singlem incorrectly parse sample name with paired-end data

[fplazaonate]

Hi @wwood ,

Many thanks for developing singlem. This is great tool that deserves more attention.

It seems singlem incorrectly parse sample name with paired-end data as it just removes the file extension:

singlem/singlem/singlem.py

Line 35 in 4a6803d

class FastaNameToSampleName:

Could you fix this?

Best,
Florian

[wwood]

Hi,

Thanks for kind words.

Can you be a bit more specific? You mean it doesn't remove the e.g. .1 or _1 bit?

[fplazaonate]

Yes, that's it.
In the output file, the sample name is 'sample_1' instead of 'sample'

[wwood]

Ah right. I made the decision not to wade into parsing the different possibilities there. Is there some general solution?

[fplazaonate]

You can add an option where the user explicitly provides the sample name.
The alternative is to find a shared substring between the forward and reverse file.
EDIT: the first option is probably the best as the user may provide several fastq files from different sequencing runs.

[adityabandla]

Looking for the same feature as I have samples sequenced across multiple runs