organism source of isolation and country source

Question

[mlagadodji]

Hello, Does anyone know how to retrieve organism source and country of isolation from NCBI or Genbank set of data with perl or python scripts?

Answer 1

[natasha.sernova]

There was a post before in biostars:

How To Extract Title And /Isolation_Source From A List Of Genbank Accession Numbers

Answer 2

[priyasanthanam1997]

from Bio import SeqIO gb_file = "filename_of_gb.txt"

for gb_record in SeqIO.parse(open(gb_file,"r"), "genbank") : for feat in gb_record.features: if feat.type == 'source': source = gb_record.features[0] for qualifiers in source.qualifiers: if qualifiers == 'isolation_source': isolation_source = source.qualifiers['isolation_source'] C = " Name %s \t Organism %s \t isolation_source %s " % (gb_record.name,gb_record.annotations["source"],isolation_source[0]) f = open('Newfile.xls','a') print(C,file = f) f.close()

[priyasanthanam1997]

Use the above python script to retrieve isolation source from the save genbank file