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Duplicate expansion support #419
Merged
jnwei
merged 9 commits into
setup-improvements
from
setup-improvements_additional-scripts
May 13, 2024
Merged
Duplicate expansion support #419
jnwei
merged 9 commits into
setup-improvements
from
setup-improvements_additional-scripts
May 13, 2024
Commits on Mar 19, 2024
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Commits on Mar 20, 2024
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Add duplicate chain file support to alignment DB script
This makes it more straightforward to create an alignment database directly from the flattened RODA downloads
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Add script for expanding the alignment dir with duplicates
This adds support for duplicate chain expansion for the alignment dir format. This script can be run on the flattened non-redundant RODA alignments to add explicit directories for all of the duplicate chains in the duplicate_chains file, symlinked to their representative chain alignment directory.
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Commits on May 6, 2024
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Add more efficient script to generate all-seqs FASTA
The previous data_dir_to_fasta.py script is very slow and requires fully reparsing mmCIF files. This new script is much faster and uses the sequence information from the alignment data instead. Note that this will not include chains for which alignments could not be generated, but we can't use those during training anyways.
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