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afombravo / 2FAST2Q

A Python3 program that counts sequence occurrences in raw FASTQ files.
GNU General Public License v3.0
7 stars 2 forks source link

TypeError: encoding without a string argument #7

Closed vuhongai closed 2 years ago

vuhongai commented 2 years ago

Hello,

I encountered this problem "TypeError: encoding without a string argument" with my fastq file, eventhough it seems the code doing well with the test fastq file (example.fastq.gz) provided here.

Untitled

Here's the hyperparameter that I used (no feature table provide): python -m fast2q -c --s ./test.fastq --o ./ --us ATACCGTCCCAGGGC --ds ATTCAATCAGCCATA --mo EC --cp 12 --l 66

Do you have any clue how to solve it please? Best regards, Ai

afombravo commented 2 years ago

Hi. Sorry for this, that is indeed a legitimate error that I have now fixed. I will upload to PyPI tomorrow and then you can pip install the new version. However, I updated github with the working version already if you want to download the program directly.

Best, Afonso

afombravo commented 2 years ago

The new fix has been uploaded to PyPI and you can run the program as you were after doing "pip install fast2q==2.4.2". Also, regarding your hyperparameters, when running in "EC" mode, you do not need to specify --l as the length will always be the length of the sequence that program finds in between the up and downstream sequences. In this case, the indicated length is ignored. You can later filter this out if you want using the output file as the sequence of all the found features will be there.

vuhongai commented 2 years ago

Thank you very much, you response so fast. I appreciate it. And it worked!