From e8d0ce39cf60b8311d9b749189a29025ad476144 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 23 Aug 2018 18:26:00 +0200
Subject: [PATCH] Fix random order of fasta headers in maf_to_bed

---
 tools/maf/maf_to_bed.py  | 8 +++++---
 tools/maf/maf_to_bed.xml | 2 +-
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/tools/maf/maf_to_bed.py b/tools/maf/maf_to_bed.py
index 764168990ab..6347924cf2a 100644
--- a/tools/maf/maf_to_bed.py
+++ b/tools/maf/maf_to_bed.py
@@ -6,6 +6,7 @@ from __future__ import print_function
 
 import os
 import sys
+from collections import OrderedDict
 
 from bx.align import maf
 
@@ -23,14 +24,15 @@ def __main__():
     primary_spec = None
 
     if "None" in species:
-        species = set()
+        species = OrderedDict()
         try:
             for i, m in enumerate(maf.Reader(open(input_filename, 'r'))):
                 for c in m.components:
                     spec, chrom = maf.src_split(c.src)
                     if not spec or not chrom:
-                        spec = chrom = c.src
-                    species.add(spec)
+                        spec = c.src
+                    species[spec] = None
+            species = species.keys()
         except Exception:
             print("Invalid MAF file specified", file=sys.stderr)
             return
diff --git a/tools/maf/maf_to_bed.xml b/tools/maf/maf_to_bed.xml
index 2464296cc2a..e7e56b6d32d 100644
--- a/tools/maf/maf_to_bed.xml
+++ b/tools/maf/maf_to_bed.xml
@@ -22,7 +22,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="input1" value="4.maf"/>
+            <param name="input1" value="4.maf" ftype="maf"/>
             <param name="species" value="hg17"/>
             <param name="complete_blocks" value="partial_disallowed"/>
             <output name="out_file1" file="cf_maf_to_bed.dat"/>