--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/maf/interval2maf.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,139 @@
+#!/usr/bin/env python
+
+"""
+Reads a list of intervals and a maf. Produces a new maf containing the
+blocks or parts of blocks in the original that overlapped the intervals.
+
+If a MAF file, not UID, is provided the MAF file is indexed before being processed.
+
+NOTE: If two intervals overlap the same block it will be written twice.
+
+usage: %prog maf_file [options]
+   -d, --dbkey=d: Database key, ie hg17
+   -c, --chromCol=c: Column of Chr
+   -s, --startCol=s: Column of Start
+   -e, --endCol=e: Column of End
+   -S, --strandCol=S: Column of Strand
+   -t, --mafType=t: Type of MAF source to use
+   -m, --mafFile=m: Path of source MAF file, if not using cached version
+   -I, --mafIndex=I: Path of precomputed source MAF file index, if not using cached version
+   -i, --interval_file=i:       Input interval file
+   -o, --output_file=o:      Output MAF file
+   -p, --species=p: Species to include in output
+   -P, --split_blocks_by_species=P: Split blocks by species
+   -r, --remove_all_gap_columns=r: Remove all Gap columns
+   -l, --indexLocation=l: Override default maf_index.loc file
+   -z, --mafIndexFile=z: Directory of local maf index file ( maf_index.loc or maf_pairwise.loc )
+"""
+
+#Dan Blankenberg
+from galaxy import eggs
+import pkg_resources; pkg_resources.require( "bx-python" )
+from bx.cookbook import doc_optparse
+import bx.align.maf
+import bx.intervals.io
+from galaxy.tools.util import maf_utilities
+import sys
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def __main__():
+    index = index_filename = None
+    mincols = 0
+    
+    #Parse Command Line
+    options, args = doc_optparse.parse( __doc__ )
+    
+    if options.dbkey: dbkey = options.dbkey
+    else: dbkey = None
+    if dbkey in [None, "?"]:
+        maf_utilities.tool_fail( "You must specify a proper build in order to extract alignments. You can specify your genome build by clicking on the pencil icon associated with your interval file." )
+    
+    species = maf_utilities.parse_species_option( options.species )
+    
+    if options.chromCol: chromCol = int( options.chromCol ) - 1
+    else: 
+        maf_utilities.tool_fail( "Chromosome column not set, click the pencil icon in the history item to set the metadata attributes." )
+    
+    if options.startCol: startCol = int( options.startCol ) - 1
+    else: 
+        maf_utilities.tool_fail( "Start column not set, click the pencil icon in the history item to set the metadata attributes." )
+    
+    if options.endCol: endCol = int( options.endCol ) - 1
+    else: 
+        maf_utilities.tool_fail( "End column not set, click the pencil icon in the history item to set the metadata attributes." )
+    
+    if options.strandCol: strandCol = int( options.strandCol ) - 1
+    else: 
+        strandCol = -1
+    
+    if options.interval_file: interval_file = options.interval_file
+    else: 
+        maf_utilities.tool_fail( "Input interval file has not been specified." )
+    
+    if options.output_file: output_file = options.output_file
+    else: 
+        maf_utilities.tool_fail( "Output file has not been specified." )
+    
+    split_blocks_by_species = remove_all_gap_columns = False
+    if options.split_blocks_by_species and options.split_blocks_by_species == 'split_blocks_by_species':
+        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
+    if options.mafType:
+        if options.indexLocation:
+            index = maf_utilities.maf_index_by_uid( options.mafType, options.indexLocation )
+        else:
+            index = maf_utilities.maf_index_by_uid( options.mafType, options.mafIndexFile )
+        if index is None:
+            maf_utilities.tool_fail( "The MAF source specified (%s) appears to be invalid." % ( options.mafType ) )
+    elif options.mafFile:
+        index, index_filename = maf_utilities.open_or_build_maf_index( options.mafFile, options.mafIndex, species = [dbkey] )
+        if index is None:
+            maf_utilities.tool_fail( "Your MAF file appears to be malformed." )
+    else:
+        maf_utilities.tool_fail( "Desired source MAF type has not been specified." )
+    
+    #Create MAF writter
+    out = bx.align.maf.Writer( open(output_file, "w") )
+    
+    #Iterate over input regions 
+    num_blocks = 0
+    num_regions = None
+    for num_regions, region in enumerate( bx.intervals.io.NiceReaderWrapper( open( interval_file, 'r' ), chrom_col = chromCol, start_col = startCol, end_col = endCol, strand_col = strandCol, fix_strand = True, return_header = False, return_comments = False ) ):
+        src = maf_utilities.src_merge( dbkey, region.chrom )
+        for block in index.get_as_iterator( src, region.start, region.end ):
+            if split_blocks_by_species:
+                blocks = [ new_block for new_block in maf_utilities.iter_blocks_split_by_species( block ) if maf_utilities.component_overlaps_region( new_block.get_component_by_src_start( dbkey ), region ) ]
+            else:
+                blocks = [ block ]
+            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()
+                    out.write( block )
+                    num_blocks += 1
+    
+    #Close output MAF
+    out.close()
+    
+    #remove index file if created during run
+    maf_utilities.remove_temp_index_file( index_filename )
+    
+    if num_blocks:
+        print "%i MAF blocks extracted for %i regions." % ( num_blocks, ( num_regions + 1 ) )
+    elif num_regions is not None:
+        print "No MAF blocks could be extracted for %i regions." % ( num_regions + 1 )
+    else:
+        print "No valid regions have been provided."
+    
+if __name__ == "__main__": __main__()