rcsb.exdb 1.33__py3-none-any.whl → 1.34__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- rcsb/exdb/seq/PolymerEntityExtractor.py +3 -2
- {rcsb_exdb-1.33.dist-info → rcsb_exdb-1.34.dist-info}/METADATA +1 -1
- {rcsb_exdb-1.33.dist-info → rcsb_exdb-1.34.dist-info}/RECORD +5 -5
- {rcsb_exdb-1.33.dist-info → rcsb_exdb-1.34.dist-info}/WHEEL +0 -0
- {rcsb_exdb-1.33.dist-info → rcsb_exdb-1.34.dist-info}/licenses/LICENSE +0 -0
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@@ -9,6 +9,7 @@
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# 9-Jan-2024 dwp Turn off use of uniprot_exdb DB for enriching protein entity details file (data not used)
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# 10-Dec-2024 dwp Sort extracted polymer entity sequence data by entity ID (alphabetically), to ensure consistent
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# ordering between coasts (order of sequence data influences results of mmseqs2 sequence searching)
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# 2-Feb-2026 dwp Handle case of missing 'rcsb_entity_source_organism.source_type'
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#
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##
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__docformat__ = "google en"
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@@ -115,7 +116,7 @@ class PolymerEntityExtractor(object):
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begSeqNum = 1
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endSeqNum = seqLen
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srcId = tD["pdbx_src_id"]
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srcType = tD["source_type"]
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srcType = tD["source_type"] if "source_type" in tD else None
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taxId = tD["ncbi_taxonomy_id"] if "ncbi_taxonomy_id" in tD else -1
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if srcName and taxId == -1:
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missingSrcD.setdefault(srcName, []).append(rId)
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@@ -138,7 +139,7 @@ class PolymerEntityExtractor(object):
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pD = eD["rcsb_polymer_entity"]
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taxCount = pD["rcsb_source_taxonomy_count"]
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except Exception:
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if srcType == "synthetic":
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if srcType is not None and srcType == "synthetic":
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taxCount = 0
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else:
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logger.warning("%s (srcName %r) no source taxonomy count type %r", rId, srcName, srcType)
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@@ -33,7 +33,7 @@ rcsb/exdb/examples-seq/testReferenceSequenceUtils.py,sha256=JIpQsyVfU9sx-50ludlD
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rcsb/exdb/seq/AnnotationExtractor.py,sha256=8iCE8LJR7QH8ilSWDkpKYQSfVuSvorlnM9VHIIYcRoY,2741
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rcsb/exdb/seq/LigandNeighborMappingExtractor.py,sha256=PpRWunQHZ6j8s6MCu1tuY59cocEoUvM3bIUcsvQ-Ijo,3431
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rcsb/exdb/seq/LigandNeighborMappingProvider.py,sha256=vzy2tJGB6IgDNgSHyzGU3TuTOV9cfWI_eLRkO3apQtk,3741
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rcsb/exdb/seq/PolymerEntityExtractor.py,sha256=
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rcsb/exdb/seq/PolymerEntityExtractor.py,sha256=7Vf50e4aCwBJ_0nMuPrlMLU3dyQMD_T2w-YtoawKInc,15144
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rcsb/exdb/seq/ReferenceSequenceAnnotationAdapter.py,sha256=VXStOXoZcbFGYOm5eYiqn599BNksG87h3kzK_aQz2Xc,31160
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rcsb/exdb/seq/ReferenceSequenceAnnotationProvider.py,sha256=2fbNeH1VkxEPpny0lfaTJ-UGEXQjxTdQbUoeiTRbJuU,9560
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rcsb/exdb/seq/ReferenceSequenceAssignmentAdapter.py,sha256=P-t4w4uvnx4qv_vBAJwKuBGjo6wOIYZ8IKzGaw2bCQ8,25935
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@@ -55,7 +55,7 @@ rcsb/exdb/wf/EntryInfoEtlWorkflow.py,sha256=YVr75Wz1BPjLr_satd28B9BeD3QL6HwmkR17
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rcsb/exdb/wf/GlycanEtlWorkflow.py,sha256=oJ6wf438K2e-eLmy8Ni3MCPxjAKgVJY38SWO885gnmg,2820
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rcsb/exdb/wf/PubChemEtlWorkflow.py,sha256=fNX3A6kf0S1XiJMz7ywNpFuuua5lT3XaUFjcCJtvQsU,11235
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rcsb/exdb/wf/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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rcsb_exdb-1.
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rcsb_exdb-1.
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rcsb_exdb-1.
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rcsb_exdb-1.
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rcsb_exdb-1.34.dist-info/METADATA,sha256=nfmbDBYh52noNUURQXRnqS8ksTzLd_46fINrsstMmkc,3845
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rcsb_exdb-1.34.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
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rcsb_exdb-1.34.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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rcsb_exdb-1.34.dist-info/RECORD,,
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File without changes
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File without changes
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