snp_network_from_gene_network.py uses a dict (chromo_num_correspondance) to translate chromosome numbering from gene_list (mart_export.txt) into integer using PLINK nomenclature :
Autosomes are coded from 1 to 22. And the following other codes can be used to specify other chromosome types:
X (X chromosome) -> 23
Y (Y chromosome) -> 24
XY (Pseudo-autosomal region of X) -> 25
MT (Mitochondrial) -> 26
Thus, genes on unlocalized sequences, unplaced sequences, and alternate loci are not take into account.
New correspondences can be added in chromo_num_correspondance.
snp_network_from_gene_network.pyuses a dict (chromo_num_correspondance) to translate chromosome numbering fromgene_list(mart_export.txt) into integer using PLINK nomenclature :Autosomes are coded from 1 to 22. And the following other codes can be used to specify other chromosome types:
X (X chromosome) -> 23
Y (Y chromosome) -> 24
XY (Pseudo-autosomal region of X) -> 25
MT (Mitochondrial) -> 26
Thus, genes on unlocalized sequences, unplaced sequences, and alternate loci are not take into account.
New correspondences can be added in
chromo_num_correspondance.