details: http://www.bx.psu.edu/hg/galaxy/rev/c3a20d503bd3 changeset: 1701:c3a20d503bd3 user: guru date: Tue Jan 13 12:18:08 2009 -0500 description: Tool to find the least common ancestor added under Taxonomy section.
2 file(s) affected in this change:
tools/taxonomy/lca.py tools/taxonomy/lca.xml
diffs (166 lines):
diff -r 03f1e9e78f74 -r c3a20d503bd3 tools/taxonomy/lca.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/taxonomy/lca.py Tue Jan 13 12:18:08 2009 -0500 @@ -0,0 +1,145 @@ +#!/usr/bin/env python +#Guruprasad Ananda +""" +This tool provides the SQL "group by" functionality. +""" +import sys, string, re, commands, tempfile, random +#from rpy import * + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit() + +def main(): + try: + inputfile = sys.argv[1] + outfile = sys.argv[2] + except: + stop_err("Syntax error: Use correct syntax: program infile outfile") + group_col = 0 + + tmpfile = tempfile.NamedTemporaryFile() + + try: + """ + The -k option for the Posix sort command is as follows: + -k, --key=POS1[,POS2] + start a key at POS1, end it at POS2 (origin 1) + In other words, column positions start at 1 rather than 0, so + we need to add 1 to group_col. + if POS2 is not specified, the newer versions of sort will consider the entire line for sorting. To prevent this, we set POS2=POS1. + """ + command_line = "sort -f -k " + str(group_col+1) +"," + str(group_col+1) + " -o " + tmpfile.name + " " + inputfile + except Exception, exc: + stop_err( 'Initialization error -> %s' %str(exc) ) + + error_code, stdout = commands.getstatusoutput(command_line) + + if error_code != 0: + stop_err( "Sorting input dataset resulted in error: %s: %s" %( error_code, stdout )) + + prev_item = "" + prev_vals = [] + remaining_vals = [] + skipped_lines = 0 + first_invalid_line = 0 + invalid_line = '' + invalid_value = '' + invalid_column = 0 + fout = open(outfile, "w") + cols = range(1,25) + block_valid = False + + for ii, line in enumerate( file( tmpfile.name )): + if line and not line.startswith( '#' ): + line = line.rstrip( '\r\n' ) + try: + fields = line.split("\t") + item = fields[group_col] + if prev_item != "": + # At this level, we're grouping on values (item and prev_item) in group_col + if item == prev_item: + # Keep iterating and storing values until a new value is encountered. + if block_valid: + for i, col in enumerate(cols): + if col >= 3: + prev_vals[i].append(fields[col].strip()) + if len(set(prev_vals[i])) > 1: + block_valid = False + break + + else: + """ + When a new value is encountered, write the previous value and the + corresponding aggregate values into the output file. This works + due to the sort on group_col we've applied to the data above. + """ + out_list = ['']*25 + out_list[0] = str(prev_item) + out_list[1] = str(prev_vals[0][0]) + out_list[2] = str(prev_vals[1][0]) + out_list[24] = str(prev_vals[23][0]) + #print >> fout, prev_vals + #sys.exit() + for k, col in enumerate(cols): + if col >= 3 and col < 24: + if len(set(prev_vals[k])) == 1: + out_list[col] = prev_vals[k][0] + else: + break + while k < 23: + out_list[k+1] = 'n' + k += 1 + + print >>fout, '\t'.join(out_list) + + block_valid = True + prev_item = item + prev_vals = [] + for col in cols: + val_list = [] + val_list.append(fields[col].strip()) + prev_vals.append(val_list) + + else: + # This only occurs once, right at the start of the iteration. + block_valid = True + prev_item = item #groupby item + for col in cols: #everyting else + val_list = [] + val_list.append(fields[col].strip()) + prev_vals.append(val_list) + + except Exception, exc: + skipped_lines += 1 + if not first_invalid_line: + first_invalid_line = ii+1 + else: + skipped_lines += 1 + if not first_invalid_line: + first_invalid_line = ii+1 + + # Handle the last grouped value + out_list = ['']*25 + out_list[0] = str(prev_item) + out_list[1] = str(prev_vals[0][0]) + out_list[2] = str(prev_vals[1][0]) + out_list[24] = str(prev_vals[23][0]) + for k, col in enumerate(cols): + if col >= 3 and col < 24: + if len(set(prev_vals[k])) == 1: + out_list[col] = prev_vals[k][0] + else: + break + while k < 23: + out_list[k+1] = 'n' + k += 1 + + print >>fout, '\t'.join(out_list) + + if skipped_lines > 0: + msg= "Skipped %d invalid lines starting with line %d. Value '%s' in column %d is not numeric." % ( skipped_lines, first_invalid_line, invalid_value, invalid_column ) + print msg + +if __name__ == "__main__": + main() \ No newline at end of file diff -r 03f1e9e78f74 -r c3a20d503bd3 tools/taxonomy/lca.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/taxonomy/lca.xml Tue Jan 13 12:18:08 2009 -0500 @@ -0,0 +1,12 @@ +<tool id="lca1" name="Least Common Ancestor" version="1.0.0"> + <description></description> + <command interpreter="python"> + lca.py $input1 $out_file1 + </command> + <inputs> + <param format="taxonomy" name="input1" type="data" label="Select taxonomy dataset"/> + </inputs> + <outputs> + <data format="taxonomy" name="out_file1" metadata_source="input1" /> + </outputs> +</tool>