nebgb

I recently had the opportunity to try out nebgb, a Genbank file parser library. The usage of the library is fairly simple with just a few lines of Python code. Upon importing nebgb, you can utilize the parse_file method to read in a Genbank file and extract information from it.

One example of how to use this library is to parse a file, extract locus information, and print it out. This can be done with the following code:

rec = nebgb.parse_file("./test/data/simple-1.gb").next()
print(rec.locus["name"])

This will print out the name of the locus in the file, in this case 'NP_034640'. Similarly, you can extract other information such as the length of the locus, the source of keywords, and specific features.

One particularly useful feature of nebgb is the ability to iterate over the sequence information in a Genbank file. This can be done using the seqiter method:

for seq in rec.seqiter:
print(seq)

This will print out the sequence information in a readable format.

Overall, I found using nebgb to be a valuable tool for parsing Genbank files. It offers a simple and intuitive interface for extracting information from these files. In addition to using parse_file method, you can also utilize the parse method to read in a string or iterator that yields lines of a Genbank file.