# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User gua110 # Date 1280420469 14400 # Node ID 07e7db914c6d2090ef7579a5e2c0583af50c39f3 # Parent 79baa9583d9390bb6341d3484aa9f55b8e3808f8 Modified Group tool by adding Mode function to the list of aggregate operations.

--- a/tools/stats/grouping.py +++ b/tools/stats/grouping.py @@ -23,6 +23,12 @@ def main(): cols.append(var.split()[1]) rounds.append(var.split()[2])

+ if 'Mode' in ops: + try: + r.library('prettyR') + except: + stop_err('R package prettyR could not be loaded. Please make sure it is installed.') + """ At this point, ops, cols and rounds will look something like this: ops: ['mean', 'min', 'c'] @@ -46,9 +52,10 @@ def main(): except: stop_err( "Group column not specified." )

+ str_ops = ['c', 'length', 'unique', 'random', 'cuniq', 'Mode'] #ops that can handle string/non-numeric inputs for k,col in enumerate(cols): col = int(col)-1 - if ops[k] not in ['c', 'length', 'unique', 'random', 'cuniq']: + if ops[k] not in str_ops: # We'll get here only if the user didn't choose 'Concatenate' or 'Count' or 'Count Distinct' or 'pick randmly', which are the # only aggregation functions that can be used on columns containing strings. try: @@ -109,7 +116,7 @@ def main(): valid = True # Before appending the current value, make sure it is numeric if the # operation for the column requires it. - if ops[i] not in ['c','length', 'unique','random','cuniq']: + if ops[i] not in str_ops: try: float( fields[col].strip()) except: @@ -128,13 +135,14 @@ def main(): due to the sort on group_col we've applied to the data above. """ out_str = prev_item - + multiple_modes = False + mode_index = None for i, op in enumerate( ops ): if op == 'cuniq': rfunc = "r.c" else: rfunc = "r." + op - if op not in ['c','length','unique','random','cuniq']: + if op not in str_ops: for j, elem in enumerate( prev_vals[i] ): prev_vals[i][j] = float( elem ) rout = eval( rfunc )( prev_vals[i] ) @@ -148,7 +156,10 @@ def main(): else: rand_index = random.randint(0,len(prev_vals[i])-1) rout = prev_vals[i][rand_index] - + + if op == 'Mode' and rout == '>1 mode': + multiple_modes = True + mode_index = i if op == 'unique': rfunc = "r.length" rout = eval( rfunc )( rout ) @@ -165,8 +176,13 @@ def main(): out_str += "\t" + str(rout) else: out_str += "\t" + str(rout) - - print >>fout, out_str + if multiple_modes and mode_index != None: + out_str_list = out_str.split('\t') + for val in prev_vals[mode_index]: + out_str = '\t'.join(out_str_list[:mode_index+1]) + '\t' + str(val) + '\t' + '\t'.join(out_str_list[mode_index+2:]) + print >>fout, out_str.rstrip('\t') + else: + print >>fout, out_str

prev_item = item prev_vals = [] @@ -195,14 +211,15 @@ def main():

# Handle the last grouped value out_str = prev_item - + multiple_modes = False + mode_index = None for i, op in enumerate(ops): if op == 'cuniq': rfunc = "r.c" else: rfunc = "r." + op try: - if op not in ['c','length','unique','random','cuniq']: + if op not in str_ops: for j, elem in enumerate( prev_vals[i] ): prev_vals[i][j] = float( elem ) rout = eval( rfunc )( prev_vals[i] ) @@ -216,7 +233,10 @@ def main(): else: rand_index = random.randint(0,len(prev_vals[i])-1) rout = prev_vals[i][rand_index] - + + if op == 'Mode' and rout == '>1 mode': + multiple_modes = True + mode_index = i if op == 'unique': rfunc = "r.length" rout = eval( rfunc )( rout ) @@ -238,7 +258,13 @@ def main(): if not first_invalid_line: first_invalid_line = ii+1

- print >>fout, out_str + if multiple_modes and mode_index != None: + out_str_list = out_str.split('\t') + for val in prev_vals[mode_index]: + out_str = '\t'.join(out_str_list[:mode_index+1]) + '\t' + str(val) + '\t' + '\t'.join(out_str_list[mode_index+2:]) + print >>fout, out_str.rstrip('\t') + else: + print >>fout, out_str

# Generate a useful info message. msg = "--Group by c%d: " %(group_col+1)

--- a/tools/stats/grouping.xml +++ b/tools/stats/grouping.xml @@ -1,4 +1,4 @@ -<tool id="Grouping1" name="Group" version="1.9.0"> +<tool id="Grouping1" name="Group" version="1.9.1"><description>data by a column and perform aggregate operation on other columns.</description><command interpreter="python"> grouping.py @@ -22,6 +22,7 @@ <param name="optype" type="select" label="Type"><option value="mean">Mean</option><option value="median">Median</option> + <option value="Mode">Mode</option><option value="max">Maximum</option><option value="min">Minimum</option><option value="sum">Sum</option> @@ -77,10 +78,12 @@

**Syntax**

-This tool allows you to group the input dataset by a particular column and perform aggregate functions like Mean, Sum, Max, Min and Concatenate on other columns. +This tool allows you to group the input dataset by a particular column and perform aggregate functions like Mean, Median, Mode, Sum, Max, Min, Count, Random draw and Concatenate on other columns.

- All invalid, blank and comment lines are skipped when performing the aggregate functions. The number of skipped lines is displayed in the resulting history item.

+- If multiple modes are present, all are reported. + -----

**Example**