zktuong / receptor_utils

Misc utilities for receptor gene 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 0.0.44:

• 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