BioPython_problemset

uniprot_sprot.fasta

3.

What does the file contain? How many records? Does it look intact? How do you know?

- File looks like a FASTA file

script for this is Biopython_2.py

#!/usr/bin/env python3

import re
import Bio.Seq
from Bio import SeqIO

sprotfasta = open ("../uniprot_sprot.fasta", "r")
count = 0

for record in sprotfasta:
        count +=1

print(count)

pfb14:files admin$ python3 BioPython_2.py 
4150232

File contains 4150232 records!



Is the file in tact? I think yes because it is recognized by SeqIO



4. 

Extract IDs from fasta file with the Bio.SeqIO module. generate a list of all the IDs in the fasta file. How many are there? 

#!/usr/bin/env python3

import re
import Bio.Seq
from Bio import SeqIO

sprotfasta = open ("../uniprot_sprot.fasta", "r")
count = 0   

for record in SeqIO.parse(sprotfasta, "fasta"):
        count +=1

print(count)

pfb14:files admin$ python3 BioPython_1.py 
555594


>>> for record in SeqIO.parse(sprotfasta, "fasta"):
>>>     print(record.id)

prints all the gene headers

>>> sprotfasta = open ("uniprot_sprot.fasta", "r")
>>> RecordID = []
>>> for record in SeqIO.parse(sprotfasta, "fasta"):
...     RecordID.append(record.id) 
... 
>>> print(len(RecordID))
555594