From 5f39620e676694d17607922b19b265291b5fe8d0 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 29 Sep 2009 21:47:59 -0400
Subject: [PATCH] Fix limiting species in interval2maf tool.

---
 tools/maf/interval2maf.py  | 4 ++++
 tools/maf/interval2maf.xml | 8 ++++++++
 2 files changed, 12 insertions(+)

diff --git a/tools/maf/interval2maf.py b/tools/maf/interval2maf.py
index 130f2ee3555..fb1730c076f 100755
--- a/tools/maf/interval2maf.py
+++ b/tools/maf/interval2maf.py
@@ -80,6 +80,8 @@ def __main__():
         split_blocks_by_species = True
         if options.remove_all_gap_columns and options.remove_all_gap_columns == 'remove_all_gap_columns':
             remove_all_gap_columns = True
+    else:
+        remove_all_gap_columns = True
     #Finish parsing command line
     
     #Open indexed access to MAFs
@@ -113,6 +115,8 @@ def __main__():
             for block in blocks:
                 block = maf_utilities.chop_block_by_region( block, src, region )
                 if block is not None:
+                    if species is not None:
+                        block = block.limit_to_species( species )
                     block = maf_utilities.orient_block_by_region( block, src, region )
                     if remove_all_gap_columns:
                         block.remove_all_gap_columns()
diff --git a/tools/maf/interval2maf.xml b/tools/maf/interval2maf.xml
index 5c82d50a5a3..ed8f97c9368 100644
--- a/tools/maf/interval2maf.xml
+++ b/tools/maf/interval2maf.xml
@@ -88,6 +88,14 @@
        <param name="split_blocks_by_species" value="dont_split_blocks_by_species"/>
        <output name="out_file1" file="fsa_interval2maf.dat" />
      </test>
+     <test>
+       <param name="input1" value="1.bed" dbkey="hg18" ftype="bed"/>
+       <param name="maf_source" value="cached"/>
+       <param name="mafType" value="28_WAY_MULTIZ_hg18"/>
+       <param name="species" value="hg18,panTro2,mm8"/>
+       <param name="split_blocks_by_species" value="dont_split_blocks_by_species"/>
+       <output name="out_file1" file="interval2maf_3from28way.maf" />
+     </test>
    </tests>
    <help>
 **What it does**