Re: Nanolyse autopkgtest broken - could someone provide a proper fastq file?
Hi Andreas,
On 2022-02-22 12:16, Andreas Tille wrote:
> by chance I realised that the autopkgtest of nanolyse was not
> working on the provided dataset. After fixing this[1] the test
> breaks unfortunately[2]:
>
> Traceback (most recent call last):
> File "/usr/bin/NanoLyse", line 33, in <module>
> sys.exit(load_entry_point('NanoLyse==1.2.0', 'console_scripts', 'NanoLyse')())
> File "/usr/lib/python3/dist-packages/nanolyse/NanoLyse.py", line 53, in main
> filter_reads(aligner, sys.stdin)
> File "/usr/lib/python3/dist-packages/nanolyse/NanoLyse.py", line 122, in filter_reads
> for record in SeqIO.parse(reads, "fastq"):
> File "/usr/lib/python3/dist-packages/Bio/SeqIO/Interfaces.py", line 74, in __next__
> return next(self.records)
> File "/usr/lib/python3/dist-packages/Bio/SeqIO/QualityIO.py", line 1085, in iterate
> for title_line, seq_string, quality_string in FastqGeneralIterator(handle):
> File "/usr/lib/python3/dist-packages/Bio/SeqIO/QualityIO.py", line 950, in FastqGeneralIterator
> raise ValueError("Sequence and quality captions differ.")
> ValueError: Sequence and quality captions differ.
>
> The problem occures when reading the perfectly random fastq file which I
> have shamelessly stolen from ncbi-blast+ package[3] and which is most
> probably a bad choice. It would be great if some educated person would
> provide a better example data set.
My educated guess is that nanolyse is correct by saying that "Sequence
and quality captions differ." The test input file should in principle
work after having text in parenthesis removed, as subsequent lines
starting with '@' and '+' in FASTQ format have to be otherwise identical
(now they are not because of the parentheses and the text in them).
> [1] https://salsa.debian.org/med-team/nanolyse/-/commit/847f0439ab66d47a512bab6fbea61268ffec4213
> [2] https://salsa.debian.org/med-team/nanolyse/-/jobs/2498940
> [3] https://salsa.debian.org/med-team/nanolyse/-/blob/master/debian/tests/data/README
Hope this helps,
Andrius
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