goatools.grouper.aart_geneproducts_all module

Product gene lists with ASCII art sections and GO IDs for each gene product.

class goatools.grouper.aart_geneproducts_all.AArtGeneProductSetsAll(grprdflt, hdrobj, **kws)

Bases: object

Product gene lists with ASCII art sections and GO IDs for each gene product.

keys_exp = {'fmtgene', 'fmtgene2', 'fmtgo', 'fmtgo2', 'itemid2name'}

all_chrints = (65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 91, 92, 93, 94, 95, 123, 124, 125, 126)

run(name, goea_nts, log)

Run gene product ASCII art.

prt_mrks(name_marks_list, prt=sys.stdout)

Print summary of all GOEAs. .. rubric:: Example

Key for GO sections: A immune B viral/bacteria C neuro D cell death E lipid F adhesion G cell cycle H chromosome I development J extracellular matrix K ion L localization M membrane N metabolic O phosphorylation P signaling Q stimulus R prolif_differ S Misc.

ABCDEFGHIJKLMNOPQRS XX.X..XXX..X.XX.XXX transient_increase XX.XXX…..X.X.XXXX consistent_increase XXXXXX..XXXXXXXXXXX late_increase ..X…..X.XX.X….X consistent_decrease ..X.XX..X.XX.XXX.XX late_decrease

prt_section_key(prt=sys.stdout)

Print the section name and its alias.

str_hdr()

Return a string representing the section headers:

get_chr2idx()

Return a dict with the ASCII art character as key and its index as value.