using python scripts in qiime2

[jdchc (Jose Daniel Chazi Capelo)]

I need to use the extract_reads_from_interleaved_file.py to get forward and reverse fastq files. I cannot find the script or even call a python script in qiime2. Is there a way to run the python script above in qiime2? or do I have to install qiime1?

[cherman2 (Chloe Herman)]

Hello @jdchc
I think that you have to install QIIME1 to run that python script. Fortunately, QIIME1 and QIIME2 are pretty compatible in terms of using QIIME1 and then moving the data back over to QIIME2. You should be able to download QIIME1 and get your two fastq files by running extract_reads_from_interleaved_file.py and then use a manifest file to import the data in QIIME2.

Besides the script and you can use cutadapt to do the same thing. This question was discussed here: importing from a single file containing both forward and reverse and different sample reads. More information on how to use this can be found in the cutadapt documentation. This isn’t a qiime2 functionality but it should get the job done

I hope that this helps
Chloe

[andrewsanchez]

Hi, @jdchc! Welcome to the forum.

@jdchc

I cannot find the script or even call a python script in qiime2.

As you indicated below this, the script you are referring to is a QIIME 1 script and will therefor not be found in a QIIME 2 environment.

Can you elaborate on the bit about not being able to call python scripts in QIIME 2? I think this might be a point of confusion because you can certainly call python scripts in a QIIME 2 environment. Keep in mind, QIIME 2 uses Python version 3.6.11, while QIIME 1 uses Python 2.7, which is why you would need a QIIME 1 installation to use that script.

Hope that helps!