changed os.system command in GetBeatAML.py script and updated tpmfromCounts.py

Author: alexandriai168

build/beatAML/GetBeatAML.py

@@ -653,7 +653,7 @@ def generate_drug_list(drug_map_path,drug_path):
             # New Transcriptomics Data
             print("Starting Transcriptomics Data")
             ##first run conversion tool
-            os.system("python tpmFromCounts.py --counts "+transcriptomics_file)
+            os.system("python tpmFromCounts.py --counts {} --out_file {}".format(transcriptomics_file,'tpm_'+transcriptomics_file))
 
 
             t_df = pd.read_csv('tpm_'+transcriptomics_file, sep = '\t')

build/utils/tpmFromCounts.py

@@ -15,7 +15,7 @@
 import argparse
 import pandas as pd
 
-def main(counts_data, genome_link, gene_column, out_file):
+def main(counts_data, genome_link, gene_column, exclude_columns, out_file):
     """
     Converts RNA count matrix to tpm matrix (transcripts per million).  
     
@@ -29,6 +29,9 @@ def main(counts_data, genome_link, gene_column, out_file):
 
     gene_column : string
         Column name of column with gene name information.  Defaults to "stable_id".
+    
+    exclude_columns : string
+        Column names of columns to exclude from patient list.  NO SPACES.  Defaults to "stable_id,display_label,description,biotype".
 
     out_file : string
         Path to output csv. No default.
@@ -42,8 +45,11 @@ def main(counts_data, genome_link, gene_column, out_file):
     counts = pd.read_csv(counts_data,sep='\t')
     counts.index=counts[gene_column]
 
+    # parse list of columns to exclude from patients list
+    exclude_cols_array = exclude_columns.split(",") # split long string by commas
+
     ##get list of patients
-    pats = set(counts.columns)-set(counts.select_dtypes(include='object')) # get patient names from column names, excluding columns were the datatype is a string
+    pats = set(counts.columns)-set(counts.select_dtypes(include='object') + exclude_columns) # get patient names from column names, excluding columns were the datatype is a string and any columns in the exclude_columns arg
 
 
     ##transcript info from grc37
@@ -84,9 +90,10 @@ def main(counts_data, genome_link, gene_column, out_file):
     parser.add_argument('--counts', default=None, help='Transcriptomics counts matrix')
     parser.add_argument('--genome_build', default="https://ftp.ensembl.org/pub/grch37/release-113/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz", help='Link to human genome build')
     parser.add_argument('--gene_col', default="stable_id", help='Name of column with gene names')
+    parser.add_argument('--exclude_col', default="stable_id,display_label,description,biotype", help='Name of column with gene names')
     parser.add_argument('--out_file', default=None, help='Output csv name.')
 
 
     args = parser.parse_args()
     print('Creating TPM from '+args.counts)
-    main(counts_data = args.counts, genome_link = args.genome_build, gene_column = args.gene_col, out_file = args.out_file)
+    main(counts_data = args.counts, genome_link = args.genome_build, gene_column = args.gene_col, exclude_columns = args.exclude_col, out_file = args.out_file)