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#!/usr/bin/env perl use strict; use IO::File; use Getopt::Long; my $Usage = <<ENDUSE; Usage: cmpcol {-i|-u|-us|-x|-x1|-x2} [options] file1[:col\#] file2[:co +l\#] Comparison modes: -i : produce intersection of file1[:col\#] and file2[:col\#] -u(s) : produce union (and identify sources) -x : produce exclusive-or, identifying sources -x1 (-x2) : produce items unique to file1 (or file2) Options: -l1 (-l2) : print whole lines from file1 or file2 -l{a|b} [str] : print whole lines from both files joined by 'str' (d +ef=:<>:) -g(v) ptn : grep (-v) -- only compare lines that (don\'t) contain /p +tn/ -c cchar : ignore material following cchar -d delim : use /delim/ as input column separator (default is white- +space) use "-d tab" for tab-delimited, "-d vb" for vert.bar-delimi +ted "-d dot" for period-delimited "-d bs" for backslash-delim +ited file1 or file2 may be 'stdin' default ':col#' for comparison is first column from each file, which +is ':1' ':-1' selects last column, ':-2' is next-to-last, etc. ':i,j' selects concatenation of columns i and j ENDUSE my %opt = (); my $cmd_okay = GetOptions( \%opt, 'i','u','us','x','x1','x2', 'l1','l2','la:s','lb:s','d=s','c=s','g=s',' +gv=s' ); my $arg_okay = ( @ARGV == 2 and $ARGV[0] ne $ARGV[1] and ( $opt{i} + $opt{u} + $opt{us} + $opt{x} + $opt{x1} + + $opt{x2} ) == 1 ); die $Usage unless ( $cmd_okay && $arg_okay ); my ( @clm, @Input ); my $lfn = ''; for ( @ARGV ) { my ( $fn, $cl ); if ( /(.*):(-?[,\d]+)$/ and ( $1 eq 'stdin' or -f $1 )) { ( $fn, $cl ) = ( $1, $2 ); } elsif ( /^stdin$/ or -f ) { ( $fn, $cl ) = ( $_, 1 ); } else { die "\n$_ is not a data file.\n$Usage"; } push @Input, new IO::File; if ( $fn eq 'stdin' ) { $Input[$#Input]->fdopen( fileno(STDIN), 'r' ); } else { $Input[$#Input]->open( "< $fn" ) or die "$fn: $! $Usage"; } push @clm, ( $cl =~ /^-/ or $cl =~ /,/ ) ? $cl : $cl - 1; } my $delim = '\s+'; if ( $opt{d} ne '' ) { my %ctrl = ( tab => "\t", dot => '\.', vb => '\|', bs => '\\\\' ); $delim = ( exists( $ctrl{$opt{d}} )) ? $ctrl{$opt{d}} : $opt{d}; } my $joiner = undef; my $jointype = ( defined( $opt{la} )) ? 'la' : ( defined( $opt{lb} )) +? 'lb' : ''; if ( $jointype ) { $joiner = ( $opt{$jointype} eq 'nl' ) ? "\n" : ( $opt{$jointype} eq 'tab' ) ? "\t" : ':<>:'; } my %tknsourc = (); my %tkndata = (); sub simple_key { return (split( /$delim/, $_[0] ))[$_[1]]; } sub multi_key { my @k = map { $_ - 1 } split /,/, $_[1]; return join( " ", (split( /$delim/, $_[0] ))[@k] ); } # Read lines from first file my $getkey = ( $clm[0] =~ /,/ ) ? \&multi_key : \&simple_key; while ( $_ = $Input[0]->getline ) { s/[\r\n]+$//; s/$opt{c}.*// if ( $opt{c} ne "" ); next if ( /^\s*$/ || ( $opt{g} ne "" && ! /$opt{g}/ ) || ( $opt{gv +} ne "" && /$opt{gv}/ )); s/^\s*// if ( $delim eq '\s+' ); # for /\s+/ delimited data, rem +ove initial whitespace first my $k = &$getkey( $_, $clm[0] ); $tknsourc{$k} .= "1"; if ( $opt{l1} || defined( $joiner )) { $tkndata{$k} .= "$_\n"; } elsif ( $opt{l2} ) { $tkndata{$k} = "($k)\n"; } } # Now do the same for second file $getkey = ( $clm[1] =~ /,/ ) ? \&multi_key : \&simple_key; while ( $_ = $Input[1]->getline ) { s/[\r\n]+$//; s/$opt{c}.*// if ( $opt{c} ne "" ); next if ( /^\s*$/ || ( $opt{g} ne "" && ! /$opt{g}/ ) || ( $opt{gv +} ne "" && /$opt{gv}/ )); s/^\s*// if ( $delim eq "\\s+" ); my $k = &$getkey( $_, $clm[1] ); $tknsourc{$k} .= "2"; if ( defined( $joiner ) && exists( $tkndata{$k} )) { if ( $tkndata{$k} =~ /\n/ ) { $tkndata{$k} =~ s/\n/\x08$_\x0b/; } else { my ( $prefix ) = ( $jointype eq 'la' ) ? ( $tkndata{$k} =~ + /^([^\x08]+)/ ) : ''; $tkndata{$k} .= "$prefix\x08$_\x0b"; } } elsif ( $opt{l2} ) { my $newval = (( ! exists( $tkndata{$k} )) || $tkndata{$k} eq " +($k)\n" ) ? "$_\n" : $tkndata{$k} . "$_\n"; $tkndata{$k} = $newval; } elsif ( $opt{l1} && ! exists( $tkndata{$k} )) { $tkndata{$k} = "($k)\n"; } } # Now print the desired results if ( $opt{i} ) { # print the intersection: all records where $tknsour +c{} contains "12" foreach my $k ( sort( keys( %tknsourc ))) { &printData( $k ) if ( $tknsourc{$k} =~ /12/ ); } } elsif ( $opt{u} || $opt{us} ) { # print the union: all records foreach my $k ( sort( keys( %tknsourc ))) { if ( $opt{us} ) { my $src = $tknsourc{$k}; $src =~ s/11+/+1/; $src =~ s/22+/2+/; print "$k <$src\n"; } else { &printData( $k ); } } } elsif ( $opt{x} ) { # print exclusive-or: all records where $tknsourc +{} doesn't show "12" foreach my $k ( sort( keys( %tknsourc ))) { if ( $tknsourc{$k} !~ /12/ ) { my $src = $tknsourc{$k}; $src =~ s/11+/+1/; $src =~ s/22+/2+/; print "$k <$src\n"; } } } elsif ( $opt{x1} ) { # print excl-or-1: all records where $tknsourc{} + doesn't show "2" foreach my $k ( sort( keys( %tknsourc ))) { &printData( $k ) if ( $tknsourc{$k} !~ /2/ ); } } elsif ( $opt{x2} ) { # print excl-or-2: all records where $tknsourc{} + doesn't show "1" foreach my $k ( sort( keys( %tknsourc ))) { &printData( $k ) if ( $tknsourc{$k} !~ /1/ ); } } sub printData { my( $k ) = @_; $_ = ( $opt{l1} or $opt{l2} or defined( $joiner )) ? $tkndata{$k} +: "$k\n"; if ( $jointype eq 'la' and /([^\x08\x0b]+)\x0b[^\x08\x0b]*\n/ ) { my $suffix = $1; s/\n/\x08$suffix\x0b/g; } if ( defined( $joiner )) { s/\x08/$joiner/g; tr/\x0b/\n/; } print; } =head1 NAME cmpcol =head1 SYNOPSIS cmpcol {-i|-u|-us|-x|-x1|-x2} [options] file1[:col\#] file2[:col\#] Comparison modes: -i : produce intersection of file1[:col\#] and file2[:col\#] -u(s) : produce union (and identify sources) -x : produce exclusive-or, identifying sources -x1 (-x2) : produce items unique to file1 (or file2) Options: -l1 (-l2) : print whole lines from file1 or file2 -l{a|b} [str] : print both whole lines joined by 'str' (def=:<>:) -g(v) ptn : grep (-v), only compare lines that (don't) contain /ptn/ -c cchar : ignore material following cchar -d delim : use /delim/ as input column separator (def=whitespace) use "-d tab": tab-delimited, "-d vb": vert.bar-delimited "-d dot": period-delimited "-d bs": backslash-delimited file1 or file2 may be 'stdin' default ':col#' for comparison is first column from each file (':1') ':-1' selects last column, ':-2' is next-to-last, etc. ':i,j' selects concatenation of columns i and j =head1 DESCRIPTION Given two lists as input (either of which could be stdin), cmpcol can output the union, intersection or differences, and will print these to stdout. One or both inputs may be treated as multi-column tables where one or more specified columns can be used to determine the set relations. By default the first space-separated token on each line of both files is used as the key field, and only the unique set of keys meeting the chosen condition is printed as output. When using one of the "-l" options to output full lines from one or both inputs, multiple occurrences of each key will be listed exhaustively with the full lines that contain them. Both "-la [sep]" and "-lb [sep]" will list full lines from both inputs, joined together one matching pair per line, with the provided "sep" string as the delimiter between the two source strings. The default separator is ":<>:". The difference between -la and -lb has to do with happens when a given key occurs more often in one input than the other. The following example will demonstrate. Given these two input files: in1: x foo y bar z faz z gar w boo in2: a moo b mar y naz y paz z noo The output of "cmpcol -la -i in1 in2" will produce four full lines by repeating one line from each input: y bar:<>:y naz y bar:<>:y paz z faz:<>:z noo z gar:<>:z noo The output of "cmpcol -lb -i in1 in2" will produce two full lines and two partial lines -- notice that the "sep" string (the default ":<>:" in this case) will be line-initial when there's an extra instance of the key in the second input, and is absent from the line when the first input has the extra instance of the key: y bar:<>:y naz :<>:y paz z faz:<>:z noo z gar It's often more useful to use "-la tab" or "-lb tab". =head1 AUTHOR David Graff <graff (at) ldc (dot) upenn (dot) edu> =cut

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