ms-extract(1)

NAME

ms-extract - Show genes in the neighborhood of specified gene

SYNOPSIS

ms-extract [--output-dir dir]
    [--adjacent-genes genes=4]
    [--max-nt-distance nucleotides=1000000]
    file.gff3 gene-list.txt

OPTIONS

--output-dir dir
    Name of the directory where gene neighborhood GFF files are stored. Default is ".".

--adjacent-genes genes=4
    Name of the directory where gene neighborhood GFF files are stored. Default is 4.

--max-nt-distance nucleotides=1000000
    Name of the directory where gene neighborhood GFF files are stored. Default is 1,000,000.

DESCRIPTION
ms-extract extracts gene neighborhoods for each gene in gene-list.txt from the given GFF3 file, writing the output to separate GFF3 files, one for each gene. The gene list file should contain one gene name per line. By default, 4 upstream and 4 downstream genes are written along with the gene of interest, as long as they overlap the maximum distance boundary of 1,000,000 nucleotides. The default number of adjacent genes and maximum distance can be overridden using --adjacent-genes and --max-nt-distance. For maximum efficiency, specify all genes of interest in a single command. This allows multiple genes to be extracted in a single pass through the input GFF file rather than sweeping it repeatedly for each gene.

SEE ALSO
ms-intersect(1), ms-stack(1), ms-plot(1)

BUGS
Please report bugs to the author and send patches in unified diff format. (man diff for more information)

AUTHOR
J. Bacon