From e56a3315f44378412bbed6cde2c5bd595273d83d Mon Sep 17 00:00:00 2001 From: jjavier-bm Date: Mon, 10 Jul 2023 11:08:11 +0100 Subject: [PATCH 1/6] fix bug in addseq for UP headers --- crops/elements/sequences.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/crops/elements/sequences.py b/crops/elements/sequences.py index 0b96d0c..779aba9 100644 --- a/crops/elements/sequences.py +++ b/crops/elements/sequences.py @@ -819,7 +819,7 @@ def add_sequence(self, newseq): if newseq.name is not None: if newseq.name in self.imer: - if self[newseq.name].imer.seqs['mainseq'] == newseq.seqs['mainseq']: + if self[newseq.name].imer[newseq.name].seqs['mainseq'] == newseq.seqs['mainseq']: addall = False else: logging.critical(errormsg) From d7c3fa3587b0b12f5929c888a49350a382edab81 Mon Sep 17 00:00:00 2001 From: jjavier-bm Date: Sun, 16 Jul 2023 16:21:38 +0100 Subject: [PATCH 2/6] fix bug in addseq for UP headers 2 --- crops/elements/sequences.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/crops/elements/sequences.py b/crops/elements/sequences.py index 779aba9..546c1b4 100644 --- a/crops/elements/sequences.py +++ b/crops/elements/sequences.py @@ -819,7 +819,7 @@ def add_sequence(self, newseq): if newseq.name is not None: if newseq.name in self.imer: - if self[newseq.name].imer[newseq.name].seqs['mainseq'] == newseq.seqs['mainseq']: + if self.imer[newseq.name].seqs['mainseq'] == newseq.seqs['mainseq']: addall = False else: logging.critical(errormsg) From d5c6bf40e215a13c86043db4981c418ce3063d84 Mon Sep 17 00:00:00 2001 From: jjavier-bm Date: Sun, 16 Jul 2023 16:27:31 +0100 Subject: [PATCH 3/6] fix issue with no chain id headers --- crops/iomod/taggers.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/crops/iomod/taggers.py b/crops/iomod/taggers.py index 30f2010..7b11a24 100644 --- a/crops/iomod/taggers.py +++ b/crops/iomod/taggers.py @@ -148,7 +148,7 @@ def retrieve_id(seqheader): headerinfo['mainid'] = seqheader[chi:i].upper() if headerinfo['chains'] is None: headerinfo['chains'] = set() - headerinfo['chains'].add(headerinfo['mainid']) + headerinfo['chains'].add('A') break # UniParc From 59c1ff01c1a6fdc77bb1616587014d7d640f8c3f Mon Sep 17 00:00:00 2001 From: jjavier-bm Date: Sat, 28 Oct 2023 14:43:26 +0100 Subject: [PATCH 4/6] chain name from Uni* to 'A' instead of mainid --- crops/iomod/taggers.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/crops/iomod/taggers.py b/crops/iomod/taggers.py index 7b11a24..a9d5867 100644 --- a/crops/iomod/taggers.py +++ b/crops/iomod/taggers.py @@ -134,7 +134,7 @@ def retrieve_id(seqheader): headerinfo['mainid'] += seqheader[i].upper() if headerinfo['chains'] is None: headerinfo['chains'] = set() - headerinfo['chains'].add(headerinfo['mainid']) + headerinfo['chains'].add('A') # UniRef elif seqheader.startswith('>UniRef'): @@ -161,7 +161,7 @@ def retrieve_id(seqheader): headerinfo['mainid'] = seqheader[1:i].upper() if headerinfo['chains'] is None: headerinfo['chains'] = set() - headerinfo['chains'].add(headerinfo['mainid']) + headerinfo['chains'].add('A') break # UniClust From cd877b72aa43b7a857542ceeac6deb6729bd6bfc Mon Sep 17 00:00:00 2001 From: jjavier-bm Date: Sat, 11 Nov 2023 12:41:39 +0000 Subject: [PATCH 5/6] set chain name of UNIPROT sequences back to mainid --- crops/iomod/taggers.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/crops/iomod/taggers.py b/crops/iomod/taggers.py index a9d5867..30f2010 100644 --- a/crops/iomod/taggers.py +++ b/crops/iomod/taggers.py @@ -134,7 +134,7 @@ def retrieve_id(seqheader): headerinfo['mainid'] += seqheader[i].upper() if headerinfo['chains'] is None: headerinfo['chains'] = set() - headerinfo['chains'].add('A') + headerinfo['chains'].add(headerinfo['mainid']) # UniRef elif seqheader.startswith('>UniRef'): @@ -148,7 +148,7 @@ def retrieve_id(seqheader): headerinfo['mainid'] = seqheader[chi:i].upper() if headerinfo['chains'] is None: headerinfo['chains'] = set() - headerinfo['chains'].add('A') + headerinfo['chains'].add(headerinfo['mainid']) break # UniParc @@ -161,7 +161,7 @@ def retrieve_id(seqheader): headerinfo['mainid'] = seqheader[1:i].upper() if headerinfo['chains'] is None: headerinfo['chains'] = set() - headerinfo['chains'].add('A') + headerinfo['chains'].add(headerinfo['mainid']) break # UniClust From 4e8a05de59b84f6cd07349e43e0b5ce181cce983 Mon Sep 17 00:00:00 2001 From: jjavier-bm Date: Sat, 11 Nov 2023 12:56:37 +0000 Subject: [PATCH 6/6] add python3.11 to tests --- setup.py | 1 + 1 file changed, 1 insertion(+) diff --git a/setup.py b/setup.py index 806da65..a648d62 100644 --- a/setup.py +++ b/setup.py @@ -147,6 +147,7 @@ def _load_suite(self, cases, pattern, directory): "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", "Topic :: Scientific/Engineering :: Bio-Informatics", ], install_requires=dependencies)