merge

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()

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**