Mercurial > repos > greg > snpeff_v2_from_pablo
comparison snpEff_2_1a/scripts/randBedIntervals.pl @ 0:f8eaa3f8194b default tip
Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani
| author | greg |
|---|---|
| date | Fri, 20 Apr 2012 14:47:09 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:f8eaa3f8194b |
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| 1 #!/usr/bin/perl | |
| 2 | |
| 3 # Number of intervals per chromosome | |
| 4 $intsPerChr = 10; | |
| 5 | |
| 6 # Max interval len | |
| 7 $maxLen = 1000; | |
| 8 | |
| 9 # Chromosome length | |
| 10 $len{'chr2L'} = 23299195; | |
| 11 $len{'chr2LHet'} = 373492; | |
| 12 $len{'chr2R'} = 21411048; | |
| 13 $len{'chr2RHet'} = 3329880; | |
| 14 $len{'chr3L'} = 24850358; | |
| 15 $len{'chr3LHet'} = 2587444; | |
| 16 $len{'chr3R'} = 28253873; | |
| 17 $len{'chr3RHet'} = 2548985; | |
| 18 $len{'chr4'} = 1368761; | |
| 19 $len{'chrdmel_mitochondrion_genome'} = 19790; | |
| 20 $len{'chrUextra'} = 29367225; | |
| 21 $len{'chrU'} = 10174655; | |
| 22 $len{'chrX'} = 22703118; | |
| 23 $len{'chrXHet'} = 206671; | |
| 24 $len{'chrYHet'} = 351384; | |
| 25 | |
| 26 foreach $chr ( sort keys %len ) { | |
| 27 $max = $len{$chr} - $maxLen - 1000; | |
| 28 | |
| 29 for( $i=0 ; $i < $intsPerChr ; $i++ ) { | |
| 30 $start = int( rand() * $max ); | |
| 31 $end = int( rand() * $maxLen ) + $start; | |
| 32 | |
| 33 print "$chr\t$start\t$end\n"; | |
| 34 } | |
| 35 } | |
| 36 |