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read.seq end with read.name when using pyfastx.Fastq in parsing long read FASTQ file #78

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QYanwei opened this issue Feb 25, 2024 · 4 comments

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@QYanwei
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QYanwei commented Feb 25, 2024

Hi,
I found an error when I use pyfastx.Fastq to parsing the long read FASTQ file.
The read.name untimely appearance in the end of read.seq string, such as 'GGCATTTTTCCGTTTGTCACTTCTTCTTCGCTATCCTGTT@390872df-5709-4012-8278-1f4969a328af ch=103 start_time=2021-01-21T19:40:20.617'.
The pyfastx version is 2.0.2. Can you check what this issue is?

code:
fq = pyfastx.Fastq('../test/ecoli.fq.gz')
for read in fq:
if '@' in read.seq:
print(read.name)
print(read.seq)
print(read.qual)

@QYanwei
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QYanwei commented Feb 25, 2024

read name error in read seq end

@aStudyingTurtle
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I have the same problem.

@lmdu
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lmdu commented Feb 27, 2024

Thanks, I will check this issue.

@lmdu
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lmdu commented Feb 28, 2024

I have fixed it in v2.1.0.

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3 participants