Mercurial > repos > fubar > jbrowse2
diff conc.awk @ 135:21bb464c1d53 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 78bf7abb931bf3d348837c7211cd3cff32486691
| author | fubar |
|---|---|
| date | Sun, 15 Dec 2024 23:47:40 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/conc.awk Sun Dec 15 23:47:40 2024 +0000 @@ -0,0 +1,57 @@ +#!/bin/awk -f +# input must be paf +# pipe to sort -n -r -k2 +# few duplicates in a 14M row paf converted from a paired bam from VGP mUroPar1 +{ + if (($1,$3,$6,$8) in concordance) + { concordance[$1,$3,$6,$8]++ } + else + { concordance[$1,$3,$6,$8] = 1 } + } + END { + for (k in concordance) {print k, concordance[k]} + } + + + + +## PAF specification +## +## Col Type Description +## 1 string Query sequence name +## 2 int Query sequence length +## 3 int Query start (0-based) +## 4 int Query end (0-based) +## 5 char Relative strand: "+" or "-" +## 6 string Target sequence name +## 7 int Target sequence length +## 8 int Target start on original strand (0-based) +## 9 int Target end on original strand (0-based) +## 10 int Number of residue matches +## 11 int Alignment block length +## 12 int Mapping quality (0-255; 255 for missing) +## +## +## chr10 135711693 0 410000 + chr10 135912142 60 410218 18 410158 32 id:f:0.999395 kc:f:1.01221 +## chr10 135711693 415000 1305000 + chr10 135912142 412798 1295808 17 890000 28 id:f:0.998493 kc:f:0.971423 +## chr10 135711693 1310000 2395000 + chr10 135912142 1300732 2385827 15 1085095 30 id:f:0.998896 kc:f:1.02767 +## chr10 135711693 2400000 25440000 + chr10 135912142 2385341 25429367 18 23044026 29 id:f:0.998716 kc:f:1.04082 +## chr10 135711693 25445000 26735000 + chr10 135912142 25429997 26720864 13 1290867 28 id:f:0.998239 kc:f:1.05397 +## chr10 135711693 26740000 37190000 + chr10 135912142 26722183 37175820 20 10453637 29 id:f:0.998842 kc:f:1.0341 +## chr10 135711693 37185000 37195000 - chr10 135912142 37175523 37185020 13 10000 22 id:f:0.993765 kc:f:1.02691 +## chr10 135711693 37195000 37285000 + chr10 135912142 37181742 37271716 18 90000 27 id:f:0.998021 kc:f:1.02883 +## chr10 135711693 37285000 38650000 + chr10 135912142 37283684 38647751 18 1365000 33 id:f:0.999466 kc:f:1.03306 +## +## #E00526:120:HYYLYCCXY:8:1206:18842:33182 179 chr10:0-100000H1 23129 0 150M chr11:0-100000H2 88118 0 +## #ATTATCTCAGCAGATGCAGAAAAGGCCTTCAATAAAAGACAACACCCCTTCAGGTTAAAAACACTCAATTAACTAGGTGTTCATGGGACATACCTCAAAATAATAAGAGCCATTTATGACAAACCCACAGACAATATCATGCTGAATGGG +## #<<F7---<<JJJFJJF-7<FFJAA7A--<<F<-A7AAA-<F777--F<-77<F--7A-AAJA-<-JJ-JFFA<-<<JAJFF<FF--AJF7FFJ<-JJFFJ7F--AA--J<F-A<JF7<AFFF-<<<FAFF-AFA7F-JF7FJAJJF<AA< NM:i:19 MD:Z:9A28T5T7T2C6T6A6C1A2G1A2A0T2C21C0A16C9A7A1 AS:i:58 +## #XS:i:58 XA:Z:chr10:0-100000H2,-22753,150M,19;chr14:0-100000H1,+33583,150M,19;chr13:0-100000H1,+48625,150M,19;chr13:0-100000H2,+35689,150M,20; E00526:120:HYYLYCCXY:8:2223:11495:36241 147 chr10:0-100000H1 30113 0 150M +## #chr10:0-100000H2 29642 0 AGAGCGCCTCTCCTCCTCCAAAGGAACACAGTTCCTCACCAGCAACAGAACAAAGCTGGACGGAGAATGACTTTGACGAGTTGAGAGAAGAAGGCTTCAGACGATCAAACTACTCCGAGCTACAGGAGGAAATTCAAACCAAAGGCAAAC +## #-<A-FF7--7-<7-A-AJJJAF7JJJFAA-FF-AFFFJJJFJJJFFAAAFJAJJJFJJJJFJFJA7AAFJF<<<A<JF7FJAAAFJJ<JJJ7<JJJJAAJJJFJJFJF<<F7JAAJJFJFJJ<AJAFJJJJJJAJJ7AJF<<-AFFF<A< NM:i:13 MD:Z:26T0G17T0G13T6C11A0C28T5T7G6C18G0 AS:i:89 XS:i:89 +## #XA:Z:chr10:0-100000H2,-29737,150M,13; ... +## #columns: readID chr1 pos1 chr2 pos2 strand1 strand2 +## #EAS139:136:FC706VJ:2:2104:23462:197393 chr1 10000 chr1 20000 + + +## #EAS139:136:FC706VJ:2:8762:23765:128766 chr1 50000 chr1 70000 + + +## #EAS139:136:FC706VJ:2:2342:15343:9863 chr1 60000 chr2 10000 + + +## #EAS139:136:FC706VJ:2:1286:25:275154 chr1 30000 chr3 40000 + - +## \ No newline at end of file