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scripts/util/pancancer_util.R

@@ -51,7 +51,9 @@ parse_summary <- function(summary_info) {
   # Output:
   #    a list of summarized classifier attributes and performance
 
+  base_dir <- NULL
   if (is.character(summary_info)) {
+    base_dir <- dirname(summary_info)
     summary_info <- readr::read_lines(summary_info)
   }
   summary_list <- list()
@@ -72,8 +74,12 @@ parse_summary <- function(summary_info) {
       next
     }
     if (line[1] == "Coefficients:") {
+      tmp_fn <- line[2]
+      if ( ! file.exists(tmp_fn)){
+        tmp_fn <- file.path( base_dir, 'classifier_coefficients.tsv' ) # maybe should use basename of not found file
+      }
       summary_list[[sub(":", "", line[1])]] <-
-        suppressMessages(readr::read_tsv(line[2]))
+        suppressMessages(readr::read_tsv(tmp_fn))
     } else if (line[1] == "") {
       disease_info <- line[2:length(line)]
       disease <- disease_info[1]

scripts/util/tcga_util.py

@@ -14,10 +14,18 @@ def get_args():
     import argparse
 
     parser = argparse.ArgumentParser()
+    #parser.add_argument('-g', '--genes',
+    #                    help='Comma separated string of HUGO gene symbols')
     parser.add_argument('-g', '--genes',
-                        help='Comma separated string of HUGO gene symbols')
+                    help='string of the genes to extract or genelist file')
+    #parser.add_argument('-t', '--diseases', default='Auto',
+    #                    help='Comma sep string of TCGA disease acronyms. '
+    #                         'If no arguments are passed, filtering will '
+    #                         'default to options given in --filter_count and '
+    #                         '--filter_prop.')
     parser.add_argument('-t', '--diseases', default='Auto',
                         help='Comma sep string of TCGA disease acronyms. '
+                             'diseases_list_file'
                              'If no arguments are passed, filtering will '
                              'default to options given in --filter_count and '
                              '--filter_prop.')
@@ -37,9 +45,13 @@ def get_args():
                         help='the alphas for parameter sweep')
     parser.add_argument('-l', '--l1_ratios', default='0,0.1,0.15,0.18,0.2,0.3',
                         help='the l1 ratios for parameter sweep')
-    parser.add_argument('-b', '--alt_genes', default='None',
-                        help='alternative genes to test performance')
-    parser.add_argument('-s', '--alt_diseases', default="Auto",
+    #parser.add_argument('-b', '--alt_genes', default='None',
+    #                    help='alternative genes to test performance')
+    parser.add_argument('-b', '--alt_genes', default=None,
+                        help='string of the alt_genes to extract or alt_genelist file to test performance')
+    #parser.add_argument('-s', '--alt_diseases', default="Auto",
+    #                    help='The alternative diseases to test performance')
+    parser.add_argument('-s', '--alt_diseases', default=None,
                         help='The alternative diseases to test performance')
     parser.add_argument('-i', '--alt_filter_count', default=15, type=int,
                         help='Min number of mutations in disease to include')
@@ -53,6 +65,8 @@ def get_args():
                         help='Keep intermediate ROC values for plotting')
     parser.add_argument('-x', '--x_matrix', default='raw',
                         help='Filename of features to use in model')
+    parser.add_argument('--x_as_raw', action='store_true',
+                        help='Treat x_matrix as "raw"')
     parser.add_argument('-e', '--shuffled', action='store_true',
                         help='Shuffle the input gene exprs matrix alongside')
     parser.add_argument('--shuffled_before_training', action='store_true',
@@ -61,10 +75,24 @@ def get_args():
                         help='Remove mutation data from y matrix')
     parser.add_argument('-z', '--drop_rasopathy', action='store_true',
                         help='Decision to drop rasopathy genes from X matrix')
+    parser.add_argument( '--drop_x_genes', default=None,
+                        help='Comma separated list of genes to be dropped from X matrix, x_genelist file ')
     parser.add_argument('-q', '--drop_expression', action='store_true',
                         help='Decision to drop gene expression values from X')
     parser.add_argument('-j', '--drop_covariates', action='store_true',
                         help='Decision to drop covariate information from X')
+    parser.add_argument( '--filename_mut', default=None,
+                        help='Filename of sample/gene mutations to use in model')
+    parser.add_argument( '--filename_mut_burden', default=None,
+                        help='Filename of sample mutation burden to use in model')
+    parser.add_argument( '--filename_sample', default=None,
+                        help='Filename of patient/samples to use in model')
+    parser.add_argument( '--filename_copy_loss', default=None,
+                        help='Filename of copy number loss')
+    parser.add_argument( '--filename_copy_gain', default=None,
+                        help='Filename of copy number gain')
+    parser.add_argument( '--filename_cancer_gene_classification', default=None,
+                        help='Filename of cancer gene classification table')
 
     args = parser.parse_args()
     return args