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thomasvangurp / epiGBS

Code for working with epiGBS data
MIT License
10 stars 7 forks source link

Comma separated vs tab separated files #5

Open thomasvangurp opened 8 years ago

thomasvangurp commented 8 years ago

Both demultiplex.py and demultiplexV2.0.py default to "barcodes.csv" as a default option; however, the code requires tab-delimited files, not comma-delimited.

NielsWagemaker commented 7 years ago

Be aware that from excell saving as tab delimited does not yet produces the correct file format (the end of line code has to be adjusted using vi.... What was the command within vi Thomas?

added:

vi type ':set list' =Shows tabs (^l) and end of line ($) type . '%s/^V^M/\r/g' where ^V^M == control-V control-M =changes file into correct format (^M = carriage-return character are replaced by \r) type . ':wq' =save and quit vi

NielsWagemaker commented 7 years ago

i believe changing line 235 to : filein = open(barcodes, 'rU') might also do the job... PLEASE don't use spaces but in bar code sheet

thomasvangurp commented 7 years ago

I've just changed the relevant lines, I think it should work now.

NielsWagemaker commented 7 years ago

did you changed the demultiplex SGBS script? i don't see the changes you made? I think my problem still leads back to the initial barcode file.... see mail... sometimes additional fields are placed in the sam file ??? see mail for picture...