Fix ValueError when parsing gap-only alignment blocks in HMMER output #4
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When HMMER outputs alignment blocks with all gaps (no sequence aligned), it uses '-' for sequence positions instead of numbers. This caused a ValueError when trying to convert '-' to int. Changes: - Handle '-' values in ali_left and ali_right by converting to None - None is semantically clearer than -1 for missing/invalid values - Gap-only blocks are preserved to maintain alignment structure - Downstream code correctly handles gaps (they're skipped in position tracking) Fixes parsing errors like: ValueError: invalid literal for int() with base 10: '-'
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That's not a nice piece of code I have there in Can you pls give an example sequence that demonstrates this behavior? |
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When HMMER outputs alignment blocks with all gaps (no sequence aligned), it uses '-' for sequence positions instead of numbers. This caused a ValueError when trying to convert '-' to int.
Changes:
Fixes parsing errors like:
ValueError: invalid literal for int() with base 10: '-'