Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Browse files

Remove raw text length calculation from hmmer3-text

Hmmer3-text parsing & indexing requires the header to be present. This means the
raw query result text needs to be appended to the header. If the query result
text length is calculated, appending is not possible since SearchIO.index_db
directly returns the text in the given range, without any modification.

Note that raw text modification may be possible, but we need to meddle with
the base `index_db` class to do this ~ which may be too messy.
  • Loading branch information...
commit 48c4ec65a6b9d6091bf0cf2a33fab79cdb8ef269 1 parent e0548f0
@bow bow authored peterjc committed
Showing with 1 addition and 2 deletions.
  1. +1 −2  Bio/SearchIO/HmmerIO/hmmer3_text.py
View
3  Bio/SearchIO/HmmerIO/hmmer3_text.py
@@ -404,8 +404,7 @@ def __iter__(self):
# (starts with the start mark)
start_offset = end_offset - len(line)
elif line.startswith(self.qresult_end):
- yield _bytes_to_string(qresult_key), start_offset, \
- end_offset - start_offset
+ yield _bytes_to_string(qresult_key), start_offset, 0
start_offset = end_offset
elif not line:
break
Please sign in to comment.
Something went wrong with that request. Please try again.