# HG changeset patch
# User trinity_ctat
# Date 1541523218 18000
# Node ID 0e3e4f24e3008a3c151480b906a7ef138c906c42
# Parent 0a4bec29a6099708571c3a9791770fffd3b6350d
Adding ctat_cravat_tissues table.
diff -r 0a4bec29a609 -r 0e3e4f24e300 data_manager/add_ctat_resource_lib.py
--- a/data_manager/add_ctat_resource_lib.py Fri Nov 02 14:17:08 2018 -0400
+++ b/data_manager/add_ctat_resource_lib.py Tue Nov 06 11:53:38 2018 -0500
@@ -1324,6 +1324,12 @@
'Normally they are assumed to reside in the build directory, ' + \
'but if that directory has not been created yet when this program ' + \
'is called, you can specify the full path to the directory where they reside.')
+ parser.add_argument('-t', '--cravat_tissues_filepath',
+ default='', \
+ help='Specify a non-default location where the Cosmic files reside. ' + \
+ 'Normally they are assumed to reside in the build directory, ' + \
+ 'but if that directory has not been created yet when this program ' + \
+ 'is called, you can specify the full path to the directory where they reside.')
# Method 1) arguments - Download and Build.
# - One can optionally utilize --build_location argument with this group of arguments.
download_and_build_args = parser.add_argument_group('Download and Build arguments')
@@ -1546,6 +1552,17 @@
data_manager_dict['data_tables']['ctat_genome_resource_libs'] = []
data_table_entry = dict(value=unique_id, name=display_name, path=genome_build_directory)
data_manager_dict['data_tables']['ctat_genome_resource_libs'].append(data_table_entry)
+
+ # Create the data table for the cravat_tissues, if the file is given:
+ if (args.cravat_tissues_filepath is not None) and (args.cravat_tissues_filepath != ""):
+ data_manager_dict['data_tables']['ctat_cravat_tissues'] = []
+ cravat_file = open(args.cravat_tissues_filepath, 'r')
+ for line in cravat_file:
+ if line[0] != '#':
+ # The line is not a comment, so parse it.
+ items = [item.strip() for item in line.split("\t")]
+ data_table_entry = dict(value=items[0], name=items[1], code=items[2], date=items[3])
+ data_manager_dict['data_tables']['ctat_cravat_tissues'].append(data_table_entry)
# Temporarily the output file's dictionary is written for debugging:
print "The dictionary for the output file is:\n\t{:s}".format(str(data_manager_dict))
diff -r 0a4bec29a609 -r 0e3e4f24e300 data_manager/add_ctat_resource_lib.xml
--- a/data_manager/add_ctat_resource_lib.xml Fri Nov 02 14:17:08 2018 -0400
+++ b/data_manager/add_ctat_resource_lib.xml Tue Nov 06 11:53:38 2018 -0500
@@ -14,7 +14,8 @@
-->
+
+
+
diff -r 0a4bec29a609 -r 0e3e4f24e300 tool-data/cravat_tissues.loc.sample
--- a/tool-data/cravat_tissues.loc.sample Fri Nov 02 14:17:08 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-Bladder Bladder Urothelial Carcinoma BLCA (TCGA) Jun 2013
-Blood-Lymphocyte Chronic Lymphocytic Leukemia CLL (ICGC) Mar 2013
-Blood-Myeloid Acute Myeloid Leukemia LAML (TCGA) Jun 2013
-Brain-Cerebellum Medulloblastoma MB (mixed source) Dec 2010
-Brain-Glioblastoma-Multiforme Glioblastoma Multiforme GBM (TCGA) Jun 2013
-Brain-Lower-Grade-Glioma Brain Lower Grade Glioma LGG (TCGA) Jun 2013
-Breast Breast Invasive Carcinoma BRCA (TCGA) Jun 12012
-Cervix Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma CESC (TCGA) Jun 2013
-Colon Colon Adenocarcinoma COAD (TCGA) Jun 2013
-Head and Neck Head and Neck Squamous Cell Carcinoma HNSC (TCGA) Jun 2013
-Kidney-Chromophobe Kidney Chromophobe KICH (TCGA) Jun 2013
-Kidney-Clear-Cell Kidney Renal Clear Cell Carcinoma KIRC (TCGA) Jun 2013
-Kidney-Papillary-Cell Kidney Renal Papillary Cell Carcinoma KIRP (TCGA) Jun 2013
-Liver-Nonviral Hepatocellular Carcinoma (Secondary to Alcohol and Adiposity) HCCA (ICGC) Mar 2013
-Liver-Viral Hepatocellular Carcinoma (Viral) HCCV (ICGC) Mar 2013
-Lung-Adenocarcinoma Lung Adenocarcinoma LUAD (TCGA) Jun 2013
-Lung-Squamous Cell Lung Squamous Cell Carcinoma LUSC (TCGA) Jun 2013
-Melanoma Melanoma ML (Yardena Samuels lab) Dec 2011
-Other General purpose OV (TCGA) Jun 2013
-Ovary Ovarian Serous Cystadenocarcinoma OV (TCGA) Jun 2013
-Pancreas Pancreatic Cancer PNCC (ICGC)) Mar 2013
-Prostate-Adenocarcinoma Prostate Adenocarcinoma PRAD (TCGA) Jun 2013
-Rectum Rectum Adenocarcinoma READ (TCGA) Jun 2013
-Skin Skin Cutaneous Melanoma SKCM (TCGA) Jun 2013
-Stomach Stomach Adenocarcinoma STAD (TCGA) Jun 2013
-Thyroid Thyroid Carcinoma THCA (TCGA) Jun 2013
-Uterus Uterine Corpus Endometriod Carcinoma UCEC (TCGA) Jun 2013
diff -r 0a4bec29a609 -r 0e3e4f24e300 tool-data/ctat_cravat_tissues.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/ctat_cravat_tissues.loc.sample Tue Nov 06 11:53:38 2018 -0500
@@ -0,0 +1,27 @@
+Bladder Bladder Urothelial Carcinoma BLCA (TCGA) Jun 2013
+Blood-Lymphocyte Chronic Lymphocytic Leukemia CLL (ICGC) Mar 2013
+Blood-Myeloid Acute Myeloid Leukemia LAML (TCGA) Jun 2013
+Brain-Cerebellum Medulloblastoma MB (mixed source) Dec 2010
+Brain-Glioblastoma-Multiforme Glioblastoma Multiforme GBM (TCGA) Jun 2013
+Brain-Lower-Grade-Glioma Brain Lower Grade Glioma LGG (TCGA) Jun 2013
+Breast Breast Invasive Carcinoma BRCA (TCGA) Jun 12012
+Cervix Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma CESC (TCGA) Jun 2013
+Colon Colon Adenocarcinoma COAD (TCGA) Jun 2013
+Head and Neck Head and Neck Squamous Cell Carcinoma HNSC (TCGA) Jun 2013
+Kidney-Chromophobe Kidney Chromophobe KICH (TCGA) Jun 2013
+Kidney-Clear-Cell Kidney Renal Clear Cell Carcinoma KIRC (TCGA) Jun 2013
+Kidney-Papillary-Cell Kidney Renal Papillary Cell Carcinoma KIRP (TCGA) Jun 2013
+Liver-Nonviral Hepatocellular Carcinoma (Secondary to Alcohol and Adiposity) HCCA (ICGC) Mar 2013
+Liver-Viral Hepatocellular Carcinoma (Viral) HCCV (ICGC) Mar 2013
+Lung-Adenocarcinoma Lung Adenocarcinoma LUAD (TCGA) Jun 2013
+Lung-Squamous Cell Lung Squamous Cell Carcinoma LUSC (TCGA) Jun 2013
+Melanoma Melanoma ML (Yardena Samuels lab) Dec 2011
+Other General purpose OV (TCGA) Jun 2013
+Ovary Ovarian Serous Cystadenocarcinoma OV (TCGA) Jun 2013
+Pancreas Pancreatic Cancer PNCC (ICGC)) Mar 2013
+Prostate-Adenocarcinoma Prostate Adenocarcinoma PRAD (TCGA) Jun 2013
+Rectum Rectum Adenocarcinoma READ (TCGA) Jun 2013
+Skin Skin Cutaneous Melanoma SKCM (TCGA) Jun 2013
+Stomach Stomach Adenocarcinoma STAD (TCGA) Jun 2013
+Thyroid Thyroid Carcinoma THCA (TCGA) Jun 2013
+Uterus Uterine Corpus Endometriod Carcinoma UCEC (TCGA) Jun 2013
diff -r 0a4bec29a609 -r 0e3e4f24e300 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample Fri Nov 02 14:17:08 2018 -0400
+++ b/tool_data_table_conf.xml.sample Tue Nov 06 11:53:38 2018 -0500
@@ -3,4 +3,8 @@
value, name, path
+
+ value, name, code, date
+
+