receptor-utils 0.0.52

Some tools I find useful for working with Ig receptor sequences

receptor_utils

Some tools I find useful for working with IG/TR receptor sequences, including support for allele sequence naming and the creation of custom IgBlast databases. Please see the documentation for further details.

Changes in version 0.0.52:

• FIx missing dependency

Changes in version 0.0.51:

• Updates to download_germline_set, to create files for IgBlast.
• New documentation sections: using AIRR-C sets with IgBlast, using AIRR-C sets with MiXCR

Changes in version 0.0.50:

• Added a new utility, download_germline_set, to download germline sets from the Open Germline Receptor Database (OGRDB)

Changes in version 0.0.49:

• Added an option to allow at_coords to be used with FASTA files containing multiple sequences
• Fixed problems in name_alleles that could be caused by erroneously long V-sequences

Changes in version 0.0.48:

• Added an option to make_igblast_ndm to specify CDR positions, for use with IMGT-gapped germline sets that do not follow the canonical alignment. Added further explanation to the documentation.

Changes in version 0.0.47:

• write_csv now takes an optional scan_all argument. If True, all records to be added are scanned for keywords and the columns are extended to include keywords found in any records

Changes in version 0.0.46:

• fix issue with naming of D novel alleles - this could cause existing alleles to be named as novel by the utilities

Changes in version 0.0.45:

• added dependency for biopython version >=1.81

Changes in version 0.0.44:

• minor fix to novel allele naming
• fixed a bug that prevented sequence subsets being shown by identical_seqs

Changes in version 0.0.43:

• remove dependency on deprecated Bio.pairwise2
• improve naming of insertions, e.g. IGHV1-203_i7g_i7a would now be IGHV1-203_i7ga

Changes in version 0.0.42:

• better handling of long target sequences

Changes in version 0.0.41:

• annotate_j: fix issue with processing FASTA input

Changes in version 0.0.40:

• The submodule name receptor_utils.number_ighv has been changed to receptor_utils.number_v to reflect its wider scope. The old name will continue to work for the time being but will raise a deprecation warning.
• In receptor_utils.simple_bio_seq, write_fasta(seqs, filename) has become write_fasta(filename, seqs) for consistency with write_csv. The old calling pattern will continue to work for the time being but will raise a deprecation warning.

Changes in version 0.0.39:

• annotate_j and make_igblast_ndm will now accept a germline set in AIRR Community JSON format, as an alternative to providing the set in FASTA format.

Changes in version 0.0.38:

• Improve reporting of issues with conserved residues
• Change URL for fetching IMGT reference sets to use https