genebe annotate

[lmanchon]

--Hi,

is "genebe annotate" command line can handle csv or tsv input file and output as same format ?

thank you --

[pstawinski]

Hi,

no, but this can be easily achieved using really simple Python script and pandas.

Here is simple code showing what you can do, instead of creating a dataframe load it from the csv file.

import pandas as pd

df = pd.DataFrame({
   'chr': ['chr1', 'chr2', 'chr1', 'chr3', 'chr2'],
   'pos': [1234567, 2345678, 3456789, 4567890, 5678901],
   'ref': ['A', 'C', 'G', 'T', 'G'],
   'alt': ['T', 'G', 'C', 'A', 'C']
})

import genebe as gnb
annotated = gnb.annotate_dataframe_variants(df,use_ensembl=False,use_refseq=True, genome='hg38', flatten_consequences=True)

annotated.to_csv('/tmp/output.tsv', sep='\t', index=False)

I hope this helps.

[lmanchon]

-Hi,

yes, you are right, i'm going to do that.
thank you --