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MrTomRod / scoary-2

Calculate assocations between genes and traits
MIT License
19 stars 1 forks source link

Scoary2 has problem with headers #10

Closed bloomarun closed 6 months ago

bloomarun commented 6 months ago

Hello @MrTomRod, I have been trying to run scoary2 for a long time now. For some strange reason, scoary2 will throw up a columns missing error. I have literally copy pasted the names in the traits file to the gene presence absence file. Why is this happening? I have pasted the error here for your ready reference.

Cheers, Arun Sai.

cols_missing={'A58', 'A131', 'A49', 'A147', 'A134', 'A113', 'A46', 'A53', 'A65', 'A117', 'A41', 'A75', 'A25', 'A83', 'A92', 'A12', 'A56', 'A59', 'A118', 'A132', 'A150', 'A51', 'A97', 'A32', 'A119', 'A23', 'A112', 'A72', 'A61', 'A68', 'A136', 'A96', 'A105', 'A43', 'A22', 'A101', 'A129', 'A2', 'A94', 'A116', 'A145', 'A37', 'A104', 'A88', 'A143', 'A8', 'A86', 'A26', 'A62', 'A144', 'A57', 'A149', 'A13', 'A63', 'A67', 'A9', 'A29', 'A142', 'A3', 'A15', 'A33', 'A107', 'A93', 'A74', 'A100', 'A78', 'A31', 'A89', 'A84', 'A98', 'A16', 'A139', 'A111', 'A120', 'A39', 'A4', 'A146', 'A45', 'A151', 'A121', 'A99', 'A36', 'A20', 'A77', 'A27', 'A87', 'A52', 'A109', 'A55', 'A6', 'A11', 'A40', 'A110', 'A73', 'A124', 'A141', 'A80', 'A64', 'A28', 'A30', 'A130', 'A95', 'A90', 'A138', 'A5', 'A127', 'A66', 'A21', 'A85', 'A79', 'A137', 'A17', 'A91', 'A81', 'A103', 'A35', 'A14', 'A18', 'A19', 'A54', 'A24', 'A133', 'A1', 'A44', 'A114', 'A82', 'A140', 'A106', 'A42', 'A125', 'A70', 'A38', 'A108', 'A47', 'A115', 'A122', 'A48', 'A102', 'A71', 'A10', 'A76', 'A69', 'A50', 'A34', 'A148', 'A126', 'A135', 'A7', 'A128', 'A60', 'A123'} restrict_to={'A58', 'A131', 'A49', 'A147', 'A134', 'A113', 'A46', 'A53', 'A65', 'A117', 'A41', 'A75', 'A25', 'A83', 'A92', 'A12', 'A56', 'A59', 'A118', 'A132', 'A150', 'A51', 'A97', 'A32', 'A119', 'A23', 'A112', 'A72', 'A61', 'A68', 'A136', 'A96', 'A105', 'A43', 'A22', 'A101', 'A129', 'A2', 'A94', 'A116', 'A145', 'A37', 'A104', 'A88', 'A143', 'A8', 'A86', 'A26', 'A62', 'A144', 'A57', 'A149', 'A13', 'A63', 'A67', 'A9', 'A29', 'A142', 'A3', 'A15', 'A33', 'A107', 'A93', 'A74', 'A100', 'A78', 'A31', 'A89', 'A84', 'A98', 'A16', 'A139', 'A111', 'A120', 'A39', 'A4', 'A146', 'A45', 'A151', 'A121', 'A99', 'A36', 'A20', 'A77', 'A27', 'A87', 'A52', 'A109', 'A55', 'A6', 'A11', 'A40', 'A110', 'A73', 'A124', 'A141', 'A80', 'A64', 'A28', 'A30', 'A130', 'A95', 'A90', 'A138', 'A5', 'A127', 'A66', 'A21', 'A85', 'A79', 'A137', 'A17', 'A91', 'A81', 'A103', 'A35', 'A14', 'A18', 'A19', 'A54', 'A24', 'A133', 'A1', 'A44', 'A114', 'A82', 'A140', 'A106', 'A42', 'A125', 'A70', 'A38', 'A108', 'A47', 'A115', 'A122', 'A48', 'A102', 'A71', 'A10', 'A76', 'A69', 'A50', 'A34', 'A148', 'A126', 'A135', 'A7', 'A128', 'A60', 'A123'} have_cols=set()

bloomarun commented 6 months ago

I would also like to add that this usually arises with csv files, somehow everything works fine with tab files.

bloomarun commented 6 months ago

Figured it out!!! I guess the error lies with giving gene list as an input while the data is actually gene counts. That is why it was throwing up an error. Anyways, now it is working. Thanks @MrTomRod. I will approach you in case of any further assistance in the future.

MrTomRod commented 6 months ago

Good to hear!