mgkegg 1.0.8

kegg color pathway object for metagenome

Kegg color pathway object for metagenome

Command line version for KEGG Pathway obejct and KEGG rest api

installation

pip install mgkegg

Usage

1. Display database release information and linked db information

   mgkegg info <dbentries>
   # displays the current statistics of the KEGG database
   mgkegg info kegg
   # displays the number of pathway entries including both the reference and organism-specific pathways
   mgkegg info pathway
   # displays the number of gene entries for the KEGG organism Homo sapiens
   mgkegg info hsa
   

2. Obtain a list of entry identifiers and associated definition

mgkegg ls <dbentries>
# returns the list of reference pathways
mgkegg ls pathway
# returns the list of human pathways
mgkegg ls pathway hsa
# returns the list of KEGG organisms with taxonomic classification
mgkegg ls organism
# returns the entire list of human genes
mgkegg ls hsa
# returns the list of a human gene and an E.coli O157 gene
mgkegg ls hsa:10458+ece:Z5100
# returns the list of a compound entry and a glycan entry
mgkegg ls cpd:C01290+gl:G00092

3. Find entries with matching query keyword or other query data

   mgkegg find <databases> <query>
   # for keywords "shiga" and "toxin" (use nop option to disable this processing)
   mgkegg find genes shiga+toxin
   # for keywords "shiga toxin"
   mgkegg find genes shiga toxin
   # for chemical formula "C7H10O5"
   mgkegg find compound C7H10O5 formula
   # for chemical formula containing "O5" and "C7"
   mgkegg find compound O5C7 formula
   # for 174.045 =< exact mass < 174.055
   mgkegg find 174.05 exact_mass
   # for 300 =< molecular weight =< 310
   mgkegg find 300-310 mol_weight
   

4. Retrieve given database entries

   mgkegg get <dbentries>
   # retrieves a compound entry and a glycan entry
   mgkegg get cpd:C01290+gl:G00092
   # retrieves a human gene entry and an E.coli O157 gene entry
   mgkegg get hsa:10458+ece:Z5100
   # retrieves amino acid sequences of a human gene and an E.coli O157 gene
   mgkegg get hsa:10458+ece:Z5100 aaseq
   # retrieves the gif image file of a compound
   mgkegg get C00002 image
   # retrieves the png image file of a pathway map
   mgkegg get hsa05130 image
   # retrieves the conf file of a pathway map
   mgkegg get hsa05130 conf
   # retrieves the kgml file of a pathway map
   mgkegg get hsa05130 kgml
   # retrieves the htext file of a brite hierarchy
   mgkegg get br:br08301
   # retrieves the json file of a brite hierarchy
   mgkegg get br:br08301 json
   

5. Download the latest kegg reference map.

   mgkegg download
   

6. Update to the latest kegg reference map if not already the lastet.

   mgkegg update
   

7. Highlight the given kegg object with the given color offline.

   mgkegg highlight --glist <gene.list> --color <color> -o <outdir>