bromberglab/varidb repository overview

usage: varidb [-h] [-q QUERY] [-Q QUERYLIST] [-t TYPE] [-T TOOLS] [-r REVISION] [-f FASTA] [-s] [-R REPORT] [-w WILDTYPE] [-p POSITION] [-m MUTATION] [-D DB] [-i] [-P PLUGINDIR] [-c CREATE] [-o OUTFILE] [-C COLUMNS [COLUMNS ...]] [-S SEPARATOR] [-H] [-j] [-F FASTA2SEGUID] [-L [LOGFILE]] [-v]

Query or create variant database

optional arguments: -h, --help show this help message and exit -q QUERY, --query QUERY single query: seguid (default), fasta sequence, or any accession id providing --type <db_name> -Q QUERYLIST, --querylist QUERYLIST query by list of querys, format: -t TYPE, --type TYPE query type: seguid (default) | fasta | <db_name> (e.g. uniprot) -T TOOLS, --tools TOOLS name/s of the tool/s (=table name/s) to query -r REVISION, --revision REVISION desired entry revision; default: latest -f FASTA, --fasta FASTA path to fasta file to use instead of id when using -Q/--querylist -s, --split split result into successful queries and list of missing entries (<outfile_name>_missing.<outfile_suffix>) -R REPORT, --report REPORT path to save detailed query report -w WILDTYPE, --wildtype WILDTYPE limit query by wildtype(s) -p POSITION, --position POSITION limit query by position(s) -m MUTATION, --mutation MUTATION limit query by mutation(s) -D DB, --db DB path to sqlite database file; default: varidb.db -i, --info prints database info -P PLUGINDIR, --plugindir PLUGINDIR path to plugins directory; default: plugins -c CREATE, --create CREATE create new database from path -o OUTFILE, --outfile OUTFILE save query result to file -C COLUMNS [COLUMNS ...], --columns COLUMNS [COLUMNS ...] columns (in that order) to print/write out; default: all -S SEPARATOR, --separator SEPARATOR separator character to use for print/write out; default: , -H, --hideheader hide header when print/write out; default: False -j, --json format output as json string -F FASTA2SEGUID, --fasta2seguid FASTA2SEGUID path to (multi)fasta file - generates seguids -L [LOGFILE], --logfile [LOGFILE] redirect logs to file -v, --verbose increase output verbosity

There are 5 possible status values in the output for each query variant:

• ok (valid variant predictions for the requested variant)
• protein (the protein is not available in the DB)
• position (the protein has no position as specified in the query variant)
• wildtype (the wildtype at the position specified in the query variant does not match the sequence residue in the DB)
• variant (the prediction for the specified mutation is not available in the DB)