From 02089369b4d1ab4e258fce36f4831bb07540df85 Mon Sep 17 00:00:00 2001
From: Rafal Gumienny <r.gumienny@unibas.ch>
Date: Fri, 20 Apr 2018 09:44:52 +0200
Subject: [PATCH] fix: SCHWED-3121 Save alignments in the output, pull out
chain_mapping
---
actions/ost-compare-structures | 31 +++++++++++++++++++++++++------
1 file changed, 25 insertions(+), 6 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index a4a821a5a..b1d2ed816 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -450,6 +450,25 @@ def _CheckConsistency(reference, model, chain_mapping, log_error):
return is_cons
+def _GetAlignmentsAsFasta(alignments):
+ """Get the alignments as FASTA formated string.
+
+ :param alignments: Alignments
+ :type alignments: list of AlignmentHandle
+ :returns: list of alignments in FASTA format
+ :rtype: list of strings
+ """
+ strings = list()
+ for alignment in alignments:
+ aln_str = ">reference:%s\n%s\n>model:%s\n%s" % (
+ alignment.GetSequence(0).name,
+ alignment.GetSequence(0).GetString(),
+ alignment.GetSequence(1).name,
+ alignment.GetSequence(1).GetString())
+ strings.append(aln_str)
+ return strings
+
+
def _ReadStructureFile(path):
"""Safely read structure file into OST entity.
@@ -618,6 +637,9 @@ def _Main():
qs_scorer.chain_mapping,
opts.consistency_checks)
reference_results["info"]["residue_names_consistent"] = is_cons
+ reference_results["info"]["mapping"] = {
+ "chain_mapping": qs_scorer.chain_mapping,
+ "alignments": _GetAlignmentsAsFasta(qs_scorer.alignments)}
skip_score = False
if opts.consistency_checks:
if not is_cons:
@@ -653,8 +675,7 @@ def _Main():
"model_name": model_name,
"reference_name": reference_name,
"global_score": 0.0,
- "best_score": 0.0,
- "chain_mapping": qs_scorer.chain_mapping}
+ "best_score": 0.0}
else:
ost.LogInfo("Computing QS-score")
try:
@@ -664,8 +685,7 @@ def _Main():
"model_name": model_name,
"reference_name": reference_name,
"global_score": qs_scorer.global_score,
- "best_score": qs_scorer.best_score,
- "chain_mapping": qs_scorer.chain_mapping}
+ "best_score": qs_scorer.best_score}
except qsscoring.QSscoreError as ex:
# default handling: report failure and set score to 0
ost.LogError('QSscore failed:', str(ex))
@@ -675,8 +695,7 @@ def _Main():
"model_name": model_name,
"reference_name": reference_name,
"global_score": 0.0,
- "best_score": 0.0,
- "chain_mapping": qs_scorer.chain_mapping}
+ "best_score": 0.0}
# Calculate lDDT
if opts.lddt:
ost.LogInfo("-" * 80)
--
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