xvazquezc / stuff

Repository for miscellaneous stuff not worth of independent repos

stuff

Place to store miscellaneous scripts

Scripts

iprs2anvio.sh

Script for parsing InterProScan annotations into table format suitable for importing into Anvi'o with anvi-import-functions

iprs2anvio.sh allows you to indicate which sources of annotation you want to export and the possibility of creating individual files for each source.

Note: tested on Linux.

Requires GNU getopt, installable in Mac using MacPorts with sudo port install getopt

Help:

iprs2anvio.sh v0.1

USAGE
iprs2anvio.sh -i iprs_output.tsv -o output_prefix
[-d|--db db_list] [-g|--go_terms] [-p|--pathways] [-r|--ipr] [-s|--split] [-h|--help]

REQUIRED
-i, --input      Output file from InterProScan in tsv format.
-o, --output     Prefix for the output file(s).

OPTIONAL
-d, --db         Only extract the annotations of specific databases. All annotations
                 will be extracted by default. For multiple databases, use a comma-separated
                 list.
-g, --go_terms   Extract GO terms.
-p, --pathways   Extract pathway annotations.
-r, --ipr        Extract InterPro cross-reference annotations.
-s, --split      Annotations from each database will be written in individual files.

MISCELLANEOUS
-h, --help       Show this help information and exits.

Deprecated

IPRS to Anvi'o scripts

Use iprs2anvio.sh instead.

iprs2anvi_go.sh parses GO terms from IPRS .tsv files to a table usable by anvi-import-functions. Output to iprs_go_matrix.tsv by default. Usage:

iprs2anvi_go.sh infile.tsv [outfile(optional)]

iprsalt2anvio.sh is similar to iprs2anvi_go.sh but also parses the output from the pathways.