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bahlolab / superSTR

A lightweight, alignment-free utility for detecting repeat-containing reads in short-read WGS, WES and RNA-seq data.
GNU General Public License v2.0
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superstr-screen.py does not complete #24

Open jay-ross opened 7 months ago

jay-ross commented 7 months ago

Hello,

I have successfully run the superSTR software for the processing and postprocessing steps without error, but the motif screening step runs until 19% and then reports an error:

"AttributeError: 'DataFrame' object has no attribute 'append'"

my code looks like this: superstr-screen.py -m manifest.txt -i input_dir/ -o screen.output.txt --swaplab --min_thresh 1 --controllab control

I am running this on 14 samples, 7 cases and 7 controls, all short-read RNA-sequencing data from fastq. Multiparse and outlier scripts seem to work fine on this data.

Any assistance would be appreciated!

jay-ross commented 7 months ago

The problem turned out to be that installing superSTR through conda has a pandas version more recent than that specified in the installation page (v1.2.2), and in newer pandas versions the append function is deprecated and causes errors. I solved this problem by installing superSTR as follows:

conda install -c bioconda -c conda-forge superstr pandas=1.2.2

lfearnley commented 7 months ago

Great, thanks for the report!

I've got a few updates to make to this repo and will add fixing this version requirement in the yml to the list.

On Wed, 27 Mar 2024, 4:58 am jay-ross, @.***> wrote:

The problem turned out to be that installing superSTR through conda has a pandas version more recent than that specified in the installation page (v1.2.2), and in newer pandas versions the append function is deprecated and causes errors. I solved this problem by installing superSTR as follows:

conda install -c bioconda -c conda-forge superstr pandas=1.2.2

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