commec v0.3.0

Features

• Add -Y / --config to provide screen configuration in YAML format, allowing customization of database structure (#19)
• Add --force and --resume to Commec Screen CLI (#20)
  • -F / --force: pre-existing screen file will be overwritten
  • -R / --resume: bypass pre-existing .screen files, only perform searches that are incomplete

Full Changelog: v0.2.0...v0.3.0

commec v0.2.0

Features

• New commec setup command to download necessary databases

Bug fixes

• Filter out deleted and invalid taxonomy ids
• Ensure immediately adjacent ranges of protein and nucleotide hits are not registered as overlapping
• Include the end of the query in nucleotide search if >50bp not covered
• Correctly name noncoding fasta created by fetch_nc_bits

Full Changelog: v0.1.2...v0.2

commec v0.1.2-alpha

Fix a few bugs that appeared when testing v0.1.1 of the commec package:

• The nucleotide search was erroneously pointing at nt_dir instead of nt_db
• Errors would appear if the # sign was present in a FASTA id
• Two FutureWarnings would appear in the file output

commec v0.1.1-alpha

Two bugfixes:

• Remove rogue "swissprot" in place of "nr" left from testing
• Change filename for cleaned FASTA (avoid file overwrite error when -o not specified and running from input directory)

commec v0.1.0-alpha

Initial release of commec

The Common Mechanism offers three sub-commands through the commec entrypoint:

    screen  Run Common Mechanism screening on an input FASTA.
    flag    Parse all .screen files in a directory and create two CSVs file of flags raised
    split   Split a multi-record FASTA file into individual files, one for each record

Full Changelog: https://github.com/ibbis-screening/common-mechanism/commits/v0.1.0