read_interpro: Read InterProScan .tsv files.

In thackl/thacklr: A Collection of R Functions and Snippets I Often Use.

Read InterProScan .tsv files.

Description

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)

Usage

read_interpro(file)

Arguments

file

Either a path to a file, a connection, or literal data (either a single string or a raw vector). Files ending in .gz, .bz2, .xz, or .zip will be automatically uncompressed. Files starting with ⁠http://⁠, ⁠https://⁠, ⁠ftp://⁠, or ⁠ftps://⁠ will be automatically downloaded. Remote gz files can also be automatically downloaded and decompressed. Literal data is most useful for examples and tests. To be recognised as literal data, the input must be either wrapped with I(), be a string containing at least one new line, or be a vector containing at least one string with a new line. Using a value of clipboard() will read from the system clipboard.

Details

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.

Value

tibble

Source

https://github.com/ebi-pf-team/interproscan/wiki/OutputFormats

thackl/thacklr documentation built on Oct. 16, 2023, 9:15 p.m.