Question: Import the quality scores from a FASTQ file in Python 3 Biopython
0
gravatar for cristian
2.9 years ago by
cristian240
cristian240 wrote:

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.

ADD COMMENTlink modified 2.9 years ago by lakhujanivijay5.1k • written 2.9 years ago by cristian240
3
gravatar for lakhujanivijay
2.9 years ago by
lakhujanivijay5.1k
India
lakhujanivijay5.1k wrote:

Try this:

from Bio import SeqIO
for record in SeqIO.parse(input_file, "fastq"):
    score=record.letter_annotations["phred_quality"]
ADD COMMENTlink written 2.9 years ago by lakhujanivijay5.1k
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