IMGT-HLA-alignments-to-alignments-matrices | # # # # # # # # # # # # # # # # # # # # # # # # #

IMGT-HLA-alignments-to-alignments-matrices is a Python library. IMGT-HLA-alignments-to-alignments-matrices has no bugs, it has no vulnerabilities and it has low support. However IMGT-HLA-alignments-to-alignments-matrices build file is not available. You can download it from GitHub.

############################################################ hlaalignmenttoalignmentmatrix ############################################################ this script aims to convert alignment files, as available on imgt-hla repository (ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/alignments/) to alignment matrices (0, 1, 2 and 3 encoding respectively a, t, c and g). then, a distance matrix can be computed, by summing the pairwise differences in the alignment matrix. ############################################################ basic usage: align2mat.py --help mat2dist.py --help align2mat.py --list --coord mat2dist.py --list with the version of the genome in which you want the coordinates of your alignment matrices, and a text file including the path to an alignment file on each line. names should not include spaces. option --help show all the other options available. ############################################################ output: .mat - alignment matrix (binary pickle) .mat2 - distance matrix (binary pickle) .ord - order of the sequences in the matrices .pos - positions kept in matrices ############################################################ additional information: in order to convert positions from alignment coordinates to genomic coordinates, you need a file describing for each alignment file the structure of present features. for instance, if you want to process the alignment file "x.txt" and get the positions as found in grch38, you will need a file called "x.txt.grch38.bio". on the first line of this file, you will have either 0 or 1, respectively if the corresponding gene is coding on the reverse strand or on the direct