Mercurial > repos > portiahollyoak > temp
annotate scripts/make.bp.bed.pl @ 21:9672fe07a232 draft default tip
planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
author | mvdbeek |
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date | Mon, 05 Dec 2016 09:58:47 -0500 |
parents | 28d1a6f8143f |
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rev | line source |
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0
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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1 #! /usr/bin/perl |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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2 |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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3 use strict; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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changeset
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4 |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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changeset
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5 my @sample=(); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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6 open (in, "<$ARGV[0]") or die "Can't open $ARGV[0] since $!\n"; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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changeset
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7 my $line=<in>; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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changeset
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8 close in; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
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9 |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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changeset
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10 my %chrs=(); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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11 my @a=split(/\t/, $line); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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12 for my $i (0..$#a) { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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13 if ($a[$i] =~ /_class$/) { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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changeset
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14 my $name=$a[$i]; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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15 $name =~ s/_class//; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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16 my $j=$i+1; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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17 my $k=$i+2; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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18 my $l=$i+3; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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19 system("cut -f7,4,6,$j,$k,$l $ARGV[0] > temp"); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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20 open (input, "<temp") or die "Can't open temp since $!\n"; |
21
9672fe07a232
planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
mvdbeek
parents:
0
diff
changeset
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21 open (output, ">$name.insertion.bp.bed") or die "Can't open $name.insertion.bp.bed since $!\n"; |
0
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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22 my $header=<input>; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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23 while (my $line=<input>) { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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24 chomp($line); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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25 my @b=split(/\t/, $line); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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26 if (($b[4] ne "0")||($b[5] ne "0")) { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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changeset
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27 my @c=split(/\:/, $b[2]); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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28 my @d=split(/\./, $c[1]); |
21
9672fe07a232
planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
mvdbeek
parents:
0
diff
changeset
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29 if ($c[0] eq "P") {next;} |
0
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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30 if ($d[0] > $d[1]) { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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31 my $temp=$d[0]; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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32 $d[0]=$d[1]; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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33 $d[1]=$temp; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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34 } |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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35 my $lower=$d[0]; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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36 my $upper=$d[1]; |
21
9672fe07a232
planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
mvdbeek
parents:
0
diff
changeset
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37 if (($lower >= 0) && ($upper >= 0)) { |
9672fe07a232
planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
mvdbeek
parents:
0
diff
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38 print output "$c[0]\t$lower\t$upper\t$b[0]\t$b[1]\t$b[3]\t$b[4]\t$b[5]\n"; |
9672fe07a232
planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
mvdbeek
parents:
0
diff
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39 } |
0
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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40 $chrs{$c[0]}=1; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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41 } |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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42 } |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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43 close input; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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changeset
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44 close output; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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45 system("rm temp"); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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46 |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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47 if ($ARGV[1] ne "") { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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48 open (input, "<$name.insertion.bp.bed") or die "Can't open $name.insertion.bp.bed since $!\n"; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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49 open (output, ">tmp") or die "Can't tmp since $!\n"; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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50 while (my $line=<input>) { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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51 chomp($line); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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52 my @a=split(/\t/, $line); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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53 if (($a[0] =~ /^\d{1,2}$/) || ($a[0] eq "X") || ($a[0] eq "Y")) {$a[0]="chr$a[0]";} |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
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54 my $strand="+"; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
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55 if ($a[4] eq "antisense") {$strand="-";} |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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56 print output "$a[0]\t$a[1]\t$a[2]\t$a[3]\t\.\t$strand\t$a[5]\t$a[6]\t$a[7]\n"; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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57 } |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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58 close input; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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changeset
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59 close output; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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60 |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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61 system("bedtools intersect -a tmp -b $ARGV[1] -f 0.1 -wo -s > tmp1"); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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62 if ($ARGV[2] eq "") { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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63 system("awk -F \"\\t\" '{OFS=\"\\t\"; if ((\$4==\$13)&&(\$6==\$15)) print \$1,\$2,\$3,\$4,\$5,\$6}' tmp1 > tmp2"); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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64 } |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
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65 else { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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66 my %family=(); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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67 open (input, "<$ARGV[2]") or die "Can't open $ARGV[2] since $!\n"; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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68 while (my $line=<input>) { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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69 chomp($line); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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70 my @a=split(/\t/, $line); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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71 $family{$a[0]}=$a[1]; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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72 } |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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73 close input; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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74 |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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changeset
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75 open (input, "<tmp1") or die "Can't open tmp1 since $!\n"; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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76 open (output, ">>tmp2") or die "Can't open tmp2 since $!\n"; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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77 while (my $line=<input>) { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
changeset
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78 chomp($line); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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79 my @a=split(/\t/, $line); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff
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80 if (($family{$a[3]} eq $family{$a[12]}) && ($a[5] eq $a[14])) { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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81 print output "$a[0]\t$a[1]\t$a[2]\t$a[3]\t$a[4]\t$a[5]\n"; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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82 } |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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83 } |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
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84 close input; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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85 close output; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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86 } |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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87 |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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88 if (-s "tmp2") { |
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89 my %to_filter=(); |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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90 open (input, "<tmp2") or die "Can't open tmp2 since $!\n"; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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91 while (my $line=<input>) { |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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92 chomp($line); |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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93 my @a=split(/\t/, $line); |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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94 $to_filter{"$a[0]\:$a[1]\:$a[2]\:$a[3]\:$a[5]"}=1; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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95 } |
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96 close input; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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97 open (input, "<tmp") or die "Can't open tmp since $!\n"; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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98 open (output, ">$name.insertion.bp.bed") or die "Can't open $name.insertion.bp.bed since $!\n"; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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99 while (my $line=<input>) { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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100 chomp($line); |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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101 my @a=split(/\t/, $line); |
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102 if (!defined $to_filter{"$a[0]\:$a[1]\:$a[2]\:$a[3]\:$a[5]"}) { |
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103 my $direction="sense"; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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104 if ($a[5] eq "-") {$direction="antisense";} |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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105 my $chr_num=$a[0]; |
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106 $chr_num =~ s/chr//; |
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107 if (($chrs{$a[0]} == 1) && (! defined $chrs{$chr_num})) {$chr_num=$a[0];} |
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108 print output "$chr_num\t$a[1]\t$a[2]\t$a[3]\t$direction\t$a[6]\t$a[7]\t$a[8]\n"; |
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109 } |
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110 } |
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111 close input; |
28d1a6f8143f
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112 close output; |
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113 } |
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114 |
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115 system("rm tmp*"); |
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116 |
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117 } |
0
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118 |
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119 } |
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120 } |
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121 |