diff draw_variants.py @ 24:248b06e86022

Added gd_genotype datatype. Modified tools to support new datatype.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/draw_variants.py	Tue May 28 16:24:19 2013 -0400
@@ -0,0 +1,78 @@
+#!/usr/bin/env python
+
+import sys
+import subprocess
+from Population import Population
+
+def run_program(prog, args, stdout_file=None, space_to_tab=False):
+    #print "args: ", ' '.join(args)
+    p = subprocess.Popen(args, bufsize=-1, executable=prog, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    (stdoutdata, stderrdata) = p.communicate()
+    rc = p.returncode
+
+    if stdout_file is not None:
+        with open(stdout_file, 'w') as ofh:
+            lines = stdoutdata.split('\n')
+            for line in lines:
+                line = line.strip()
+                if line:
+                    if space_to_tab:
+                        line = line.replace(' ', '\t')
+                    print >> ofh, line
+
+    if rc != 0:
+        print >> sys.stderr, "FAILED: rc={0}: {1}".format(rc, ' '.join(args))
+        print >> sys.stderr, stderrdata
+        sys.exit(1)
+
+################################################################################
+
+if len(sys.argv) < 10:
+    print >> sys.stderr, "Usage"
+    sys.exit(1)
+
+snp_input, indel_input, coverage_input, annotation_input, indiv_input, ref_name, min_coverage, output = sys.argv[1:9]
+individual_metadata = sys.argv[9:]
+
+p_total = Population()
+p_total.from_tag_list(individual_metadata)
+
+p1 = Population()
+p1.from_population_file(indiv_input)
+if not p_total.is_superset(p1):
+    print >> sys.stderr, 'There is an individual in the population individuals that is not in the SNP table'
+    sys.exit(1)
+
+################################################################################
+
+prog = 'mk_Ji'
+
+args = [ prog ]
+
+args.append(snp_input)
+args.append(indel_input)
+args.append(coverage_input)
+args.append(annotation_input)
+args.append(min_coverage)
+args.append(ref_name)
+
+for tag in p1.tag_list():
+    args.append(tag)
+
+run_program(prog, args, stdout_file='mk_Ji.out')
+
+################################################################################
+
+prog = 'varplot'
+
+args = [ prog ]
+args.append('-w')
+args.append('3')
+args.append('-s')
+args.append('0.3')
+args.append('-g')
+args.append('0.2')
+args.append('mk_Ji.out')
+
+run_program(prog, args, stdout_file=output)
+sys.exit(0)