Manifest

[stefdecondor31]

Marc,

I'm trying in vain to import my own manifest (version b5) with methylprep. Can you give me more explanation about this.

BR

Stef L

[willherbert27]

I am running in to the same issue, also trying to import a version b5 manifest. Downloaded .csv from https://support.illumina.com/downloads/infinium-methylationepic-v1-0-product-files.html. Getting error:

ValueError: Usecols do not match columns, columns expected but not found: ['MAPINFO', 'Color_Channel', 'IlmnID', 'Infinium_Design_Type', 'CHR', 'AddressA_ID', 'AddressB_ID', 'Genome_Build', 'Strand']

Is this manifest format for the b5 versions different than the manifest that is imported from methylprep.files.manifests when I don't include the manifest argument when running from command line? Those columns are present when I open the csv I downloaded from Illumina. Also tried and failed with the .bpm version.

[arogozhnikov]

same. Default downloaded is v2.

When downloading a reference iscan data from illumina + manifest b5, the system does not work.

[notmaurox]

I believe the quickest way to get around this issue is to overwrite the version of the manifest that MethylPrep downloads into your home directory in a folder called .methylprep_manifest_files.

If you look here: https://github.com/FoxoTech/methylprep/blob/master/methylprep/files/manifests.py
you can see what file name MethylPrep associates with each array type. I think adding your manifest to ~/.methylprep_manifest_files and updating the file name for the array you are using should work.

of course this assumes you clone the repo - change the code - and then pip install the module locally.

If you don't want to go through all these steps, just save your copy of the manifest with the same name as the one that's currently selected by default - effectively overwriting the old contents with the new