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extract-go-terms

A docker image for extracting Gene Ontology terms from a CSV file

Running

The Docker image built by the Dockerfile is designed to be used by docker-pipeline.

The image's default command is an executable python script, extract_go_terms.py, which replaces parsing and matching in go_sequence.py from YoderLab/MMAP. It produces a CSV file containing unique GO terms and the number of times they occurred in the input file

Environment Variables

Variable Description Type Required? Default
CONT_INPUT_BLAST_RESULTS_FILE CSV file in BLAST CSV format with subject titles containing [GO:xxxxxx] terms Input Yes
CONT_OUTPUT_GOTERMS_FILE Results file, in CSV format. GO terms and counts Output Yes
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dukegcb
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