--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/column_join.py	Tue Apr 01 09:30:45 2014 -0400
@@ -0,0 +1,279 @@
+#!/usr/bin/env python
+
+"""
+This tool takes a tab-delimited text file as input and creates filters on columns based on certain properties. The tool will skip over invalid lines within the file, informing the user about the number of lines skipped.
+
+usage: %prog -o output -1 input1 -2 input2 -c column1[,column2[,column3[,...]]] -g hinge1[,hinge2[,hinge3[,...]]] -f <fill_options_file> [other_input1 [other_input2 [other_input3 ...]]]
+    -o, output=0: the output pileup
+    -1, input1=1: the pileup file to start with
+    -2, input2=2: the second pileup file to join
+    -g, hinge=h: the columns to be used for matching
+    -c, columns=c: the columns that should appear in the output
+    -f, fill_options_file=f: the file specifying the fill value to use
+    other_inputs: the other input files to join
+"""
+
+import optparse, os, re, struct, sys, tempfile
+from galaxy.util.bunch import Bunch
+from galaxy.util import stringify_dictionary_keys
+import json
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+def split_nums( text ):
+    """
+    Splits a string into pieces of numbers and non-numbers, like 'abc23B3' --> [ 'abc', 23, 'B', 3 ]
+    """
+    split_t = []
+    c = ''
+    n = ''
+    for ch in text:
+        try:
+            v = int( ch )
+            n += ch
+            if c:
+                split_t.append( ''.join( c ) )
+                c = ''
+        except ValueError:
+            c += ch
+            if n:
+                split_t.append( int( ''.join( n ) ) )
+                n = ''
+    if c:
+        split_t.append( ''.join( c ) )
+    if n:
+        split_t.append( int( ''.join( n ) ) )
+    return split_t
+
+def hinge_compare( hinge1, hinge2 ):
+    """
+    Compares items like 'chr10' and 'chrM' or 'scaffold2' and scaffold10' so that
+    first part handled as text but last part as number
+    """
+    split_hinge1 = hinge1.split( '\t' )
+    split_hinge2 = hinge2.split( '\t' )
+    # quick check if either hinge is empty
+    if not ''.join( split_hinge2 ):
+        if ''.join( split_hinge1 ):
+            return 1
+        elif not ''.join( split_hinge1 ):
+            return 0
+    else:
+        if not ''.join( split_hinge1 ):
+            return -1
+    # go through all parts of the hinges and compare
+    for i, sh1 in enumerate( split_hinge1 ):
+        # if these hinge segments are the same, just move on to the next ones
+        if sh1 == split_hinge2[ i ]:
+            continue
+        # check all parts of each hinge
+        h1 = split_nums( sh1 )
+        h2 = split_nums( split_hinge2[ i ] )
+        for j, h in enumerate( h1 ):
+            # if second hinge has no more parts, first is considered larger
+            if j > 0 and len( h2 ) <= j:
+                return 1
+            # if these two parts are the same, move on to next
+            if h == h2[ j ]:
+                continue
+            # do actual comparison, depending on whether letter or number
+            if type( h ) == int:
+                if type( h2[ j ] ) == int:
+                    if h > h2[ j ]:
+                        return 1
+                    elif h < h2[ j ]:
+                        return -1
+                # numbers are less than letters
+                elif type( h2[ j ] ) == str:
+                    return -1
+            elif type( h ) == str:
+                if type( h2[ j ] ) == str:
+                    if h > h2[ j ]:
+                        return 1
+                    elif h < h2[ j ]:
+                        return -1
+                # numbers are less than letters
+                elif type( h2[ j ] ) == int:
+                    return 1
+    # if all else has failed, just do basic string comparison
+    if hinge1 > hinge2:
+        return 1
+    elif hinge1 == hinge2:
+        return 0
+    elif hinge1 < hinge2:
+        return -1
+
+def hinge_sort( infile, outfile, hinge ):
+    """Given input file name, sorts logically (text vs. numeric) into provided output file name."""
+    hinge_locs = {}
+    bad_lines = []
+    fin = open( infile, 'rb' )
+    line = fin.readline()
+    while line.strip():
+        try:
+            hinge_parts = line.split( '\t' )[ :hinge ]
+            try:
+                hinge_locs[ '\t'.join( hinge_parts ) ].append( fin.tell() - len( line ) )
+            except KeyError:
+                hinge_locs[ '\t'.join( hinge_parts ) ] = [ fin.tell() - len( line ) ]
+        except ValueError:
+            bad_line.append( line )
+        line = fin.readline()
+    fin.close()
+    fin = open( infile, 'rb' )
+    fout = open( outfile, 'wb' )
+    hinge_locs_sorted = hinge_locs.keys()
+    hinge_locs_sorted.sort( hinge_compare )
+    for hinge_loc in hinge_locs_sorted:
+        locs = hinge_locs[ hinge_loc ]
+        for loc in locs:
+            fin.seek( loc )
+            fout.write( fin.readline() )
+    fout.close()
+    fin.close()
+
+def __main__():
+    parser = optparse.OptionParser()
+    parser.add_option( '-o', '--output', dest='output', help='The name of the output file' )
+    parser.add_option( '-1', '--input1', dest='input1', help='The name of the first input file' )
+    parser.add_option( '-2', '--input2', dest='input2', help='The name of the second input file' )
+    parser.add_option( '-g', '--hinge', dest='hinge', help='The "hinge" to use (the value to compare)' )
+    parser.add_option( '-c', '--columns', dest='columns', help='The columns to include in the output file' )
+    parser.add_option( '-f', '--fill_options_file', dest='fill_options_file', default=None, help='The file specifying the fill value to use' )
+    (options, args) = parser.parse_args()
+    hinge = int( options.hinge )
+    cols = [ int( c ) for c in str( options.columns ).split( ',' ) if int( c ) > hinge ]
+    inputs = [ options.input1, options.input2 ]
+    if options.fill_options_file == 'None':
+        inputs.extend( args )
+    elif len( args ) > 0:
+        inputs.extend( args )
+    fill_options = None
+    if options.fill_options_file != 'None' and options.fill_options_file is not None:
+        try:
+            fill_options = Bunch( **stringify_dictionary_keys( json.load( open( options.fill_options_file ) ) ) )
+        except Exception, e:
+            print 'Warning: Ignoring fill options due to json error (%s).' % e
+    if fill_options is None:
+        fill_options = Bunch()
+    if 'file1_columns' not in fill_options:
+        fill_options.file1_columns = None
+    if fill_options and fill_options.file1_columns:
+        fill_empty = {}
+        for col in cols:
+            fill_empty[ col ] = fill_options.file1_columns[ col - 1 ]
+    else:
+        fill_empty = None
+    assert len( cols ) > 0, 'You need to select at least one column in addition to the hinge'
+    delimiter = '\t'
+    # make sure all files are sorted in same way, ascending
+    tmp_input_files = []
+    input_files = inputs[:]
+    for in_file in input_files:
+        tmp_file = tempfile.NamedTemporaryFile()
+        tmp_file_name = tmp_file.name
+        tmp_file.close()
+        hinge_sort( in_file, tmp_file_name, hinge )
+        tmp_file = open( tmp_file_name, 'rb' )
+        tmp_input_files.append( tmp_file )
+    # cycle through files, getting smallest line of all files one at a time
+    # also have to keep track of vertical position of extra columns
+    fout = file( options.output, 'w' )
+    old_current = ''
+    first_line = True
+    current_lines = [ f.readline().rstrip( '\r\n' ) for f in tmp_input_files ]
+    last_lines = ''.join( current_lines )
+    last_loc = -1
+    while last_lines:
+        # get the "minimum" hinge, which should come first, and the file location in list
+        hinges = [ delimiter.join( line.split( delimiter )[ :hinge ] ) for line in current_lines ]
+        hinge_dict = {}
+        for i in range( len( hinges ) ):
+            if not hinge_dict.has_key( hinges[ i ] ):
+                hinge_dict[ hinges[ i ] ] = i
+        hinges.sort( hinge_compare )
+        hinges = [ h for h in hinges if h ]
+        current, loc = hinges[0], hinge_dict[ hinges[0] ]
+        # first output empty columns for vertical alignment (account for "missing" files)
+        # write output for leading and trailing empty columns
+        # columns missing from actual file handled further below
+        current_data = []
+        if current != old_current:
+            # fill trailing empty columns with appropriate fill value
+            if not first_line:
+                if last_loc < len( inputs ) - 1:
+                    if not fill_empty:
+                        filler = [ '' for col in range( ( len( inputs ) - last_loc - 1 ) * len( cols ) ) ]
+                    else:
+                        filler = [ fill_empty[ cols[ col % len( cols ) ] ] for col in range( ( len( inputs ) - last_loc - 1 ) * len( cols ) ) ]
+                    fout.write( '%s%s' % ( delimiter, delimiter.join( filler ) ) )
+                # insert line break before current line
+                fout.write( '\n' )
+            # fill leading empty columns with appropriate fill value
+            if loc > 0:
+                if not fill_empty:
+                    current_data = [ '' for col in range( loc * len( cols ) ) ]
+                else:
+                    current_data = [ fill_empty[ cols[ col % len( cols ) ] ] for col in range( loc * len( cols ) ) ]
+        else:
+            if loc - last_loc > 1:
+                if not fill_empty:
+                    current_data = [ '' for col in range( ( loc - last_loc - 1 ) * len( cols ) ) ]
+                else:
+                    current_data = [ fill_empty[ cols[ col % len( cols ) ] ] for col in range( ( loc - last_loc - 1 ) * len( cols ) ) ]
+        # now output actual data
+        split_line = current_lines[ loc ].split( delimiter )
+        # fill empties within actual line if appropriate
+        if fill_empty:
+            new_split_line = split_line[:]
+            split_line = []
+            for i, item in enumerate( new_split_line ):
+                col = i + 1
+                if not item:
+                    try:
+                        split_line.append( fill_empty[ i + 1 ] )
+                    except KeyError:
+                        split_line.append( item )
+                else:
+                    split_line.append( item )
+        # add actual data to be output below
+        if ''.join( split_line ):
+            for col in cols:
+                if col > hinge:
+                    # if this column doesn't exist, add the appropriate filler or empty column
+                    try:
+                        new_item = split_line[ col - 1 ]
+                    except IndexError:
+                        if fill_empty:
+                            new_item = fill_empty[ col ]
+                        else:
+                            new_item = ''
+                    current_data.append( new_item )
+            # grab next line for selected file
+            current_lines[ loc ] = tmp_input_files[ loc ].readline().rstrip( '\r\n' )
+            # write relevant data to file
+            if current == old_current and current_data:
+                fout.write( '%s%s' % ( delimiter, delimiter.join( current_data ) ) )
+            elif current_data:
+                fout.write( '%s%s%s' % ( current, delimiter, delimiter.join( current_data ) ) )
+            last_lines = ''.join( current_lines )
+        else:
+            last_lines = None
+        last_loc = loc
+        old_current = current
+        first_line = False
+    # fill trailing empty columns for final line
+    if last_loc < len( inputs ) - 1:
+        if not fill_empty:
+            filler = [ '' for col in range( ( len( inputs ) - last_loc - 1 ) * len( cols ) ) ]
+        else:
+            filler = [ fill_empty[ cols[ col % len( cols ) ] ] for col in range( ( len( inputs ) - last_loc - 1 ) * len( cols ) ) ]
+        fout.write( '%s%s' % ( delimiter, delimiter.join( filler ) ) )
+    fout.write( '\n' )
+    fout.close()
+    for f in tmp_input_files:
+        os.unlink( f.name )
+
+if __name__ == "__main__" : __main__()