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47 lines
1.4 KiB
Python
47 lines
1.4 KiB
Python
# Copyright 2024 by Samuel Prince. All rights reserved.
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#
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# This file is part of the Biopython distribution and governed by your
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# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
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# Please see the LICENSE file that should have been included as part of this
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# package.
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"""Bio.SearchIO base classes for Infernal-related code."""
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from Bio.SearchIO._model import Hit
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class _BaseInfernalParser:
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"""Abstract class for Infernal parser objects."""
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def _add_hit_to_dict(self, hit_attrs, hsp, hit_dict):
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"""Add a hit information to the hit container (PRIVATE)."""
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# add the hit to the container dict, creating a new
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# entry if it does not exist yet
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hid = hit_attrs["id"]
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if not hid in hit_dict:
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hit_dict[hid] = {
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"attrs": hit_attrs,
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"hsps": []
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}
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else:
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assert hit_dict[hid]["attrs"]["query_id"] == hit_attrs["query_id"]
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assert hit_dict[hid]["attrs"]["description"] == hit_attrs["description"]
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hit_dict[hid]["hsps"].append(hsp)
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def _hit_to_list(self, hit_dict):
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"""Create a Hit list from the hit container (PRIVATE)."""
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hit_list = []
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for hit_info in hit_dict.values():
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hit = Hit(hit_info["hsps"])
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for attr, value in hit_info["attrs"].items():
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setattr(hit, attr, value)
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hit_list.append(hit)
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return hit_list
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