Python scripts for finding any QTL near SNPs in the Sorghum QTL Atlas.
The primary query_qtl_atlas.py script requires a local SQLite database be generated using exported Sorghum QTL Atlas data (in Excel format). A helper script is provided to simplify database generation (see instructions below).
python query_qtl_atlas.py -h
usage: query_qtl_atlas.py [-h] --input INPUT --output OUTPUT
[--database DATABASE] [--distance DISTANCE]
[--qtl_length QTL_LENGTH] [--column COLUMN]
[--substring SUBSTRING]
This script was designed to find any QTLs near SNPs in the Sorghum QTL Atlas
(https://aussorgm.org.au/sorghum-qtl-atlas/search/)
optional arguments:
-h, --help show this help message and exit
--database DATABASE The SorghumQtlAtlas database to use.
--distance DISTANCE The maximum distance (in kb) from a SNP to search for
QTL (default: 10).
--qtl_length QTL_LENGTH
The maximum length (in kb) of a QTL to include
(default: 5000).
--column COLUMN To search for specific substrings within columns, use
the following index numbers: { 0: index, 1: QTL Id, 2:
Publication, 3: Population, 4: Trait Description, 5:
LG:Start-End (v3.0), 6: Genes Under QTL (v3.0), 7:
Synteny, 8: Chr, 9: Start, 10: Stop}. Ex. --column 2
(this will use the Publication column to look for
substrings). Multiple columns may also be designated:
--column 2,8
--substring SUBSTRING
Substring to search for within column (designated in
--column). Ex. --column 4 --substring wax. Multiple
substrings may be designated: --column 3,8 --substring
bap,2
required arguments:
--input INPUT The name of the input file (CSV). File structure:
markerName,chromosome,position Or:
markerName,chromosome,start,stop -- both with a header
--output OUTPUT The output file to be created (CSV).Generate SQLite database from each SQA trait Excel table (see Sorghum QTL Atlas):
python generate_atlas_database.py -h
usage: generate_atlas_database.py [-h] --input INPUT [--database DATABASE]
This script was designed to build a local instance of the Sorghum QTL Atlas
(https://aussorgm.org.au/sorghum-qtl-atlas/search/)
optional arguments:
-h, --help show this help message and exit
--database DATABASE The SorghumQtlAtlas database output name. (Default:
SorghumQtlAtlas.db)
required arguments:
--input INPUT The name of the input files (Excel) as a comma-
separated list. Ex. Atlas_leaf.xlsx,Atlas_maturity.xlsx