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ParkinsonLab / Metatranscriptome-Workshop

Metatranscriptomics Tutorial
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TypeError: unhashable type: 'SeqRecord' #2

Closed pwang16 closed 6 years ago

pwang16 commented 6 years ago

Hi Billy Taj,

Thanks a lot for your reply. I have a problem after I run the command in the Step 5–Remove abundant rRNA sequences: ./2_Infernal_Filter.py mouse1_mouse_blat.fastq mouse1_rRNA.infernalout mouse1_unique_mRNA.fastq mouse1_unique_rRNA.fastq

After I return and run it, It shows:

Traceback (most recent call last): File "./2_Infernal_Filter.py", line 33, in mRNA_seqs.add(sequence) TypeError: unhashable type: 'SeqRecord'

What can i do next? Best regards, Peng

billytaj commented 6 years ago

which step is this? Do you have the prerequisite packages for python installed? SeqRecord is part of BioPython

pwang16 commented 6 years ago

Step 5–Remove abundant rRNA sequences.

I am sure I have installed the BioPython.

billytaj commented 6 years ago

I just reran the tutorial from step 1 through to 5. I see no errors. can you comfirm that every other step happened without incident?

In order to do a bugtrace, I need to reproduce your problem. so far, I can't.

pwang16 commented 6 years ago

Okay. Thanks very much for your time and reply. I can do it and to see if other steps have incident or not.

Best regards, Peng

pwang16 commented 6 years ago

Hi Billy Taj,

I stoped at the Step10 when I use "./8_Gene_EC_Map.py". It shows the error information: "0 genes were mapped with Diamond to 0 unique enzyme functions."

Does swiss_map.tsv belongingto the old version cause the 0 genes mapped? Because I downloaded the new swiss_db database.

Thanks, Peng

billytaj commented 6 years ago

original issue was resolved. no need to keep this open for multiple issues

pwang16 commented 6 years ago

Thank you for your reply. I am looking forward to your update!

From: Billy Taj notifications@github.com Reply-To: ParkinsonLab/Metatranscriptome-Workshop reply@reply.github.com Date: Saturday, September 1, 2018 at 12:11 AM To: ParkinsonLab/Metatranscriptome-Workshop Metatranscriptome-Workshop@noreply.github.com Cc: Peng Wang pwang16@unl.edu, Author author@noreply.github.com Subject: Re: [ParkinsonLab/Metatranscriptome-Workshop] TypeError: unhashable type: 'SeqRecord' (#2)

sorry, didn't realize you left a question: This tutorial was meant as a standalone workshop demo. It's only guaranteed to work with the pre-computed files we supplied. As you can tell, there's many variations that are possible, so we can't really guarantee that this particular workshop is flexible enough for your specific needs, without your personal intervention.

That being said, we're aware of the situation, and we're working on something to address this.

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