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new file: cell2loc.py
[GalaxyCodeBases.git] / perl / bsim / overlapMeerkat.pl
blobbd8fd56c052fc2059af91f054cec987d77f23dd4
1 #!/usr/bin/env perl
2 use strict;
3 use warnings;
4
5 die "Usage: $0 <SimLst> <AnalyseRes> [Shift=10]\n" if @ARGV <2;
6
7 my $total=shift;
8 my $result=shift;
9 my $shift=shift;
10 $shift = 10 unless defined $shift;
11 open TT,$total or die $!;
12 open RT,$result or die $!;
13 my %hash;
14
15 while(<TT>){
16 chop;
17 my @a=split;
18 #print $a[3]."\n";
19 next unless(/\w/);
20 for( my $kk=$a[3]-$shift;$kk<$a[3]+$shift;$kk++){
21 $hash{$kk}=1;
22 }
23
24 }
25 close TT;
26
27 sub docheck($$$) {
28 my ($chr,$start,$end) = @_;
29 my $ret = 0;
30 ($start,$end) = sort {$a <=> $b} ($start,$end);
31 for my $p ($start .. $end) {
32 if (exists $hash{$p}) {
33 $ret = 1;
34 last;
35 }
36 }
37 return $ret;
38 }
39
40 while(<RT>){
41 chomp;
42 my @a=split;
43 my ($cnt,$chr,$start,$end,$chr2,$start2,$end2)=(1);
44 if (@a == 11) { # invers & tandem_dup
45 ($chr,$start,$end) = @a[5,6,7];
46 } elsif (@a == 14 or @a == 15) { # ins & del_ins
47 ($chr,$start,$end) = @a[5,6,7];
48 ($chr2,$start2,$end2) = @a[9,10,11];
49 $cnt=2 if $chr2 ne '-';
50 } elsif (@a == 13) { # transl_inter
51 ($chr,$start,$end) = @a[5,6,6];
52 ($chr2,$start2,$end2) = @a[8,9,9];
53 $cnt=2 if $chr2 ne '-';
54 } else {
55 die "Unknown format:[$_]\n"
56 }
57 #print $a[2]."\n";
58 my $ret = docheck($chr,$start,$end);
59 $ret = docheck($chr2,$start2,$end2) if ($cnt==2) and ($ret==0);
60 print "$_\n" if $ret;
61 }
62 close RT;
63
64 __END__
65 grep \> simout_*.Ref.fa | sed 's/^simout_m//'|sed 's/.Ref.fa:>/\t/'|sed 's/Ref_/Ref:/g'|sed 's/Vir_/Vir:/'|sed 's/R_/R:/'|sed 's/_/ /g'|cat -n >simed.lst
66
67 $ ./overlapMeerkat.pl simed.lst all.variants|awk '{print $1"\t"$2}'|uniq|sort|uniq
68 11 invers
69 11 invers_f
70 11 invers_r
71 11 tandem_dup
72 13 transl_inter
73 14 del_ins
74 15 del_inso
75 15 inso
76 15 inss
77
78 wc -l all.variants 117 # cat Meerkat/*2*.variants > all.variants
79 ./overlapMeerkat.pl simed.lst all.variants 100 |wc -l 82
80
81 $ wc -l simed.lst
82 700 simed.lst
83
84 $ wc -l Meerkat/*2*.variants
85 8 Meerkat/bwa2gx.variants
86 86 Meerkat/bwa2hg18.variants
87 23 Meerkat/meth2gx.variants
88 117 total
89
90 ./overlapMeerkat.pl simed.lst Meerkat/bwa2gx.variants |wc -l 3
91 ./overlapMeerkat.pl simed.lst Meerkat/meth2gx.variants |wc -l 5
92 ./overlapMeerkat.pl simed.lst Meerkat/bwa2hg18.variants |wc -l 71
93
94 __DAT__
95 invers_f NA 273_0 31 1 chr18 11929626 11930843 1217 1000 BP:TE_TE
96 invers_r NA 270 32 1 chr18 11929606 11930823 1217 1000 BP:TE_TE
97 tandem_dup NA 50 97 2 chr18 12616569 12617117 548 -47 BP:_TE
98
99 del_ins FoSTeS 1574_0 5 1 chr18 15924715 18626457 2701741 - - - 41 BP:_TE
100 invers_f NA 1189 10 1 chr18 61614378 61615078 700 1000 BP:_
101 invers_r NA 1358 7 1 chr18 61614358 61615058 700 1000 BP:_
102 tandem_dup NA 772 47 1 chr18 22015346 22016298 952 20 BP:TE_TE
103 tandem_dup NA 300 101 2 chr18 43138397 43138712 315 -49 BP:_
104
105 del_inso FoSTeS 815_0/474_0 5/18 20/2 chr6 147769523 147769543 19 chr18 56863663 58638709 1775047 -13/2 BP:__TE_TE
106 inso NA 760_0/754_0 6/6 2/6 chr1 188536417 188536417 -1 chr18 10930057 10930057 1 -20/-20 BP:TE_TE__
107 inso NA 682_0/589_0 7/9 2/9 chr1 246112340 246112340 -1 chr18 66074916 66074916 1 -2/-2 BP:__TE_TE
108 inso NA 504_0/497_0 15/16 1/10 chr11 80370988 80370988 -1 chr18 66199314 66199314 1 -34/-34 BP:TE_TE__
109 inso NA 831_0/752_0 5/6 5/6 chr11 89609742 89609742 -1 chr18 20675062 20675062 1 -28/-28 BP:__TE_TE
110 inso NA 554_0/544_0 12/12 2/5 chr13 89361761 89361761 -1 chr18 40628245 40628245 1 -10/-10 BP:TE_TE__
111 inso NA 482_0/477_0 18/18 2/10 chr13 94154988 94154988 -1 chr18 31841819 31841819 1 -20/-20 BP:__TE_TE
112 inso NA 552_0/543_0 12/12 2/10 chr13 94154988 94154988 -1 chr18 33366658 33366658 1 -24/-24 BP:___
113 inso NA 572_0/582_0 11/10 2/10 chr13 94154988 94154988 -1 chr18 33414001 33414001 1 -25/-25 BP:__TE_TE
114 inso NA 832_0/823_0 5/5 2/10 chr13 94154988 94154988 -1 chr18 33840728 33840728 1 -31/-31 BP:___
115 inso NA 547_0/533_0 12/12 2/6 chr14 88453875 88453875 -1 chr18 47355345 47355345 1 -4/-4 BP:TE_TE_TE_TE
116 inso NA 460_0/459_0 21/21 1/7 chr15 80290558 80290558 -1 chr18 10204472 10204472 1 -35/-35 BP:___
117 inso NA 548_0/534_0 12/12 1/7 chr15 80290577 80290577 -1 chr18 10373958 10373958 1 -39/-39 BP:__TE_TE
118 inso NA 549_0/535_0 12/12 1/10 chr18 10727847 10727847 -1 chr8 122638945 122638945 1 -2/-2 BP:___
119 inso NA 637_0/718_0 8/6 1/3 chr18 41924326 41924326 -1 chr3 52215635 52215635 1 3/3 BP:___
120 inso NA 503_0/501_0 15/15 1/6 chr18 50103558 50103558 -1 chr20 43152025 43152025 1 -2/-2 BP:__TE_TE
121 inso NA 553_0/565_0 12/11 2/18 chr18 68315631 68315631 -1 chr8 110628783 110628783 1 -12/-12 BP:__TE_TE
122 inso NA 445_0/443_0 25/25 2/10 chr18 70013527 70013527 -1 chr3 89469319 89469319 1 -30/-30 BP:__TE_TE
123 inso NA 465_0/463_0 20/20 2/10 chr18 70123134 70123134 -1 chr3 89469319 89469319 1 -27/-27 BP:TE_TE_TE_TE
124 inso NA 517_0/481_0 14/18 2/1 chr2 12668402 12668402 -1 chr18 14194320 14194320 1 -25/-25 BP:TE_TE__
125 inso NA 827_0/639_0 5/8 1/5 chr2 32227442 32227442 -1 chr18 50012628 50012628 1 -40/-40 BP:TE_TE_TE_TE
126 inso NA 469_0/468_0 19/19 1/7 chr20 43152025 43152025 -1 chr18 50430831 50430831 1 -29/-29 BP:TE_TE_TE_TE
127 inso NA 746_0/678_0 6/7 6/2 chr20 56114021 56114021 -1 chr18 26134579 26173402 38824 -9/-21 BP:___
128 inss NA 514_0/518_0 14/14 1/4 chr1 28801685 28801685 -1 chr18 77358872 77358872 1 -31/-31 BP:TE_TE__
129 inss NA 607_0/610_0 9/9 1/13 chr11 89609742 89609742 -1 chr18 27827051 27827051 1 -28/-28 BP:___
130 inss NA 522_0/519_0 13/14 1/4 chr13 72703887 72703887 -1 chr18 77358872 77358872 1 -9/-9 BP:TE_TE__
131 inss NA 680_0/609_0 7/9 2/8 chr13 72703887 72703887 -1 chr18 79263837 79263837 1 -30/-30 BP:TE_TE__
132 inss NA 758_0/684_0 6/7 1/10 chr18 10930057 10930057 -1 chr2 222878521 222878521 1 -25/-25 BP:__SR_SR
133 inss NA 689_0/633_0 7/8 1/4 chr18 26134579 26134579 -1 chr9 10858712 10858712 1 -20/-20 BP:__TE_TE
134 inss NA 834_0/824_0 5/5 1/2 chr18 26134579 26134579 -1 chrX 145458414 145458414 1 -41/-41 BP:___
135 inss NA 608_0/581_0 9/10 1/5 chr18 26173402 26173402 -1 chrX 145458414 145458414 1 -29/-29 BP:___
136 inss NA 611_0/600_0 9/9 11/1 chr18 45311409 45311409 -1 chr19 3982132 3982132 1 -33/-33 BP:TE_TE__
137 inss NA 635_0/790_0 8/5 1/6 chr18 50012628 50012628 -1 chr2 127641529 127641529 1 -6/-6 BP:TE_TE__
138 inss NA 470_0/479_0 19/18 1/5 chr18 61462044 61462044 -1 chr7 54378346 54378346 1 -18/-18 BP:__TE_TE
139 inss NA 829_0/717_0 5/6 1/5 chr18 61462044 61462044 -1 chr7 143940165 143940165 1 -2/-2 BP:___
140 inss NA 546_0/532_0 12/12 1/6 chr18 62500026 62500026 -1 chr7 54378346 54378346 1 -6/-6 BP:SR_SR_TE_TE
141 inss NA 527_0/508_0 13/14 1/4 chr18 68315630 68315630 -1 chr3 89469299 89469299 1 1/1 BP:__TE_TE
142 inss NA 545_0/531_0 12/12 1/10 chr18 69680373 69680373 -1 chr3 89469300 89469300 1 -37/-37 BP:TE_TE_TE_TE
143 inss NA 688_0/686_0 7/7 1/6 chr18 69714982 69714982 -1 chr3 89469319 89469319 1 -38/-38 BP:__TE_TE
144 inss NA 499_0/492_0 16/16 1/16 chr18 71159390 71159390 -1 chr3 8842566 8842566 1 -4/-4 BP:__TE_TE
145 inss NA 440_0/439_0 28/28 1/17 chr18 72319702 72319702 -1 chr3 8842566 8842566 1 -9/-9 BP:__TE_TE
146 inss NA 505_0/502_0 15/15 1/17 chr18 72711991 72711991 -1 chr3 8842566 8842566 1 -21/-21 BP:TE_TE_TE_TE
147 inss NA 449_0/453_0 24/23 1/5 chr20 25658177 25658177 -1 chr18 49300016 49300016 1 -6/-6 BP:TE_TE__
148 inss NA 551_0/571_0 12/11 1/5 chr20 25658177 25658177 -1 chr18 49418901 49418901 1 -26/-26 BP:TE_TE_SR_SR
149 inss NA 451_0/450_0 24/24 1/7 chr20 43152004 43152004 -1 chr18 54763252 54763252 1 -22/-22 BP:TE_TE_TE_TE
150 inss NA 641_0/685_0 8/7 2/7 chr3 192474316 192474316 -1 chr18 10930055 10930055 1 -29/-29 BP:TE_TE__
151 transl_inter NA 570 11 8 chr1 66753472 -1 chr18 70444674 -1 -50 BP:TE_
152 transl_inter NA 791 5 5 chr1 107988319 1 chr18 35980668 -1 -42 BP:_TE
153 transl_inter NA 755_0 6 1 chr10 64140812 1 chr18 10930055 -1 -29 BP:TE_
154 transl_inter NA 523_0 13 2 chr10 80363269 -1 chr18 66130374 -1 3 BP:_TE
155 transl_inter NA 512 14 15 chr11 25649769 -1 chr18 75846882 -1 -43 BP:TE_
156 transl_inter NA 789_0 5 11 chr12 11624029 -1 chr18 56863664 -1 -8 BP:_TE
157 transl_inter NA 513 14 10 chr13 18843690 -1 chr18 14216367 -1 -45 BP:TE_TE
158 transl_inter NA 590 9 13 chr14 66621359 1 chr18 22506567 -1 -45 BP:_
159 transl_inter NA 632 8 20 chr15 66008014 -1 chr18 79263837 -1 -15 BP:TE_
160 transl_inter NA 536 12 13 chr18 7650940 -1 chr3 87425411 1 -45 BP:TE_
161 transl_inter NA 833 5 6 chr18 10930057 1 chr9 36676099 -1 -13 BP:_TE
162 transl_inter NA 757_0 6 1 chr18 26134579 1 chr20 56114021 1 -21 BP:_
163 transl_inter NA 759 6 1 chr18 26134579 1 chr3 18033189 -1 -21 BP:_TE
164 transl_inter NA 826 5 6 chr18 26134579 -1 chr4 27670343 -1 -11 BP:_
165 transl_inter NA 716 6 7 chr18 39236217 -1 chr3 166976579 1 -44 BP:TE_
166 transl_inter NA 725 6 20 chr18 39236217 -1 chr8 52954930 1 29 BP:TE_
167 transl_inter NA 452 24 7 chr18 43989113 1 chr19 3982132 -1 -15 BP:_
168 transl_inter NA 436 30 8 chr18 50862264 1 chr20 43152025 -1 -8 BP:TE_TE
169 transl_inter NA 480_0 18 8 chr18 56863663 1 chr6 147769543 1 2 BP:TE_
170 transl_inter NA 462 20 6 chr18 58742568 -1 chr7 143940183 -1 -6 BP:_
171 transl_inter NA 657 7 19 chr18 60932220 -1 chr5 142136757 -1 -44 BP:_TE
172 transl_inter NA 828_0 5 3 chr18 66074917 1 chr7 48942925 1 -39 BP:TE_
173 transl_inter NA 604_0 9 2 chr18 70444674 -1 chr7 48942943 1 -33 BP:_
174 transl_inter NA 605_0 9 6 chr18 70444674 -1 chr6 24593189 1 -43 BP:_
175 transl_inter NA 458 21 12 chr18 75846882 -1 chr5 140515479 1 -43 BP:_
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