sc2calc is a command-line utility to convert genomic coordinates and
mutations on the SARS-CoV-2 genome between nucleotide and aa positions.
No installation is required, just run ./sc2calc. The script accepts
a wide range of notations, see the examples below.
The script reads from stdin, writes to stdout. Here are examples:
./sc2calc
12345C # What does SNP C at 12345 translate to?
nt:12345C # Same, being explicit that it's nt
G12345C # Same and will error if 12345 is not a G
12345TA # What do SNPs TA at 12345 translate to?
12345:GT>TA # Same and errors if 12345 is not GT
12345 GT TA # Same, VCF columns 2, 4, 5
ABC 12345 GT TA # Same, VCF columns 1, 2, 4, 5
ins:12345:atg # Insertion of atg at 12345
12344 A AACG # Same, using VCF idiom for insertion
a12345aacg # Same, different notation
nt:a12345aacg # Same, different notation
ABC 12344 A AACG # VCF with label column 1
ABC 12344 AG AACGG # Same, extended VCF idiom (end + start)
del:12345:3 # Deletion of 3nt at 12345
del:12345:gtg # Same and will error if 12345 is not GTG
12345:3- # Same
12344 agtg a # Same, using VCF idiom for deletion
Inverse, translating back from AA to nt:
S:456 # What nt position (leftmost) is aa 456 on S?
S:356Y # What nt mutations give substitution ?>Y at 456?
S:X356Y # Same but errors is 456 is not X
aa:S:X356Y # Same but explicit about AA
sc2calc - SARS-CoV-2 genomic coordinate converter
Copyright (C) 2021 Marco van Zwetselaar io@zwets.it
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.