CODEWITHSUNDEEP
pythonbiopython
modi2020
modi2020

Reputation: 31

I don't understand how to specify a path for a file I want to open in python

I am a new user to Python and I tried to import genbank and fasta format files. In their documentation, they provide an example that illustrates how we can import datasets into Python. specifically, they provide the following example in the Biopython Tutorial and Cookbook, page 16:

from  Bio  import  SeqIO

for  seq_record  in  SeqIO.parse("ls_orchid.gbk",  "genbank"):
    print  seq_record.id
    print  repr(seq_record.seq)
    print  len(seq_record)

Now, they mention in page 14 that the Biopython source code contains this file which is true. However, how does python know through the Bio import SeqIO where the file exactly is? Note that I tried the above code after installing biopython and its components but it never worked?

Also, can I just specify the path for the genbank file and open it somehow!

Thank you

Upvotes: 2

Views: 1510

Answers (3)

sreisman
sreisman

Reputation: 668

It seems that you need to save the ls_orchid.gbk file in the same directory as your python script, otherwise you would need to specify the full path to the file. You can also just download any genbank file from NCBI and add it to the directory, or specify its location as such

for seq_record in SeqIO.parse("~/File Location/File Name", "genbank")

Upvotes: 1

Putra
Putra

Reputation: 1

i put Genbank and FASTA in C:\Python27 I could parse all kind of other file formats such as Newick, PhyloXML, etc U should contact the developers for further information

Upvotes: -1

Peter de Rivaz
Peter de Rivaz

Reputation: 33509

According to http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc10

You need to copy the files to your local directory

When this tutorial was originally written, this search gave us only 94 hits, which we saved as a FASTA formatted text file and as a GenBank formatted text file (files ls_orchid.fasta and ls_orchid.gbk, also included with the Biopython source code under docs/tutorial/examples/).

If you run the search today, you’ll get hundreds of results! When following the tutorial, if you want to see the same list of genes, just download the two files above or copy them from docs/examples/ in the Biopython source code. In Section 2.5 we will look at how to do a search like this from within Python.

Upvotes: 1

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