receptor-utils 0.0.67

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 0.0.66:

• Added support for 10X Cell Ranger reference sets
• Added options and a utility to download/extract leader sequences for V alleles

Changes in version 0.0.66:

• Added -f MIXCR option to download_germline set
• Added make_mixcr_json utility
• If necessary, add fake alleles to sequence names when making aux, ndm files for igblast

Changes in version 0.0.65:

• Further fixes to imports

Changes in version 0.0.64:

• Fix import of aux_formats (whch regressed in 0.0.63)

Changes in version 0.0.63:

• In extract_imgt_refs, include obviously incomplete V sequences (length <= 280) unless the functional_only option is set
• upgrade setuptools dependency. If you have trouble installing receptor_utils, please upgrade pip.

Changes in version 0.0.62:

• Fix import of aux_formats
• Add support for C genes in download_germline_set

Changes in version 0.0.61:

• Internal restructing of aux_formats.py: no change to functionality

Changes in version 0.0.61:

• Fix handing of incomplete codon at 3' end in create_alignment

Changes in version 0.0.60:

• New script create_alignment: creates an alignment of alleles from a single gene, showing nucleotide sequences with amino acid translations and silent/nonsilent mutations. Supports V, D, and J sequence types with type-specific formatting including CDR region delineation for V sequences.

Changes in version 0.0.57:

• annotate_j: better handling of non-standard motifs and prioritzation of results. Canonical [WF]GxG motifs are always preferred, but non-standard motifs such as [WF]A.G (seen in TRGJP1, TRGJP2, TRAJ16) and [CWF][AG].G (seen in TRAJ35) are accommodated with a warning. likewise solutions with no stop codons are preferred, but stop codons are accommodated if necessary as they may be excised during recombination.

Changes in version 0.0.56:

• annotate_j: accommodate (with warning) the non-standard motif [CWF][AG].G seen in TRAJ35

Changes in version 0.0.55:

• annotate_j: accommodate (with warning) the non-standard motif [WF]A.G seen in TRGJP1, TRGJP2, TRAJ16

Changes in version 0.0.54:

• Fix name of ungapped file in download_germline_set
• Improve naming of novel D alleles

Changes in version 0.0.53:

• Fix bug in download_germline_set that masked the correct error message when multiple sets were selected

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