changeset 5:83f2acca2387 draft

Deleted selected files

--- a/matrix_manipulate/aggregate.pl~	Thu Jun 13 16:54:15 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,219 +0,0 @@
-#!/usr/bin/perl
-
-##############################################################################
-##############################################################################
-##
-## aggregate.pl
-##
-##############################################################################
-##############################################################################
-##
-## Written by Josh Stuart in the lab of Stuart Kim, Stanford University.
-##
-##  Email address: [e-mail]
-##          Phone: [phone]
-##
-## Postal address: Department of Developmental Biology
-##                 Beckman Center Room B314
-##                 279 Campus Dr.
-##                 Stanford, CA 94305
-##
-##       Web site: http://www.smi.stanford.edu/people/stuart
-##
-##############################################################################
-##############################################################################
-##
-## Written: 00/00/02
-## Updated: 00/00/02
-##
-##############################################################################
-##############################################################################
-
-## Support for MEDIAN calculation added by Alex Williams, 2007
-
-require "$ENV{MYPERLDIR}/lib/libfile.pl";
-require "$ENV{MYPERLDIR}/lib/libstats.pl";
-
-use strict;
-use warnings;
-
-my @flags   = (
-                  [    '-q', 'scalar',     0,     1]
-                , [    '-k', 'scalar',     1, undef]
-                , [    '-d', 'scalar',  "\t", undef]
-                , [    '-h', 'scalar',     0, undef]
-                , [  '-sig', 'scalar',     3, undef]
-                , [    '-f', 'scalar','mean', undef]
-                , ['--file', 'scalar',   '-', undef]
-			    , ['--emptyval', 'scalar',     'NaN',     undef]
-			    , ['--test', 'scalar',     0,     1]
-              );
-
-my %args = %{&parseArgs(\@ARGV, \@flags)};
-
-if(exists($args{'--help'}))
-{
-   print STDOUT <DATA>;
-   exit(0);
-}
-
-my $emptyVal = $args{'--emptyval'};
-my $runTest  = $args{'--test'}; # <-- this doesn't do anything right now. Theoretically it should run a test to make sure the values actually work for a few known cases (sanity check for this program)
-my $verbose  = not($args{'-q'});
-my $col      = int($args{'-k'}) - 1;
-my $delim    = $args{'-d'};
-my $function = lc($args{'-f'}); # lower-case whatever the function name was
-my $headers  = $args{'-h'};
-my $sigs     = $args{'-sig'};
-my $file     = $args{'--file'};
-
-my $sprintf_ctrl = '%.' . $sigs . 'f';
-
-
-if ($function ne 'mean' && $function ne 'median') {
-	die "ERROR in aggregate.pl: You must specify a function ( -f  FUNCTION_NAME ). The supported functions are mean and median.\n";
-}
-
-# my ($ids, $rows) = &readIds($file, $col, $delim);
-# my $data = &readDataMatrix($file, $col, $delim, \$max_cols);
-my ($data, $ids, $rows, $max_cols) = &readDataAndIds($file, $col, $delim);
-
-for(my $i = 0; $i < scalar(@{$rows}) and $i < $headers; $i++) {
-   print $$ids[$i], $delim, join($delim, @{$$data[$i]}), "\n";
-}
-
-for(my $i = $headers; $i < scalar(@{$rows}); $i++)
-{
-   my $id = $$ids[$i];
-
-   my $useMedian = ($function eq 'median');
-   my $useMean   = ($function eq 'mean');
-
-   my @sum;
-   my @count;
-   my @medianCalcArray; # this is actually just a list of all the items in the column for each key
-   # Note: medianCalcArray is an array of ARRAYS.
-
-   for(my $j = 0; $j < $max_cols; $j++) {
-      $sum[$j] = 0;
-      $count[$j] = 0;
-   }
-
-   #my @r = @{$$rows[$i]};
-
-   for(my $k = 0; $k < scalar(@{$$rows[$i]}); $k++) {
-	   my $row = $$rows[$i][$k];
-	   
-	   #print "Row is $row\n";
-	   for(my $j = 0; $j < $max_cols; $j++) {
-		   my $thisEntry = $$data[$row][$j];
-		   if(defined($thisEntry)) {
-			   if($thisEntry =~ /^\s*[\d+\.eE-]+\s*$/) {
-				   $count[$j]++;
-				   $sum[$j] += $thisEntry;
-				   if ($useMedian) {
-					   if (!defined($medianCalcArray[$j])) {
-						   @{$medianCalcArray[$j]} = ();
-					   }
-					   push(@{$medianCalcArray[$j]}, $thisEntry);
-					   #print "$j: $k: $row: ";
-					   #print @{$medianCalcArray[$j]};
-					   #print "\n";
-				   }
-			   }
-		   }
-	   }
-   }
-
-   my @agg;
-   for(my $j = 0; $j < $max_cols; $j++) {
-      $agg[$j] = ${emptyVal};
-      if($useMean) {
-         $agg[$j] = ($count[$j] > 0) ? sprintf($sprintf_ctrl, ($sum[$j] / $count[$j])) : ${emptyVal};
-      }
-	  if($useMedian) {
-		  # Only calculate the median if we actually specifically want it... otherwise it slows us down
-		  if (defined($medianCalcArray[$j]) && (scalar(@{$medianCalcArray[$j]}) > 0) ) {
-			  $agg[$j] = vec_median(\@{$medianCalcArray[$j]}); # <-- vec_median is in libstats.pl
-		  }
-	  }
-	  if ($useMean && $useMedian) { die "Error in arguments to aggregate.pl: You cannot specify both *mean* AND *median* at the same time! (We would be overwriting the storage variable!) You will have to run the program twice, once with each option.\n"; }
-   }
-
-   print STDOUT $id, (($max_cols > 0) ? ($delim . join($delim, @agg)) : ""), "\n";
-}
-
-exit(0);
-
-
-__DATA__
-syntax: aggregate.pl [OPTIONS]
-
-Combines the numeric data across rows with the same key. Useful if you have experiments
-with replicates. See below for a complete example.
-
-Example usage:  aggregate.pl -f median MYFILE
-
-OPTIONS are:
-
--q: Quiet mode (default is verbose)
-
--k COL: Use the column COL as the key column. The script uses the entries found
-        on each line of this column as keys. Duplicates are merged by applying
-        an aggregation function for each value in their records.
-
--d DELIM: Set the field delimiter to DELIM (default is tab).
-
--h NUM: The number of headers in the input file (default is 0).
-
--f FUNCTION: Set the aggregation function to FUNCTION (default is mean). The
-             possible values are:
-
-                 mean: The mean of the values (default)  (-f mean)
-
-                 median: The median of the values.  (-f median)
-
---emptyval VALUE: Sets the "empty"/"no data" values to VALUE. (default is NaN)
-             If an output value has no input data, then this will be the output.
-
-EXAMPLE:
-
-Works like this:
-
-If the input file INPUTFILE has five columns like below (tab-delimited, although
-spaces are shown here): (Note that Column 3 (C3) is blank for all rows except
-for the last one)
-
-Column_1  Column_2  C3  C4  C5
-v                v   v   v   v
--------------------------------- (Sample file is below)
-Experiment_Alpha 1       0   77
-Experiment_Alpha 2       0
-Expr_Beta        10
-Expr_Beta        30
-Experiment_Alpha 3       6
-Expr_Beta            5
-
-
-And you type:   aggregate.pl -f mean THE_FILE
-
-Then the output will be the *mean* values for each experiment, across all rows:
-
-Experiment_Alpha   2.0   NaN   3.0   77
-Expr_Beta          20    5     NaN   NaN
-
-Note that the "77" case (the last item in the first row) is the corect mean,
-because the other Experiment_Alpha items for that column do not have any data ta
-all. Even though there are 3 rows labeled "Experiment_Alpha", only one of them
-has data for the last column (column 4), so 77 is the mean. The output is always
-a matrix (although it could be a single-column matrix). Empty values are padded
-with NaN (although you can change this with --emptyval).
-
-
-TO DO / FUTURE WORK:
-
-Future possibility (NOT IMPLEMENTED YET): smean: Standardized mean (mean/stddev).
-
-KNOWN BUGS / ISSUES:
-
-None so far.

Binary file matrix_manipulate/floatMatrix.pyc has changed

--- a/matrix_manipulate/quartile_norm.pl	Thu Jun 13 16:54:15 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,102 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-use Getopt::Long;
-
-my $out = '-';
-my $q = 75;
-my @col;
-my @also;
-my $names = 1;
-my $target = 1000;
-my $skip = 0;
-my $min=1;
-GetOptions("quant=i"=>\$q, "target=i"=>\$target, "col=i@"=>\@col, "out=s"=>\$out, "also=i@"=>\@also, "skip=i"=>\$skip, "min=i"=>\$min);
-
-my $in = shift @ARGV;
-
-die usage() unless $in && @col;
-
-open(OUT, ($out eq '-') ? '<&STDOUT' : ">$out") || die "Can't open $out\n";
-open(IN, ($in eq '-') ? '<&STDIN' : $in) || die "Can't open $in\n";
-
-@also = (1) if !@also && !grep {$_ eq '1'} @col;
-
-map {$_--} @col;
-map {$_--} @also;
-
-my @d;
-my $cnt = 0;
-my $head ='';
-while(<IN>) {
-        if ($skip) {
-                --$skip;
-                $head .= $_;
-                next;
-        }
-        chomp;
-        my @f = split /\t/;
-        if ($col[0] eq '-2') {
-                @col = (1..$#f);
-        }
-        for (@col) {
-                push @{$d[$_]}, $f[$_];
-        }
-        for (@also) {
-                push @{$d[$_]}, $f[$_];
-        }
-        ++$cnt;
-}
-for (@col) {
-        my @t = grep {$_>=$min} @{$d[$_]};
-        @t = sort {$a <=> $b} @t;
-        my $t=quantile(\@t, $q/100);
-        for (@{$d[$_]}) {
-                $_= sprintf "%.4f", $target*$_/$t;
-        }
-}
-
-my @out = (sort {$a <=> $b} (@col, @also));
-
-print OUT $head;
-
-for (my $i=0;$i<$cnt;++$i) {
-        for my $j (@out) {
-                print OUT "\t" unless $j == $out[0];
-                print OUT $d[$j][$i];
-        }
-        print OUT "\n";
-}
-
-
-sub usage {
-<<EOF;
-Usage: $0 -c COL [opts] FILE
-
-Returns an upper quartile normalization of data in column(s) COL
-of file FILE.
-
-Col is 1-based, zeroes are ignores when calculating upper quartile
-
-Options:
-   -c|col COL    normalize this column of data (can specify more than once, or -1 for all but first col)
-   -q|quant INT  quantile to use (75)
-   -t|target INT target to use (1000)
-   -a|also COL   output these columns also
-   -o|out FILE   output to this file instead of stdout
-   -m|min INT    minimum value (1)
-   -s|skip INT   skip header rows
-EOF
-}
-
-sub quantile {
-        my ($a,$p) = @_;
-        my $l = scalar(@{$a});
-        my $t = ($l-1)*$p;
-        my $v=$a->[int($t)];
-        if ($t > int($t)) {
-                return $v + $p * ($a->[int($t)+1] - $v);
-        } else {
-                return $v;
-        }
-}