This script is designed to perform kaas or KofamKOALA result. These files will be produced: *.kegg_anno.xls, *.kegg_pathway_stata.xls, *.K_codes_not_in_pathway_map.list.
- wget windows: http://gnuwin32.sourceforge.net/packages/wget.htm, unix: https://www.gnu.org/software/wget/
python kaas_kofam2pathwayAnalysis.py annot_kegg.txt [org]
annot_kegg.txt the first column should be the gene ID; Kd+ can be one or more in one row; the same geneID can be in one or more row.
Get from kaas or KofamKOALA result
org Organisms code of KEGG. eg. eco (Escherichia coli K-12 MG1655), The default value is "ko", Use "ko00001.keg" annotations not species-specific
See: https://www.genome.jp/kegg/catalog/org_list.html
1. Use "ko00001.keg" annotations:
python kaas_kofam2pathwayAnalysis.py annot_kegg.txt
2. Use species-specific annotations:
python kaas_kofam2pathwayAnalysis.py annot_kegg.txt ecohttps://zhuanlan.zhihu.com/p/375740435?
This script is convert the GO annotation with GO annotation with wego format, TSV format (interproscan.sh and eggnog-mapper) to GENE2TERM format. (Recommended interpro results)
eggNOG: http://eggnog5.embl.de/
interpro: https://www.ebi.ac.uk/interpro/search/sequence/
python3 (>=3.8.1)
goatools （pip install goatools, Tested: goatools v1.1.6）
pandas（pip install pandas, Tested: pandas v1.0.1 ）
R (>=3.6.2 )
ggplot2 (>=3.3.5)
dplyr (>=1.0.7)
python GO_anno_from_tab.py -i eggnog_result.emapper.annotations
python GO_anno_from_tab.py -i go.wego
python GO_anno_from_tab.py -i interpro.out.txthttps://zhuanlan.zhihu.com/p/426424799?
goatools: Klopfenstein D V, Zhang L, Pedersen B S, et al. GOATOOLS: A Python library for Gene Ontology analyses[J]. Scientific reports, 2018, 8(1): 1-17.
ggplot2: Valero-Mora P M. ggplot2: elegant graphics for data analysis[J]. Journal of Statistical Software, 2010, 35: 1-3.