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Coverage Mode Option Not Affecting TM Scores in HTML Output #355

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khatrics16 opened this issue Sep 22, 2024 · 0 comments
Open

Coverage Mode Option Not Affecting TM Scores in HTML Output #355

khatrics16 opened this issue Sep 22, 2024 · 0 comments

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@khatrics16
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I am using the following commands to generate HTML files from Foldseek result files by varying the coverage mode to output different TM scores: query-normalized, target-normalized, and both query and target-normalized TM scores.

foldseek easy-search MW355455-CDS-0004.pdb Foldseek_db/anti_crispr_db query_target.html tmp --format-mode 3 --alignment-type 1 --cov-mode 0
foldseek easy-search MW355455-CDS-0004.pdb Foldseek_db/anti_crispr_db target.html tmp --format-mode 3 --alignment-type 1 --cov-mode 1
foldseek easy-search MW355455-CDS-0004.pdb Foldseek_db/anti_crispr_db query.html tmp --format-mode 3 --alignment-type 1 --cov-mode 2

Expected Behavior:
The generated HTML files should display different TM scores based on the specified coverage mode:
--cov-mode 0: TM score normalized by both query and target.
--cov-mode 1: TM score normalized by target.
--cov-mode 2: TM score normalized by query.

Actual Behavior:
All the generated HTML files show the same TM scores, which suggests that the coverage mode option might not be working as expected.

Has anyone else experienced a similar issue with Foldseek? Is there a workaround or a fix for ensuring that the coverage mode is properly applied to the TM score calculation?

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