Open dstern opened 2 years ago
:exclamation: Make to check out our User Guide.
Does not seem like big deal, but causes alphafold2 to crash, because af2 expects #=GC at bottom (in their module remove_empty_columns_from_stockholm_msa - https://github.com/deepmind/alphafold/blob/0be2b30b98f0da7aecb973bde04758fae67eb913/alphafold/data/parsers.py) This is a problem when using custom multiple sequence alignments as input.
in conversion to Stockholm format, #=GC RF placed at top of alignment
Please make sure to execute the reproduction steps.
reformat.pl a3m sto file.a3m file.sto
Please make sure to post the complete output of the tool you called. Please use gist.github.com.
Providing context helps us come up with a solution and improve our documentation for the future.
Include as many relevant details about the environment you experienced the issue in.
:exclamation: Make to check out our User Guide.
Expected Behavior
=GC line is recommended at bottom of alignment (https://en.wikipedia.org/wiki/Stockholm_format##=GC)
Does not seem like big deal, but causes alphafold2 to crash, because af2 expects #=GC at bottom (in their module remove_empty_columns_from_stockholm_msa - https://github.com/deepmind/alphafold/blob/0be2b30b98f0da7aecb973bde04758fae67eb913/alphafold/data/parsers.py) This is a problem when using custom multiple sequence alignments as input.
Current Behavior
in conversion to Stockholm format, #=GC RF placed at top of alignment
Steps to Reproduce (for bugs)
Please make sure to execute the reproduction steps.
reformat.pl a3m sto file.a3m file.sto
HH-suite Output (for bugs)
Please make sure to post the complete output of the tool you called. Please use gist.github.com.
Context
Providing context helps us come up with a solution and improve our documentation for the future.
Your Environment
Include as many relevant details about the environment you experienced the issue in.