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epi2me-labs / pychopper

cDNA read preprocessing
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"no reverse complement" warnings #59

Closed omarkr8 closed 5 months ago

omarkr8 commented 6 months ago

Hi,

using pychopper as part of a pipeline elsewhere, it seems to process the fastqs fine, but will always come up with the same "warning" for each sample in a batch. read-out might look like : _Using kit: PCS109 Configurations to consider: "+:SSP,-VNP|-:VNP,-SSP" WARNING: No reverse complement for R found, returning argument.WARNING: No reverse complement for R found, returning argument.WARNING: No reverse complement for W found, returning argument.WARNING: No reverse complement for K found, returning argument.Counting fastq records in input file: shb_results/quality_filtering/barcode13_AR1.fastq

so in particular the "WARNING: No reverse complement for R found, returning argument." is troubling me. seems to imply there are Rs,Ws, and Ks in my sequence? i think for another experiment it was a separate set of letters. my gut feeling is that it's to do with file names somehow getting passed as sequence. unsure if its a pychopper issue or I concatenated my fastq.gzs wrong.

in any case, would be good to know what triggers this.

nrhorner commented 6 months ago

Hi @omarkr8

This is strange. The error message appears to be coming from here https://github.com/epi2me-labs/pychopper/blob/513b0c389eadc338fb521f8c9f37a39cf59edf2e/pychopper/seq_utils.py#L21

which is not actually used in the pychopper workflow. Also if your input sequences contained non-DNA characters, pychopper would fail at the sequence reading stage.

Are you calling base_complement from elsewhere?

omarkr8 commented 6 months ago

i am unsure. pychopper is used as part of the Natrix2 pipeline (https://github.com/dbeisser/Natrix2/tree/dev), which is where im getting these errors.

could you explain what you mean by base_complement not being in the workflow?

nrhorner commented 6 months ago

Hi @omarkr8

The error message you are getting appears to be coming from pychopper/seq_utils.base_complement which is not actually called by any part of the pychopper code (and shouldn't actually be in the the repository). So I'm unsure why you are getting this warning message.

What version of pychopper are you using?

omarkr8 commented 6 months ago

from init.py it says version 2.7.2.

my guess is the devs from the pipeline im using just havent updated the tools.

nrhorner commented 6 months ago

Yes I would recommend updating to 2.7.9

nrhorner commented 5 months ago

Closing from lack of response Please open another ticket if this issue arises again