read_interpro | R Documentation |
Columns are: 1. protein_id - Protein Accession (e.g. P51587) 2. protein_md5 - Sequence MD5 digest (e.g. 14086411a2cdf1c4cba63020e1622579) 3. protein_length - Sequence Length (e.g. 3418) 4. analysis - Analysis (e.g. Pfam / PRINTS / Gene3D) 5. signature_id - Signature Accession (e.g. PF09103 / G3DSA:2.40.50.140) 6. signature_desc - Signature Description (e.g. BRCA2 repeat profile) 7. start - Start location 8. end - Stop location 9. score - is the e-value (or score) of the match reported by member database method (e.g. 3.1E-52) 10. status - is the status of the match (T: true) 11. date - is the date of the run 12. interpro_id - (InterPro annotations - accession (e.g. IPR002093) - optional column; only displayed if -iprlookup option is switched on) 13. interpro_desc - (InterPro annotations - description (e.g. BRCA2 repeat) - optional column; only displayed if -iprlookup option is switched on) 14. go_terms - (GO annotations (e.g. GO:0005515) - optional column; only displayed if –goterms option is switched on) 15. pathway_terms - (Pathways annotations (e.g. REACT_71) - optional column; only displayed if –pathways option is switched on)
read_interpro(file)
file |
Either a path to a file, a connection, or literal data (either a single string or a raw vector). Files ending in Literal data is most useful for examples and tests. To be recognised as
literal data, the input must be either wrapped with Using a value of |
Because 'readr::read_tsv' expects a fixed number of columns, but interpro columsn 12-15 are optional, warnings like 15 cols expected, 11 cols seen should be ignored.
tibble
https://github.com/ebi-pf-team/interproscan/wiki/OutputFormats
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