From ce485ed9d64a602d23e963960d9add34db6a5173 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 17 Apr 2020 09:00:41 +0200
Subject: [PATCH] Set ss_pred and ss_conf to None if not available in a3m/hhm
parsing
---
modules/bindings/pymod/hhblits.py | 32 ++++++++++++++++++++-----------
1 file changed, 21 insertions(+), 11 deletions(-)
diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index 0ddaf7842..d2ec85b2d 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -302,6 +302,7 @@ def ParseA3M(a3m_file):
:return: Dictionary containing "ss_pred" (:class:`list`), "ss_conf"
(:class:`list`) and "msa" (:class:`~ost.seq.AlignmentHandle`).
+ If not available, "ss_pred" and "ss_conf" entries are set to None.
'''
profile_dict = dict()
state = 'NONE'
@@ -331,12 +332,16 @@ def ParseA3M(a3m_file):
elif state == 'msa':
msa_seq[len(msa_seq)-1] += line.rstrip()
- profile_dict['ss_pred'] = list()
- profile_dict['ss_conf'] = list()
- for i in range(0, len(pred_seq_txt)):
- profile_dict['ss_pred'].append(pred_seq_txt[i])
- profile_dict['ss_conf'].append(int(conf_seq_txt[i]))
-
+ if len(pred_seq_txt) > 0:
+ profile_dict['ss_pred'] = list()
+ profile_dict['ss_conf'] = list()
+ for i in range(0, len(pred_seq_txt)):
+ profile_dict['ss_pred'].append(pred_seq_txt[i])
+ profile_dict['ss_conf'].append(int(conf_seq_txt[i]))
+ else:
+ profile_dict['ss_pred'] = None
+ profile_dict['ss_conf'] = None
+
# post processing
# MSA
profile_dict['msa'] = None
@@ -374,6 +379,7 @@ def ParseHHM(profile):
:return: Dictionary containing "ss_pred" (:class:`list`), "ss_conf"
(:class:`list`), "msa" (:class:`~ost.seq.AlignmentHandle`) and
"consensus" (:class:`~ost.seq.SequenceHandle`).
+ If not available, "ss_pred" and "ss_conf" entries are set to None.
'''
profile_dict = dict()
state = 'NONE'
@@ -416,11 +422,15 @@ def ParseHHM(profile):
elif state == 'consensus':
consensus_txt += line.rstrip()
- profile_dict['ss_pred'] = list()
- profile_dict['ss_conf'] = list()
- for i in range(0, len(pred_seq_txt)):
- profile_dict['ss_pred'].append(pred_seq_txt[i])
- profile_dict['ss_conf'].append(int(conf_seq_txt[i]))
+ if len(pred_seq_txt) > 0:
+ profile_dict['ss_pred'] = list()
+ profile_dict['ss_conf'] = list()
+ for i in range(0, len(pred_seq_txt)):
+ profile_dict['ss_pred'].append(pred_seq_txt[i])
+ profile_dict['ss_conf'].append(int(conf_seq_txt[i]))
+ else:
+ profile_dict['ss_pred'] = None
+ profile_dict['ss_conf'] = None
# post processing
# MSA
--
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