'\t'+str(new_curr_start)+'\t'+str(new_curr_end)+'\t'+curr_attrs[3]+'\n'
count += 1
if count == 1000000:
Expand Down

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