Updates for issue 90

Config/configure_PRONTO.ini

@@ -7,72 +7,93 @@ inpred_node = OUS
 data_path = /data/sample_data/analysis_results/
 ;Please modify this if you need to specify file encoding as "ISO-8859-1" or other encoding standards in your local environment to read special Norwegian characters.
 encoding_sys = utf-8
-;Specify the number of columns you want to do the filtering (NB: this will also make the script to generate the number of output tables):
-filter_col_nu = 5
+;Specify the number of top filter sections with highest priority, these sections will be named staring with FILTER0 in this configure. (NB: the other filter sections will use the comnbined results from all FILTER0):
+top_filter = 3
+;Specify the number of filter sections with low priority. (NB: this will also make the script to generate the number of output tables):
+filter_col_nu = 4
 ;Specify the number of max rows of the table per slide starting from the 8th slide in report. This is used to split long tables.
 table_max_rows_per_slide = 14
 ;Please modify this for local env if you use MTF files to import the clinical data into meta file. Specify the version of year of the MTF files.
 material_file_version = 2026
 
-[FILTER1]
+[FILTER0-1]
+;pecify the column name need to be filtered:
+filter_column = CPSR_ACMG_class,CPSR_ClinVar_class
+;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:
+key_word = Likely_Pathogenic,Pathogenic
+;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,Genomic_location,DNA_change,cDNA_change,Protein_change_short,Coding_status,Depth_tumor_DNA,AF_tumor_DNA,Depth_normal_DNA,AF_normal_DNA,Depth_tumor_RNA,AF_tumor_RNA,TSO500_LocalApp_class,Class_judgement_comments
+;Specify the column name to add in the right end of the table to verify this filter condition. NB: if this value is given, a new column will be added into the tables in the report. Same column name in different filter sections will be merged into one filter column.
+filter_column_add = Filter_rescued
+;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 = pathogenic_germline
+
+[FILTER0-2]
+;pecify the column name need to be filtered:
+filter_column = Gene_symbol,Protein_change_short
+;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:
+key_word = TERT
+;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,Genomic_location,DNA_change,cDNA_change,Protein_change_short,Coding_status,Depth_tumor_DNA,AF_tumor_DNA,Depth_normal_DNA,AF_normal_DNA,Depth_tumor_RNA,AF_tumor_RNA,TSO500_LocalApp_class,Class_judgement_comments
+;Specify the column name to add in the right end of the table to verify this filter condition. NB: if this value is given, a new column will be added into the tables in the report. Same column name in different filter sections will be merged into one filter column.
+filter_column_add = Filter_rescued
+;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 = TERT
+
+[FILTER0-3]
+;In this filter section, the input data is the combined table generated from FILTER0.
 ;Specify the column name need to be filtered:
 filter_column = Class_judgement
 ;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:
 key_word = LikSOM,SOM,LikGL,incon,include
-;Specify if you want to output all columns based on the filter. 'True' means yes, and a default output table 'workingTable' will be generated in the output folder extra_files:
-all_col_output = True
 ;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,Genomic_location,DNA_change,cDNA_change,Protein_change_short,Coding_status,Depth_tumor_DNA,AF_tumor_DNA,Depth_normal_DNA,AF_normal_DNA,Depth_tumor_RNA,AF_tumor_RNA,TSO500_LocalApp_class,Class_judgement_comments
 ;Specify the miniment number of Depth_tumor for data to choose:
 min_depth_tumor_DNA = 0
 ;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_Appendix
 
-[FILTER2]
-;In this filter section, the input data is the first table generated from FILTER1.
+[FILTER1]
+;In this filter section, the input data is the combined table named 'workingTable' generated from all sections of FILTER0.
 ;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 = False
 ;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,Ensembl_transcript_ID,Exon_number,Protein_change_short,Coding_status,AF_tumor_DNA
+columns = Gene_symbol,Ensembl_transcript_ID,Exon_number,Protein_change_short,Coding_status,AF_tumor_DNA,Filter_rescued
 ;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 = sequence_summary
 
-[FILTER3]
-;In this filter section, the input data is the first table generated from FILTER1.
+[FILTER2]
+;In this filter section, the input data is the combined table named 'workingTable' generated from all sections of FILTER0.
 ;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
-all_col_output = False
 ;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,Genomic_location,DNA_change,cDNA_change,Protein_change_short,Coding_status,Depth_tumor_DNA,AF_tumor_DNA
+columns = Gene_symbol,Genomic_location,DNA_change,cDNA_change,Protein_change_short,Coding_status,Depth_tumor_DNA,AF_tumor_DNA,Filter_rescued
 ;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 = AllReporVariants_CodingRegion
 
-[FILTER4]
-;In this filter section, the input data is the first table generated from FILTER1.
+[FILTER3]
+;In this filter section, the input data is the combined table named 'workingTable' generated from all sections of FILTER0.
 ;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 = False
 ;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,Protein_change_short,Coding_status,AF_tumor_DNA
 ;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 = AllReporVariants_AltProtein
 
-[FILTER5]
-;In this filter section, the input data is the first table generated from FILTER1.
+[FILTER4]
+;In this filter section, the input data is the combined table named 'workingTable' generated from all sections of FILTER0.
 ;Specify the column name need to be filtered:
 filter_column = Reporting_judgement
 ;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 = BioMar,VUSpot,AddRes,GLrel
-all_col_output = False
 ;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,Coding_status,Functional_domain,AF_tumor_DNA,CPSR_ACMG_class,Reporting_judgement
+columns = Gene_symbol,Coding_status,Functional_domain,AF_tumor_DNA,CPSR_ACMG_class,Reporting_judgement,Filter_rescued
 ;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 = Main_Findings