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gaarangoa / deeparg

A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes. It provides two models,deepARG-SS and deepARG-LS.
MIT License
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Question: columns in file test.clean.deeparg.align.daa.tsv #5

Closed imonteroo closed 7 months ago

imonteroo commented 8 months ago

Hello. I have just installed and ran tets of deeparg for short reads and it worked perfectly. My question is about file test.clean.deeparg.align.daa.tsv generated. What is the meaning of each column? Thanks in advance

gaarangoa commented 8 months ago

this is the output from diamond alignment (here): 

                    BH[i[0]][2][8],  # alignment gene start
                    BH[i[0]][2][9],  # alignment gene end
                    i[0],  # read-id
                    i[1],  # predicted type
                    x_bh,  # best hit
                    str(i[2]),  # probability
                    BH[i[0]][2][2],  # identity
                    BH[i[0]][2][3],  # alignment length
                    BH[i[0]][2][-1],  # bitscore
                    BH[i[0]][2][-2],  # evalue
                    '1'  # count