scientific_name_to_common-name_converter / rename fasta file header's scientific name to common name
Convert scientific names to common names and vice versa
Required file: https://www.uniprot.org/docs/speclist.txt
Python: 2.7
to run (change the path as yours)
[1] import convert_scientific_name_to_common_names
Function to get a general scientific name to common name dictionary
[2] n2c, c2n = convert_scientific_name_to_common_names.convert(path = 'C:/Users/rahul/',specfile="speclist.txt",outfile="Sci2Com.csv")
output:
A csv file "Sci2Com.csv" in your folder and a python dictionary
[3] n2c['Homo sapiens']
[4] 'Human'
[5] n2c['Pan paniscus']
[6] 'Bonobo'
[7] c2n['Human']
'Homo sapiens'
[8] c2n['Cat']
'Felis catus'
Function to make a fasta file with concise header and common names - useful before phylogeny analysis
Rename fasta file header's scientific name to common name before phylogeny analysis
Download 'Description Table (csv) after selecting 'Common Name' from the NCBI BLAST output page
Change the path and file names as yours and run:
