Mercurial > repos > bornea > dotplot_runner
comparison Dotplot_Release/SaintConvert.pl @ 0:dfa3436beb67 draft
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| author | bornea |
|---|---|
| date | Fri, 29 Jan 2016 09:56:02 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:dfa3436beb67 |
|---|---|
| 1 #!/usr/bin/perl | |
| 2 | |
| 3 # 17/12/2013 | |
| 4 | |
| 5 if($#ARGV==0){ | |
| 6 print "This program takes non-SaintExpress formatted data and converts it to look like it.\n"; | |
| 7 print "\nusage:\n $0\n-i [csv saint output file]\n\n"; | |
| 8 die; | |
| 9 } | |
| 10 else{ | |
| 11 $i=0; | |
| 12 while($i<=$#ARGV){ | |
| 13 if($ARGV[$i] eq '-i'){ | |
| 14 $i++; | |
| 15 $ifile=$ARGV[$i]; | |
| 16 } | |
| 17 else{ | |
| 18 die "\Incorrect program usage\n\n"; | |
| 19 } | |
| 20 $i++; | |
| 21 } | |
| 22 } | |
| 23 | |
| 24 $i=0; | |
| 25 $file=''; | |
| 26 open(IFILE,"<$ifile") || die "$ifile can't be opened: $!"; | |
| 27 { local $/=undef; $file=<IFILE>; } | |
| 28 @lines=split /[\r\n]+/, $file; | |
| 29 foreach $line (@lines) { | |
| 30 if($line =~ /^Bait/){ | |
| 31 } | |
| 32 elsif($line =~ /^([^\t]+)\t([^\t]+)\t([^\t]+)\t([^\t]+)/){ | |
| 33 $bait[$i]=$1; | |
| 34 $prey[$i]=$2; | |
| 35 $spec[$i]=$3; | |
| 36 $fdr[$i]=$4; | |
| 37 $i++; | |
| 38 } | |
| 39 else{ | |
| 40 } | |
| 41 } | |
| 42 close(IFILE); | |
| 43 $line_count=$i; | |
| 44 | |
| 45 open(OFILE, ">mockSaintExpress.txt"); | |
| 46 print OFILE "Bait\tPrey\tPreyGene\tSpec\tSpecSum\tAvgSpec\tNumReplicates\tctrlCounts\tAvgP\tMaxP\tTopoAvgP\tTopoMaxP\tSaintScore\tFoldChange\tBFDR\tboosted_by\n"; | |
| 47 | |
| 48 for($i=0; $i<$line_count; $i++){ | |
| 49 print OFILE "$bait[$i]\t111\t$prey[$i]\t111\t111\t$spec[$i]\t111\t111\t111\t111\t111\t111\t111\t111\t$fdr[$i]\t111\n"; | |
| 50 } | |
| 51 close(OFILE); | |
| 52 |