diff span_wrapper.py @ 0:1f0c4f0a9c3b draft

Initial version of SPAN for ToolShed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/span_wrapper.py	Thu Nov 15 11:04:49 2018 -0500
@@ -0,0 +1,67 @@
+#!/usr/bin/env python
+
+import os
+import sys
+import subprocess
+argv = sys.argv[1:]
+print 'Arguments {0}'.format(argv)
+
+SPAN_JAR = os.environ.get("SPAN_JAR")
+# span.jar from Docker container
+# SPAN_JAR = "/root/span.jar"
+print 'Using SPAN Peak Analyzer distributive file {0}'.format(SPAN_JAR)
+
+# #if $action.action_selector
+#     #if str($control.control_selector) == "with_control"
+#         span_wrapper.py model with_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${control.control_file}"
+#     #else
+#         span_wrapper.py model without_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}"
+#     #end if
+# #else
+#     #if $control.control_selector
+#         span_wrapper.py peaks with_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${control.control_file}" "${fdr}" "${gap}" "${action.peaks_file}"
+#     #else
+#         span_wrapper.py peaks without_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${fdr}" "${gap}" "${action.peaks_file}"
+#     #end if
+# #end if
+
+# See http://artyomovlab.wustl.edu/aging/span.html for command line options
+action = argv[0]
+control = argv[1]
+if action == 'model':
+    if control == 'with_control':
+        (chrom_sizes, treatment_file, bin, model_file, control_file) = argv[2:]
+        cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --control {} --bin {}'.format(
+            SPAN_JAR, chrom_sizes, treatment_file, control_file, bin
+        )
+        print "MODEL FILE" + model_file
+    elif control == 'without_control':
+        (chrom_sizes, treatment_file, bin, model_file) = argv[2:]
+        cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --bin {}'.format(
+            SPAN_JAR, argv[2], argv[3], argv[4]
+        )
+        print "MODEL FILE" + model_file
+    else:
+        raise Exception("Unknown control option {}".format(control))
+
+elif action == "peaks":
+    if control == 'with_control':
+        (chrom_sizes, treatment_file, bin, model_file, control_file, fdr, gap, peaks_file) = argv[2:]
+        cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --control {} --bin {} --fdr {} --gap {} --peaks {}'.format(
+            SPAN_JAR, chrom_sizes, treatment_file, control_file, bin, fdr, gap, peaks_file
+        )
+        print "MODEL FILE" + model_file
+    elif control == 'without_control':
+        (chrom_sizes, treatment_file, bin, model_file, fdr, gap, peaks_file) = argv[2:]
+        cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --bin {} --fdr {} --gap {} --peaks {}'.format(
+            SPAN_JAR, chrom_sizes, treatment_file, bin, fdr, gap, peaks_file
+        )
+        print "MODEL FILE" + model_file
+    else:
+        raise Exception("Unknown control option {}".format(control))
+else:
+    raise Exception("Unknown action command {}".format(action))
+
+
+print 'Launching SPAN: {0}'.format(cmd)
+subprocess.check_call(cmd, cwd=None, shell=True)