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micompy

micompy

 
 

test_data

test_data

 
 

.gitignore

.gitignore

 
 

README.txt

README.txt

 
 

big_clusters.csv

big_clusters.csv

 
 

composition_matrix.csv

composition_matrix.csv

 
 

genome_name_map.csv

genome_name_map.csv

 
 

quarts.csv

quarts.csv

 
 

sc_pfam_overlaps.csv

sc_pfam_overlaps.csv

 
 

sc_pfam_pres.csv

sc_pfam_pres.csv

 
 

single_copy_pfams_cpr.csv

single_copy_pfams_cpr.csv

 
 

test.py

test.py

 
 

type.csv

type.csv

 
 

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Prereqs python:

* biopython
* pandas
* tqdm
* scipy
* matplotlib

binaries in path:

* makeblastdb
* blastn
* hmmersearch
* prokka

Notes : 

It is built around linux so some stuff brutally uses *nix commands (e.g. find, sed, ...)

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Library and tools for microbial comparative genomics [highly experimental and in dev]

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