calc_motifs

calc_motifs creates motif files for RSS and leader fields, based on the features produced by parse_imgt_annotations. Only annotations of sequences marked as ‘functional’ are considered.

calc_motifs also creates a file containing definitions of other motif parameters for the locus. These are copied from the values used for human locus, but may be modified if necessary. The following values are included:

Parameter	Definition
J_TRP_MOTIF	The J amino acid motif to search for. May be a single value, or a Python list, e.g. [“FGXG”, “WGXG”]
J_TRP_OFFSET	The number of codons between and including the start of the J motif and the final codon before the J-SPLICE
J_SPLICE	The expected nt sequence of the J-SPLICE
V_RSS_SPACING	The expected length of the V-SPACER
J_RSS_SPACING	The expected length of the J-SPACER
D_5_RSS_SPACING	The expected length of the 5’ D-SPACER (0 if this is not a heavy chain)
D_3_RSS_SPACING	The expected length of the 3’ D-SPACER (0 if this is not a heavy chain)

Please refer to Annotating the rhesus macaque IGH locus for example usage of this and the other ‘individual’ commands.

Given a set of gene features, create motif matrices

usage: calc_motifs [-h] locus feat_file

Positional Arguments

locus

locus (e.g. IGH, TRA)

feat_file

feature file, created, for example, by parse_imgt_annotations