Import the quality scores from a FASTQ file in Python 3 Biopython
Hi,
I would like to import the FASTQ scores in Python. I have figured the 'seq' attribute from the records in a FASTQ object but does anybody know how to extract the quality score as well, please?
from Bio import SeqIO
records = SeqIO.parse("assembly.fastq", "fastq")
for i, record in enumerate(records):
if i == 1:
print(record.seq)
break
Thanks.
Best, C.
• 6,474 views
•
link
updated
by
lakhujanivijay
•
written
by
biomagician
•
written
by
biomagician
1 answer
Try this:
from Bio import SeqIO
for record in SeqIO.parse(input_file, "fastq"):
score=record.letter_annotations["phred_quality"]
• 0 views
•
link
written
by
lakhujanivijay
Log in to answer this question.
More posts like this
-
How to output FASTQ file with four lines per sequence?
written by Apex92 •
-
SeqIO object get cleared away after being accessed
written by zincjiang •
-
When running this code on a fasta file and a max() arg error occurs
written by rt2421 •
-
No output when trying to obtain protein sequence from PDB file
written by shome •
-
How to remove features from GBK files with biopython ?
written by hugo.avila
-
comlement fastq file using Biopython
written by Andrei Makhon •
-
Select records from fasta file by SeqIO (Biopython)
written by dmitri.ivanovsky •
-
remove sequences with non-canonical nucleotides from fasta file
written by grant.hovhannisyan
-
Using Biopython to search a fasta file for specific uniprots
written by chrisgbeldam •
-
Problem with downloading CDS sequences using Biopython
written by cl10101 •
