[galaxy-dev] [hg] galaxy 3358: Initial version of DNA code filter tool

details: http://www.bx.psu.edu/hg/galaxy/rev/b36c13131ac7 changeset: 3358:b36c13131ac7 user: Kelly Vincent <kpvincent@bx.psu.edu> date: Mon Feb 08 23:52:56 2010 -0500 description: Initial version of DNA code filter tool diffstat: test-data/dna_filter_in1.bed | 49 ++++++++++ test-data/dna_filter_out1.bed | 4 + test-data/dna_filter_out2.bed | 39 ++++++++ test-data/dna_filter_out3.bed | 41 ++++++++ test-data/dna_filter_out4.bed | 24 +++++ tool_conf.xml.sample | 1 + tools/stats/dna_filtering.py | 195 ++++++++++++++++++++++++++++++++++++++++++ tools/stats/dna_filtering.xml | 114 ++++++++++++++++++++++++ 8 files changed, 467 insertions(+), 0 deletions(-) diffs (506 lines): diff -r dedb7be9aa44 -r b36c13131ac7 test-data/dna_filter_in1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna_filter_in1.bed Mon Feb 08 23:52:56 2010 -0500 @@ -0,0 +1,49 @@ +chr1 256 257 A N M N - M N U N N A N D N G N N K N N N +chr1 468 469 C C C N M N N K . N C U N H N G N N M N S +chr1 582 583 G G G N G R N R N - N M N V K N N N G C R +chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R +chr1 4792 4793 A A M K N W S S N N Y N N N N N M R N R N +chr1 6119 6120 G G M N S N N W B N S D N N H V N B W N N +chr1 6357 6358 G G N M K N G - N N G U N N N B N N K N S +chr1 6433 6434 G G N R N N C N N N . N N . N N N N N R N +chr1 39160 39161 T T T N N Y N - N N N N N N N V N N N N Y +chr1 41920 41921 G C G N M C G N A N G N K N W S N N N V N +chr1 42100 42101 T T T Y R W N N N V N M R N N G N M Y N K +chr1 45026 45027 C A C N N Y N S Y N N X N A D N N K N N A +chr1 45161 45162 C T C . N X H V N N C R N Y N N N N R N Y +chr2 45407 45408 C N C S B N N N N N C N Y N N T K G N C N +chr2 45788 45789 T T T N W S N Y N R Y N S N W M N C T N C +chr2 46243 46244 T T T N W N N B V N U N T N N Y C N U N N +chr2 47814 47815 A C A S N X D N N H W N G N Y C N N M R N +chr2 48073 48074 A G A Y W . N K N N N G N N N G N N N Y N +chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N +chr2 51304 51305 A G N N C N W - N S Y N . N N G N N N W R +chr2 51324 51325 T T N R N N N N N - N U N W A N N N N N N +chr2 52065 52066 T C T N N N S N . N T N M N S W N T Y C N +chr2 53130 53131 T C T K R . N B N N T N N M N Y N N Y N N +chr2 53505 53506 A A A M N N Y N N N N - K N W N N N S N R +chr2 53559 53560 T T T N N V R V N N T N U N N B N M N V Y +chr2 55607 55608 A N A U S N N H R K N N N Y N N G N N N N +chr10 55659 55660 T N T C N K N N N U N S N N N V C R S N N +chr10 55734 55735 T N T G N C N M M G C N B N . N G N N N N +chr10 55870 55871 C G C N H G - N N N C N H K N M G N N N N +chr10 56024 56025 A T A N D U N Y B N N X N N Y N T N - N N +chr10 56100 56101 T T A W N N W N S N K M N R N R N R N G N +chr10 56120 56121 A - A N A N N Y N N N W V N N Y G N N W N +chr10 56137 56138 A A A N A Y H . Y N G N . D N N T N N N N +chr10 56174 56175 A T A Y A N N N N N N N N N . S T Y N B N +chr10 59373 59374 A G A N N N N N N T N S N N N G N N N V N +chr10 68912 68913 G T G R N B R N H N U W Y N N N N N N N T +chr10 72946 72947 T A N N N N N N B N N . B D W U N U N D A +chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R +chr18 78200 78201 G G G N N H N N V N G N N N N A A N K X N +chr18 81076 81077 T A T B N N G N N X W N X N V N N D N N N +chr18 81198 81199 A T A N N N N - N N X N K T N M N K X N W +chr18 81216 81217 G A G Y N N D N X N N N N A N S N N N D N +chr18 81398 81399 G T G N - W N N M N G C N K N S N N N N K +chr18 91548 91549 A A A S N X H S R N A K N N N N U A R N N +chr18 93895 93896 T T T H N N V W Y N N N - N N N N N N Y N +chr18 98172 98173 T T T N . N N N S N T N Y N N Y X D V N Y +chr18 110904 110905 T - A A N A N A W A N N A X N W N N N N N +chr18 140324 140325 A A A N M N N Y N S N V N N X N C N N . M +chr18 160592 160593 C G G G N G N G N G N N G N N M T N Y N N \ No newline at end of file diff -r dedb7be9aa44 -r b36c13131ac7 test-data/dna_filter_out1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna_filter_out1.bed Mon Feb 08 23:52:56 2010 -0500 @@ -0,0 +1,4 @@ +chr1 582 583 G G G N G R N R N - N M N V K N N N G C R +chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R +chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N +chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R diff -r dedb7be9aa44 -r b36c13131ac7 test-data/dna_filter_out2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna_filter_out2.bed Mon Feb 08 23:52:56 2010 -0500 @@ -0,0 +1,39 @@ +chr1 256 257 A N M N - M N U N N A N D N G N N K N N N +chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R +chr1 4792 4793 A A M K N W S S N N Y N N N N N M R N R N +chr1 6119 6120 G G M N S N N W B N S D N N H V N B W N N +chr1 6357 6358 G G N M K N G - N N G U N N N B N N K N S +chr1 6433 6434 G G N R N N C N N N . N N . N N N N N R N +chr1 39160 39161 T T T N N Y N - N N N N N N N V N N N N Y +chr1 41920 41921 G C G N M C G N A N G N K N W S N N N V N +chr1 42100 42101 T T T Y R W N N N V N M R N N G N M Y N K +chr2 45788 45789 T T T N W S N Y N R Y N S N W M N C T N C +chr2 46243 46244 T T T N W N N B V N U N T N N Y C N U N N +chr2 47814 47815 A C A S N X D N N H W N G N Y C N N M R N +chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N +chr2 51304 51305 A G N N C N W - N S Y N . N N G N N N W R +chr2 51324 51325 T T N R N N N N N - N U N W A N N N N N N +chr2 53130 53131 T C T K R . N B N N T N N M N Y N N Y N N +chr2 53505 53506 A A A M N N Y N N N N - K N W N N N S N R +chr2 53559 53560 T T T N N V R V N N T N U N N B N M N V Y +chr2 55607 55608 A N A U S N N H R K N N N Y N N G N N N N +chr10 55659 55660 T N T C N K N N N U N S N N N V C R S N N +chr10 55734 55735 T N T G N C N M M G C N B N . N G N N N N +chr10 56024 56025 A T A N D U N Y B N N X N N Y N T N - N N +chr10 56100 56101 T T A W N N W N S N K M N R N R N R N G N +chr10 56120 56121 A - A N A N N Y N N N W V N N Y G N N W N +chr10 56137 56138 A A A N A Y H . Y N G N . D N N T N N N N +chr10 56174 56175 A T A Y A N N N N N N N N N . S T Y N B N +chr10 59373 59374 A G A N N N N N N T N S N N N G N N N V N +chr10 68912 68913 G T G R N B R N H N U W Y N N N N N N N T +chr10 72946 72947 T A N N N N N N B N N . B D W U N U N D A +chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R +chr18 78200 78201 G G G N N H N N V N G N N N N A A N K X N +chr18 81076 81077 T A T B N N G N N X W N X N V N N D N N N +chr18 81198 81199 A T A N N N N - N N X N K T N M N K X N W +chr18 81216 81217 G A G Y N N D N X N N N N A N S N N N D N +chr18 81398 81399 G T G N - W N N M N G C N K N S N N N N K +chr18 91548 91549 A A A S N X H S R N A K N N N N U A R N N +chr18 98172 98173 T T T N . N N N S N T N Y N N Y X D V N Y +chr18 110904 110905 T - A A N A N A W A N N A X N W N N N N N +chr18 160592 160593 C G G G N G N G N G N N G N N M T N Y N N diff -r dedb7be9aa44 -r b36c13131ac7 test-data/dna_filter_out3.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna_filter_out3.bed Mon Feb 08 23:52:56 2010 -0500 @@ -0,0 +1,41 @@ +chr1 468 469 C C C N M N N K . N C U N H N G N N M N S +chr1 582 583 G G G N G R N R N - N M N V K N N N G C R +chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R +chr1 6119 6120 G G M N S N N W B N S D N N H V N B W N N +chr1 6357 6358 G G N M K N G - N N G U N N N B N N K N S +chr1 6433 6434 G G N R N N C N N N . N N . N N N N N R N +chr1 39160 39161 T T T N N Y N - N N N N N N N V N N N N Y +chr1 41920 41921 G C G N M C G N A N G N K N W S N N N V N +chr1 42100 42101 T T T Y R W N N N V N M R N N G N M Y N K +chr1 45026 45027 C A C N N Y N S Y N N X N A D N N K N N A +chr1 45161 45162 C T C . N X H V N N C R N Y N N N N R N Y +chr2 45407 45408 C N C S B N N N N N C N Y N N T K G N C N +chr2 45788 45789 T T T N W S N Y N R Y N S N W M N C T N C +chr2 46243 46244 T T T N W N N B V N U N T N N Y C N U N N +chr2 48073 48074 A G A Y W . N K N N N G N N N G N N N Y N +chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N +chr2 51324 51325 T T N R N N N N N - N U N W A N N N N N N +chr2 52065 52066 T C T N N N S N . N T N M N S W N T Y C N +chr2 53130 53131 T C T K R . N B N N T N N M N Y N N Y N N +chr2 53559 53560 T T T N N V R V N N T N U N N B N M N V Y +chr2 55607 55608 A N A U S N N H R K N N N Y N N G N N N N +chr10 55659 55660 T N T C N K N N N U N S N N N V C R S N N +chr10 55734 55735 T N T G N C N M M G C N B N . N G N N N N +chr10 55870 55871 C G C N H G - N N N C N H K N M G N N N N +chr10 56100 56101 T T A W N N W N S N K M N R N R N R N G N +chr10 56120 56121 A - A N A N N Y N N N W V N N Y G N N W N +chr10 56174 56175 A T A Y A N N N N N N N N N . S T Y N B N +chr10 59373 59374 A G A N N N N N N T N S N N N G N N N V N +chr10 68912 68913 G T G R N B R N H N U W Y N N N N N N N T +chr10 72946 72947 T A N N N N N N B N N . B D W U N U N D A +chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R +chr18 78200 78201 G G G N N H N N V N G N N N N A A N K X N +chr18 81076 81077 T A T B N N G N N X W N X N V N N D N N N +chr18 81198 81199 A T A N N N N - N N X N K T N M N K X N W +chr18 81216 81217 G A G Y N N D N X N N N N A N S N N N D N +chr18 81398 81399 G T G N - W N N M N G C N K N S N N N N K +chr18 93895 93896 T T T H N N V W Y N N N - N N N N N N Y N +chr18 98172 98173 T T T N . N N N S N T N Y N N Y X D V N Y +chr18 110904 110905 T - A A N A N A W A N N A X N W N N N N N +chr18 140324 140325 A A A N M N N Y N S N V N N X N C N N . M +chr18 160592 160593 C G G G N G N G N G N N G N N M T N Y N N diff -r dedb7be9aa44 -r b36c13131ac7 test-data/dna_filter_out4.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna_filter_out4.bed Mon Feb 08 23:52:56 2010 -0500 @@ -0,0 +1,24 @@ +chr1 582 583 G G G N G R N R N - N M N V K N N N G C R +chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R +chr1 6119 6120 G G M N S N N W B N S D N N H V N B W N N +chr1 6433 6434 G G N R N N C N N N . N N . N N N N N R N +chr1 41920 41921 G C G N M C G N A N G N K N W S N N N V N +chr1 45161 45162 C T C . N X H V N N C R N Y N N N N R N Y +chr2 45788 45789 T T T N W S N Y N R Y N S N W M N C T N C +chr2 46243 46244 T T T N W N N B V N U N T N N Y C N U N N +chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N +chr2 51304 51305 A G N N C N W - N S Y N . N N G N N N W R +chr2 51324 51325 T T N R N N N N N - N U N W A N N N N N N +chr2 52065 52066 T C T N N N S N . N T N M N S W N T Y C N +chr2 53559 53560 T T T N N V R V N N T N U N N B N M N V Y +chr10 55734 55735 T N T G N C N M M G C N B N . N G N N N N +chr10 55870 55871 C G C N H G - N N N C N H K N M G N N N N +chr10 56120 56121 A - A N A N N Y N N N W V N N Y G N N W N +chr10 59373 59374 A G A N N N N N N T N S N N N G N N N V N +chr10 72946 72947 T A N N N N N N B N N . B D W U N U N D A +chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R +chr18 81198 81199 A T A N N N N - N N X N K T N M N K X N W +chr18 98172 98173 T T T N . N N N S N T N Y N N Y X D V N Y +chr18 110904 110905 T - A A N A N A W A N N A X N W N N N N N +chr18 140324 140325 A A A N M N N Y N S N V N N X N C N N . M +chr18 160592 160593 C G G G N G N G N G N N G N N M T N Y N N diff -r dedb7be9aa44 -r b36c13131ac7 tool_conf.xml.sample --- a/tool_conf.xml.sample Mon Feb 08 21:33:12 2010 -0500 +++ b/tool_conf.xml.sample Mon Feb 08 23:52:56 2010 -0500 @@ -49,6 +49,7 @@ <tool file="filters/headWrapper.xml" /> <tool file="filters/tailWrapper.xml" /> <tool file="filters/trimmer.xml" /> + <tool file="stats/dna_filtering.xml" /> </section> <section name="Filter and Sort" id="filter"> <tool file="stats/filtering.xml" /> diff -r dedb7be9aa44 -r b36c13131ac7 tools/stats/dna_filtering.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/stats/dna_filtering.py Mon Feb 08 23:52:56 2010 -0500 @@ -0,0 +1,195 @@ +#!/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 [options] + -i, --input=i: tabular input file + -o, --output=o: filtered output file + -c, --cond=c: conditions to filter on + -n, --n_handling=n: how to handle N and X + -l, --columns=l: columns + -t, --col_types=t: column types + +""" + +#from __future__ import division +import os.path, re, string, sys +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +from bx.cookbook import doc_optparse + +# Older py compatibility +try: + set() +except: + from sets import Set as set + +#assert sys.version_info[:2] >= ( 2, 4 ) + +def get_operands( filter_condition ): + # Note that the order of all_operators is important + items_to_strip = [ '==', '!=', ' and ', ' or ' ] + for item in items_to_strip: + if filter_condition.find( item ) >= 0: + filter_condition = filter_condition.replace( item, ' ' ) + operands = set( filter_condition.split( ' ' ) ) + return operands + +def stop_err( msg ): + sys.stderr.write( msg ) + sys.exit() + +def __main__(): + #Parse Command Line + options, args = doc_optparse.parse( __doc__ ) + input = options.input + output = options.output + cond = options.cond + n_handling = options.n_handling + columns = options.columns + col_types = options.col_types + + try: + in_columns = int( columns ) + assert col_types #check to see that the column types variable isn't null + in_column_types = col_types.split( ',' ) + except: + stop_err( "Data does not appear to be tabular. This tool can only be used with tab-delimited data." ) + + # Unescape if input has been escaped + cond_text = cond.replace( '__eq__', '==' ).replace( '__ne__', '!=' ).replace( '__sq__', "'" ) + orig_cond_text = cond_text + # Expand to allow for DNA codes + dot_letters = [ letter for letter in string.uppercase if letter not in \ + [ 'A', 'T', 'U', 'G', 'C', 'K', 'M', 'R', 'Y', 'S', 'W', 'B', 'V', 'H', 'D', 'N', 'X' ] ] + codes = {'A': [ 'A', 'M', 'R', 'W', 'V', 'H', 'D' ], + 'T': [ 'T', 'U', 'K', 'Y', 'W', 'B', 'H', 'D' ], + 'G': [ 'G', 'K', 'R', 'S', 'B', 'V', 'D' ], + 'C': [ 'C', 'M', 'Y', 'S', 'B', 'V', 'H' ], + 'U': [ 'T', 'U', 'K', 'Y', 'W', 'B', 'H', 'D' ], + 'K': [ 'K', 'G', 'T' ], + 'M': [ 'M', 'A', 'C' ], + 'R': [ 'R', 'A', 'G' ], + 'Y': [ 'Y', 'C', 'T' ], + 'S': [ 'S', 'C', 'G' ], + 'W': [ 'W', 'A', 'T' ], + 'B': [ 'B', 'C', 'G', 'T' ], + 'V': [ 'V', 'A', 'C', 'G' ], + 'H': [ 'H', 'A', 'C', 'T' ], + 'D': [ 'D', 'A', 'G', 'T' ], + '.': dot_letters, + '-': [ '-' ]} + # Add handling for N and X + if n_handling == "all": + codes[ 'N' ] = [ 'G', 'A', 'T', 'C', 'U', 'K', 'M', 'R', 'Y', 'S', 'W', 'B', 'V', 'H', 'D', 'N', 'X' ] + codes[ 'X' ] = [ 'G', 'A', 'T', 'C', 'U', 'K', 'M', 'R', 'Y', 'S', 'W', 'B', 'V', 'H', 'D', 'N', 'X' ] + for code in codes.keys(): + if code != '.' and code != '-': + codes[code].append( 'N' ) + codes[code].append( 'X' ) + else: + codes[ 'N' ] = dot_letters + codes[ 'X' ] = dot_letters + # Expand conditions to allow for DNA codes + try: + match_replace = {} + pat = re.compile( "c\d+\s*[!=]=\s*[\w']+" ) + matches = pat.findall( cond_text ) + for match in matches: + if match.find( '==' ) > 0: + match_parts = match.split( '==' ) + new_match = '(%s in codes[%s] and %s in codes[%s])' % ( match_parts[0], match_parts[1], match_parts[1], match_parts[0] ) + elif match.find( '!=' ) > 0 : + match_parts = match.split( '!=' ) + new_match = '(%s not in codes[%s] or %s not in codes[%s])' % ( match_parts[0], match_parts[1], match_parts[1], match_parts[0] ) + else: + raise Exception + if match_parts[1].find( "'" ) >= 0: + assert match_parts[1].replace( "'", '' ) in [ 'G', 'A', 'T', 'C', 'U', 'K', 'M', 'R', 'Y', 'S', 'W', 'B', 'V', 'H', 'D', 'N', 'X', '-', '.' ] + else: + assert match_parts[1].startswith( 'c' ) + match_replace[match] = new_match + for match in match_replace.keys(): + cond_text = cond_text.replace(match, match_replace[match]) + if len( match_replace ) == 0: + raise Exception + except: + stop_err( "One of your conditions is invalid. Make sure to use only '!=' or '==', valid column numbers, and valid base values." ) + + # Attempt to determine if the condition includes executable stuff and, if so, exit + secured = dir() + operands = get_operands( cond_text ) + for operand in operands: + try: + check = int( operand ) + except: + if operand in secured: + stop_err( "Illegal value '%s' in condition '%s'" % ( operand, cond_text ) ) + + # Prepare the column variable names and wrappers for column data types + cols, type_casts = [], [] + for col in range( 1, in_columns + 1 ): + col_name = "c%d" % col + cols.append( col_name ) + col_type = in_column_types[ col - 1 ] + type_cast = "%s(%s)" % ( col_type, col_name ) + type_casts.append( type_cast ) + + col_str = ', '.join( cols ) # 'c1, c2, c3, c4' + type_cast_str = ', '.join( type_casts ) # 'str(c1), int(c2), int(c3), str(c4)' + assign = "%s = line.split( '\\t' )" % col_str + wrap = "%s = %s" % ( col_str, type_cast_str ) + skipped_lines = 0 + first_invalid_line = 0 + invalid_line = None + lines_kept = 0 + total_lines = 0 + out = open( output, 'wt' ) + # Read and filter input file, skipping invalid lines + code = ''' +for i, line in enumerate( file( input ) ): + total_lines += 1 + line = line.rstrip( '\\r\\n' ) + if not line or line.startswith( '#' ): + skipped_lines += 1 + if not invalid_line: + first_invalid_line = i + 1 + invalid_line = line + continue + try: + %s = line.split( '\\t' ) + %s = %s + if %s: + lines_kept += 1 + print >> out, line + except Exception, e: + skipped_lines += 1 + if not invalid_line: + first_invalid_line = i + 1 + invalid_line = line +''' % ( col_str, col_str, type_cast_str, cond_text ) + + valid_filter = True + try: + exec code + except Exception, e: + out.close() + if str( e ).startswith( 'invalid syntax' ): + valid_filter = False + stop_err( 'Filter condition "%s" likely invalid. See tool tips, syntax and examples.' % orig_cond_text ) + else: + stop_err( str( e ) ) + + if valid_filter: + out.close() + valid_lines = total_lines - skipped_lines + print 'Filtering with %s, ' % orig_cond_text + if valid_lines > 0: + print 'kept %4.2f%% of %d lines.' % ( 100.0*lines_kept/valid_lines, total_lines ) + else: + print 'Possible invalid filter condition "%s" or non-existent column referenced. See tool tips, syntax and examples.' % orig_cond_text + if skipped_lines > 0: + print 'Skipped %d invalid lines starting at line #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line ) + +if __name__ == "__main__" : __main__() diff -r dedb7be9aa44 -r b36c13131ac7 tools/stats/dna_filtering.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/stats/dna_filtering.xml Mon Feb 08 23:52:56 2010 -0500 @@ -0,0 +1,114 @@ +<tool id="dna_filter" name="DNA Filter" version="1.0.0"> + <description>filter column data on DNA ambiguity codes using simple expressions</description> + <command interpreter="python"> + dna_filtering.py + --input=$input + --output=$out_file1 + --cond="$cond" + --n_handling=$n_handling + --columns=${input.metadata.columns} + --col_types="${input.metadata.column_types}" + </command> + <inputs> + <param format="tabular" name="input" type="data" label="Filter" help="Query missing? See TIP below."/> + <param name="cond" size="40" type="text" value="c8=='G'" label="With following condition" help="Double equal signs, ==, must be used as shown above. To filter for an arbitrary string, use the Select tool."> + <validator type="empty_field" message="Enter a valid filtering condition, see syntax and examples below."/> + </param> + <param name="n_handling" type="select" label="Do you want N (and X) to match A or C or G or T OR nothing?"> + <option value="all">N = A or C or G or T</option> + <option value="none">N = nothing</option> + </param> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="input"/> + </outputs> + <tests> + <test> + <param name="input" value="dna_filter_in1.bed" /> + <param name="cond" value="c8=='G'" /> + <param name="n_handling" value="all" /> + <output name="out_file1" file="dna_filter_out1.bed" /> + </test> + <test> + <param name="input" value="dna_filter_in1.bed" /> + <param name="cond" value="(c10==c11 or c17==c18) and c6!='C' and c23=='R'" /> + <param name="n_handling" value="all" /> + <output name="out_file1" file="dna_filter_out2.bed" /> + </test> + <test> + <param name="input" value="dna_filter_in1.bed" /> + <param name="cond" value="c4=='B' or c9==c10" /> + <param name="n_handling" value="none" /> + <output name="out_file1" file="dna_filter_out3.bed" /> + </test> + <test> + <param name="input" value="dna_filter_in1.bed" /> + <param name="cond" value="c7!='Y' and c9!='U'" /> + <param name="n_handling" value="none" /> + <output name="out_file1" file="dna_filter_out4.bed" /> + </test> + </tests> + <help> + +.. class:: warningmark + +Double equal signs, ==, must be used as *"equal to"* (e.g., **c1 == 'G'**) + +.. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* + +.. class:: infomark + +**TIP:** This tool is intended primarily for comparing column values (such as "c5==c12"), although it is also possible to filter on specific values (like "c6!='G'"). Be aware that when searching for specific values, any possible match is considered. So if you search on "c6!='G'", rows will be excluded when c6 is G, K, R, S, B, V, or D (plus N or X if you set that to equal "all"), because it is possible those values could be G. + +----- + +**Syntax** + +The filter tool allows you to restrict the dataset using simple conditional statements. + +- Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file +- Make sure that multi-character operators contain no white space ( e.g., **!=** is valid while **! =** is not valid ) +- When using 'equal-to' operator **double equal sign '==' must be used** ( e.g., **c1=='chr1'** ) +- Non-numerical values must be included in single or double quotes ( e.g., **c6=='C'** ) +- Filtering condition can include logical operators, but **make sure operators are all lower case** ( e.g., **(c1!='chrX' and c1!='chrY') or c6=='+'** ) + +----- + +**DNA Codes** + +The following are the DNA codes used for filtering:: + + Code Meaning + ---- --------------------------- + A A + T T + U T + G G + C C + K G or T + M A or C + R A or G + Y C or T + S C or G + W A or T + B C, G or T + V A, C or G + H A, C or T + D A, G or T + X A, C, G or T + N A, C, G or T + . not (A, C, G or T) + - gap of indeterminate length + +----- + +**Example** + +- **c8=='A'** selects lines in which the eighth column is A, M, R, W, V, H, D and N or X if appropriate +- **c12==c15** selects lines where the value in the twelfth column could be the same as the fifteenth and the fifteenth column could be the same as the twelfth column (based on appropriate codes) +- **c9!=c19** selects lines where column nine could not be the same as column nineteen and column nineteen could not be the same as column nine (using appropriate codes) + +</help> +</tool>