diff make_phylip_hooks.py @ 35:ea52b23f1141

Bug fixes for Draw variants, Phylip, and gd_d_tools

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make_phylip_hooks.py	Wed Nov 20 13:46:10 2013 -0500
@@ -0,0 +1,47 @@
+#!/usr/bin/env python
+
+def exec_before_job(app, inp_data=None, out_data=None, tool=None, param_dict=None):
+    pass
+
+def exec_after_process(app, inp_data=None, out_data=None, param_dict=None, tool=None, stdout=None, stderr=None):
+    output_name = 'output1'
+
+    ## check for output
+    try:
+        first_output = out_data[output_name]
+    except:
+        return
+
+    ## check for collected datasets
+    try:
+        collected_dict = param_dict['__collected_datasets__']['primary'][output_name]
+    except:
+        return
+
+    if len(collected_dict.keys()) == 0:
+        return
+
+    ## check for fasta file
+    try:
+        fasta_file = inp_data['fasta_input']
+    except:
+        return
+
+    ## find missing fasta header
+    first_output_name = None
+    with open(fasta_file.get_file_name()) as fh:
+        for line in fh:
+            if line[0] != '>':
+                continue
+            name = line[1:]
+            name = name.strip()
+            name = name.split()[0]
+            name = name.replace('_', '-')
+            if name not in collected_dict:
+                first_output_name = name
+                break
+
+    ## fix name
+    if first_output_name is not None:
+        first_output.name = '%s (%s)' % (first_output.name, first_output_name)
+