From e5998ab4e85775286d498ae89e961f66005f47ba Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Thu, 9 Aug 2018 14:16:25 +0200
Subject: [PATCH] SCHWED-3472: skip dssp lines in hhr files and better document
parsing.
---
modules/bindings/pymod/hhblits.py | 21 +++++++++++++++++++--
1 file changed, 19 insertions(+), 2 deletions(-)
diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index 74e44c77a..0a1045171 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -215,6 +215,12 @@ def ParseHHblitsOutput(output):
return seq.CreateAlignment(s1, s2)
try:
while True:
+ # Lines which we are interested in:
+ # - "Done!" -> end of list
+ # - "No ..." -> next item in list
+ # - "T <hit_id> <start> <data> <end>"
+ # - "Q <query_id> <start> <data> <end>"
+ # -> rest is to be skipped
line = lines.next()
if len(line.strip()) == 0:
continue
@@ -238,19 +244,30 @@ def ParseHHblitsOutput(output):
lines.next()
continue
assert entry_index != None
+ # Skip all "T ..." and "Q ..." lines besides the one we want
if line[1:].startswith(' Consensus'):
continue
if line[1:].startswith(' ss_pred'):
continue
if line[1:].startswith(' ss_conf'):
continue
+ if line[1:].startswith(' ss_dssp'):
+ continue
if line.startswith('T '):
end_pos = line.find(' ', 22)
- assert end_pos != -1
+ # this can fail if we didn't skip all other "T ..." lines
+ if end_pos == -1:
+ error_str = "Unparsable line '%s' for entry No %d" \
+ % (line.strip(), entry_index + 1)
+ raise AssertionError(error_str)
templ_str += line[22:end_pos]
if line.startswith('Q '):
end_pos = line.find(' ', 22)
- assert end_pos != -1
+ # this can fail if we didn't skip all other "Q ..." lines
+ if end_pos == -1:
+ error_str = "Unparsable line '%s' for entry No %d" \
+ % (line.strip(), entry_index + 1)
+ raise AssertionError(error_str)
query_str += line[22:end_pos]
except StopIteration:
if len(query_str) > 0:
--
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