InPreD / PRONTO

rePort geneRator fOr iNpred Tumor bOards
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Bool reads `Faulse` in the `configure_PRONTO.ini` file #26

Closed marrip closed 7 months ago

marrip commented 7 months ago

I found that there are several variables in the afore mentioned file that read Faulse. Should this be a bool with False? Example here all_col_output:

[FILTER2]
;In this filter section, the input data is the first table generated from FILTER1.
;Specify the column name need to be filtered:
filter_column = Coding_status
;Specify the key word for the filter column. If there are multiple keywords need to be filtered at the same time, please split them with ','. You can use ' && ' to combine the keywords startswith '!' as one filter condition. And '!' means NOT:
key_word = !x:noncoding_variant && !synonymous_variant
all_col_output = Faulse
;Specify the column names need to be transfered to new data file. Split the column names with ','. NB: the column contents must be the same as they are in the sheet.
columns = Gene_symbol,Change_summary,Ensembl_transcript_ID,Genomic_location,Exon_number,Protein_change_short,Coding_status,Functional_domain,Depth_tumor_DNA,AF_tumor_DNA,Depth_normal_DNA,AF_normal_DNA,TSO500_LocalApp_class
;Specify the output result file name. Please note that you type should not exceed 31 characters and not contain any of the characters ':' ' \'  '/'  '?'  '*'  '['  or ']':
output_table = preMTBTable_Vigdis

For FILTER1 the same variable is True but for 3-5 it's the same as in the example. Is that intentional?

xiaoliz0 commented 7 months ago

Yes, this is used to generate different intermediate tables.

marrip commented 7 months ago

Sorry, but is all_col_output a Boolean?

xiaoliz0 commented 7 months ago

Sorry, but is all_col_output a Boolean?

Ah, yes. It is a typing mistake in the configure file. I will fix it in the next releasing. Thanks for your checking. :)