goatools.parsers.david_chart module

Manages data from a DAVID Chart file.

class goatools.parsers.david_chart.DavidChartReader(fin_davidchart)

Bases: object

Manages data from a DAVID Chart file.

prt_flds = ['Category', 'GO', 'name', 'Count', 'Perc', 'PValue', 'List_Total', 'Pop_Hits', 'Pop_Total', 'Fold_Enrichment', 'Bonferroni', 'Benjamini', 'FDR', 'Genes']

fld2col_widths = {'Benjamini': 8, 'Bonferroni': 8, 'Category': 10, 'Count': 4, 'FDR': 8, 'Fold_Enrichment': 6, 'GO': 11, 'Genes': 15, 'List_Total': 4, 'PValue': 8, 'Perc': 4, 'Pop_Hits': 4, 'Pop_Total': 5, 'name': 30}

fld2prtfmt = {'Benjamini': '{Benjamini:8.2e}', 'Bonferroni': '|{Bonferroni:8.2e}', 'Category': '{Category:10}', 'Count': '{Count:8}', 'FDR': '{FDR:8.2e}', 'Fold_Enrichment': '{Fold_Enrichment:6.4f}', 'GO': '{GO:10}', 'Genes': '{Genes:30}', 'List_Total': '{List_Total:8}', 'PValue': '{PValue:8.2e}', 'Perc': '{Perc:4.1f}', 'Pop_Hits': '{Pop_Hits:8}', 'Pop_Total': '{Pop_Total:8}', 'name': '{name:30}'}

wr_xlsx(fout_xlsx, nts)

Write specified namedtuples into an Excel spreadsheet.

prt_mdtbl(nts, prt_flds=None, prt=sys.stdout)

Write specified namedtuples into an Excel spreadsheet.

prt_num_sig(prt=sys.stdout, alpha=0.05)

Print the number of significant GO terms.

get_num_sig(alpha=0.05)

Print the number of significant results using various metrics.