Download fasta file with protein accession biopython

Active Oldest Votes. Improve this answer. Maximilian Peters Maximilian Peters Sign up or log in Sign up using Google. Sign up using Facebook. Sign up using Email and Password. Post as a guest Name. Email Required, but never shown. The Overflow Blog. Podcast Who is building clouds for the independent developer? Exploding turkeys and how not to thaw your frozen bird: Top turkey questions Featured on Meta.

It was chosen because it is a small genome, so the example is very quick to run. This is how this file starts out, showing the first gene and some of the second entry:. In total ignoring the comments my program has under 20 lines which I'll explain below :. This is a universal format, you can read it with any text editor or spreadsheet - Microsoft Excel is also a good choice.

SeqIO , so we must tell Python to load this ready for us:. Now we create a sequence record iterator, using the Bio. SeqIO parse function. Biopython uses the term iterator to mean an lump of code we can use to step through the records in a file i. The records created by Bio. SeqIO are SeqRecord objects, which in general will have an id, name, descrption and sequence. For some file formats additional annotation of sub-features may also be present.

In the Bio. Just like a normal string in python, sequence objects also have a 'count' method which we can use to find the number of times nucleotide is present:. BlueSky BlueSky 2 2 bronze badges.

Whether you want a large number of files or just one file is, I guess, a personal choice. A multifasta file is fairly standard though. I don't think you can create individual files for each sequence using epost and efetch ; you will have to either use a bash script or postprocess the efetch output using the unix tool split. Sign up or log in Sign up using Google.

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