Searches current directory for zip files that contains genbank files, then extracts and renames them.

zip_file_extractor.py

#!/usr/bin/python
# zip_file_extractor.py
#
# Searches current directory for zip files that contains genbank files, then extracts and renames them.
#
# Usage: python zip_file_extractor.py
#
# 4/17/2020 - Initial script (Chloe Smith)
# 4/27/2020 - Implemented file renaming (Bryon Drown)

from zipfile import ZipFile
import os

#starts the program
print('Extract .gbk file from ZIP')

# iterate through files in the current directory
for file in os.listdir("."):
    
    filename=os.fsdecode(file)
    
    # calling the zip folders to go through the extraction
    if filename.endswith(".zip"):
    
        print('Extracting ' + filename)
        
        output = os.path.splitext(filename)[0] + '.gbk' # determine name of output file

        with ZipFile(filename, 'r') as zipObj: # reads the zip files
            
            # iterate through archived files
            for archivedFile in zipObj.namelist():
                
                # find the file of interest
                if archivedFile.endswith('region001.gbk'):
                
                    with open(output, 'bw') as outfile:

                        print('Genbank file found, writing to ' + output)
                        
                        # instead of extracting and renaming the file, just read contents and write to output
                        outfile.write(zipObj.read(archivedFile))
                    
print('Complete')