fixes to tbl_transfer_prealigned oob_clip

ncbi.py

@@ -64,15 +64,19 @@ def tbl_transfer_common(cmap, ref_tbl, out_tbl, alt_chrlens, oob_clip=False):
  raise Exception("this line has only one column?")
  row[0] = int(row[0])
  row[1] = int(row[1])
+ strand = None
  if row[1] >= row[0]:
+ strand = '+'
  row[0] = cmap.mapChr(refSeqID, altid, row[0], -1)[1]
  row[1] = cmap.mapChr(refSeqID, altid, row[1], 1)[1]
  else:
  # negative strand feature
+ strand = '-'
  row[0] = cmap.mapChr(refSeqID, altid, row[0], 1)[1]
  row[1] = cmap.mapChr(refSeqID, altid, row[1], -1)[1]
 
  if row[0] and row[1]:
+ # feature completely within bounds
  feature_keep = True
  elif row[0] == None and row[1] == None:
  # feature completely out of bounds
@@ -81,12 +85,39 @@ def tbl_transfer_common(cmap, ref_tbl, out_tbl, alt_chrlens, oob_clip=False):
  else:
  # feature overhangs end of sequence
  if oob_clip:
- if row[0] == None:
- row[0] = '<1'
- if row[1] == None:
- row[1] = '>{}'.format(alt_chrlens[altid])
+ if strand == '+':
+ # clip pos strand feature
+ if row[0] == None:
+ # clip the beginning
+ if row[2] == 'CDS':
+ # for CDS features, clip in multiples of 3
+ r = (row[1] if row[1] is not None else alt_chrlens[altid])
+ row[0] = '<{}'.format((r % 3) + 1)
+ else:
+ row[0] = '<1'
+ if row[1] == None:
+ # clip the end
+ row[1] = '>{}'.format(alt_chrlens[altid])
+ else:
+ # clip neg strand feature
+ if row[0] == None:
+ # clip the beginning (right side)
+ r = alt_chrlens[altid]
+ if row[2] == 'CDS':
+ # for CDS features, clip in multiples of 3
+ l = (row[1] if row[1] is not None else 1) # new left
+ r = r - ((r-l+1) % 3) # create new right in multiples of 3 from left
+ if (r-l) < 3:
+ # less than a codon remains, drop it
+ feature_keep = False
+ continue
+ row[0] = '>{}'.format(r)
+ if row[1] == None:
+ # clip the end (left side)
+ row[1] = '<1'
  feature_keep = True
  else:
+ # drop the partially out of bounds feature
  feature_keep = False
  continue
  line = '\t'.join(map(str, row))