receptor-utils 0.0.48

Some tools I find useful for working with Ig receptor sequences

receptor_utils

Some tools I find useful for working with Ig 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 0.0.47:

• 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