New to coding. New to Pytho/biopython; this is my first question online, ever. How do I open a compressed fasta.gz file to extract info and perform calcuations in my function. Here is a simplified example of what I'm trying to do (I've tried different ways), and what the error is. The gzip command I'm using doesn't seem to work.?
with gzip.open("practicezip.fasta.gz", "r") as handle:
for record in SeqIO.parse(handle, "fasta"):
print(record.id)
Traceback (most recent call last):
File "<ipython-input-192-a94ad3309a16>", line 2, in <module>
for record in SeqIO.parse(handle, "fasta"):
File "C:\Users\Anaconda3\lib\site-packages\Bio\SeqIO\__init__.py", line 600, in parse
for r in i:
File "C:\Users\Anaconda3\lib\site-packages\Bio\SeqIO\FastaIO.py", line 122, in FastaIterator
for title, sequence in SimpleFastaParser(handle):
File "C:\Users\Anaconda3\lib\site-packages\Bio\SeqIO\FastaIO.py", line 46, in SimpleFastaParser
if line[0] == ">":
IndexError: index out of range
Are you using python3?
This ("r" --> "rt") could solve your problem.
import gzip
from Bio import SeqIO
with gzip.open("practicezip.fasta.gz", "rt") as handle:
for record in SeqIO.parse(handle, "fasta"):
print(record.id)