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This repository was archived by the owner on Mar 15, 2024. It is now read-only.

Commit ef3e6e2

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author
[email protected]
committed
fix bug
1 parent cdfaa02 commit ef3e6e2

19 files changed

+25172
-21501
lines changed

‎ClustersPloter.sh‎

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@@ -56,7 +56,9 @@ date
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fi
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ls -l $prefix.prepare.data.log $prefix.plot.log $prefix.prepare.data.error $prefix.plot.error
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ls -ltrh $prefix.prepare.data.log $prefix.plot.log
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echo
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ls -ltrh $prefix.prepare.data.error $prefix.plot.error
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if [ -s $prefix.plot.error ];
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then

‎env.sh‎

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11
export PATH=/zfssz5/BC_PUB/Software/03.Soft_ALL/samtools-1.7:/ifs4/BC_PUB/biosoft/pipeline/newblc/03.Soft_ALL/bcftools-1.3.1:$PATH
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. /zfssz4/BC_COM_P0/F18FTSECKF1389/ASPjisD/software/minimap2/minimap2-2.11_x64-linux/env.sh
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#. /zfssz4/BC_COM_P0/F18FTSECKF1389/ASPjisD/software/minimap2/minimap2-2.11_x64-linux/env.sh

‎example/out1.html‎

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@@ -2024,13 +2024,15 @@ <h1>./out1, you can zoom in/out or drag, thanks https://github.com/ariutta/svg-p
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<g class='myth'><title><tspan>feature_id -> pO83_CORR.NC_017659.1.5460.147060.1.+</tspan>
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<g class='myth'><title><tspan>feature_id -> pO83_CORR.NC_017659.1.5460.147060.1.+</tspan>
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<tspan>track name -> pO83_CORR</tspan>
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<tspan>ref start-end -> NC_017659.1:5460-147060</tspan></title><path id="pO83_CORR.NC_017659.1.5460.147060.1.+" path d="M884.036827195467 149 L884.036827195467 151 L20439.4157223796 151 L20439.4157223796 149 Z" clip-path="url(#cut-pO83_CORR-NC_017659.1-1)" style="fill:orange;stroke:black;stroke-width:0;opacity:0.5"/></g>
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<tspan>ref start-end -> NC_017659.1:5460-147060</tspan></title>
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<path id="pO83_CORR.NC_017659.1.5460.147060.1.+" d="M884.036827195467 149 L884.036827195467 151 L20439.4157223796 151 L20439.4157223796 149 Z" clip-path="url(#cut-pO83_CORR-NC_017659.1-1)" style="fill:orange;stroke:black;stroke-width:0;opacity:0.5"/></g>
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<g class='myth'><title><tspan>feature_id -> pO83_CORR.indel.NC_017659.1.fake.5460.147060.1.+</tspan>
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<g class='myth'><title><tspan>feature_id -> pO83_CORR.indel.NC_017659.1.fake.5460.147060.1.+</tspan>
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<tspan>track name -> pO83_CORR.indel</tspan>
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<tspan>ref start-end -> NC_017659.1.fake:5460-147060</tspan></title><path id="pO83_CORR.indel.NC_017659.1.fake.5460.147060.1.+" path d="M649.401558073654 349 L649.401558073654 351 L20204.7804532578 351 L20204.7804532578 349 Z" clip-path="url(#cut-pO83_CORR.indel-NC_017659.1.fake-1)" style="fill:orange;stroke:black;stroke-width:0;opacity:0.5"/></g>
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<tspan>ref start-end -> NC_017659.1.fake:5460-147060</tspan></title>
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<path id="pO83_CORR.indel.NC_017659.1.fake.5460.147060.1.+" d="M649.401558073654 349 L649.401558073654 351 L20204.7804532578 351 L20204.7804532578 349 Z" clip-path="url(#cut-pO83_CORR.indel-NC_017659.1.fake-1)" style="fill:orange;stroke:black;stroke-width:0;opacity:0.5"/></g>
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<g class='myth'><title><tspan>pO83_CORR.NC_017659.1.5460.147060.1.+ -> pO83_CORR.indel.NC_017659.1.fake.5460.147060.1.+</tspan>
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<tspan>query -> NC_017659.1.fake:5460:147060</tspan>
@@ -2045,13 +2047,15 @@ <h1>./out1, you can zoom in/out or drag, thanks https://github.com/ariutta/svg-p
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<g class='myth'><title><tspan>feature_id -> pO83_CORR.NC_017659.1.2101.5468.1.+</tspan>
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<g class='myth'><title><tspan>feature_id -> pO83_CORR.NC_017659.1.2101.5468.1.+</tspan>
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<tspan>track name -> pO83_CORR</tspan>
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<tspan>ref start-end -> NC_017659.1:2101-5468</tspan></title><polygon id="pO83_CORR.NC_017659.1.2101.5468.1.+" points="420.152266288952,149 420.152266288952,151 885.279745042493,151 885.279745042493,149 " style="fill:orange;stroke:black;stroke-width:0;opacity:0.5"/></g>
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<tspan>ref start-end -> NC_017659.1:2101-5468</tspan></title>
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<polygon id="pO83_CORR.NC_017659.1.2101.5468.1.+" points="420.152266288952,149 420.152266288952,151 885.279745042493,151 885.279745042493,149 " style="fill:orange;stroke:black;stroke-width:0;opacity:0.5"/></g>
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<g class='myth'><title><tspan>feature_id -> pO83_CORR.indel.NC_017659.1.fake.1891.5257.1.+</tspan>
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<g class='myth'><title><tspan>feature_id -> pO83_CORR.indel.NC_017659.1.fake.1891.5257.1.+</tspan>
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<tspan>track name -> pO83_CORR.indel</tspan>
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<tspan>ref start-end -> NC_017659.1.fake:1891-5257</tspan></title><polygon id="pO83_CORR.indel.NC_017659.1.fake.1891.5257.1.+" points="156.515580736544,349 156.515580736544,351 621.504957507082,351 621.504957507082,349 " style="fill:orange;stroke:black;stroke-width:0;opacity:0.5"/></g>
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<tspan>ref start-end -> NC_017659.1.fake:1891-5257</tspan></title>
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<polygon id="pO83_CORR.indel.NC_017659.1.fake.1891.5257.1.+" points="156.515580736544,349 156.515580736544,351 621.504957507082,351 621.504957507082,349 " style="fill:orange;stroke:black;stroke-width:0;opacity:0.5"/></g>
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<g class='myth'><title><tspan>pO83_CORR.NC_017659.1.2101.5468.1.+ -> pO83_CORR.indel.NC_017659.1.fake.1891.5257.1.+</tspan>
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<tspan>query -> NC_017659.1.fake:1891:5257</tspan>
@@ -2065,13 +2069,15 @@ <h1>./out1, you can zoom in/out or drag, thanks https://github.com/ariutta/svg-p
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<g class='myth'><title><tspan>feature_id -> pO83_CORR.NC_017659.1.1.1898.1.+</tspan>
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<g class='myth'><title><tspan>feature_id -> pO83_CORR.NC_017659.1.1.1898.1.+</tspan>
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<tspan>track name -> pO83_CORR</tspan>
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<tspan>ref start-end -> NC_017659.1:1-1898</tspan></title><polygon id="pO83_CORR.NC_017659.1.1.1898.1.+" points="130.138101983003,149 130.138101983003,151 392.25566572238,151 392.25566572238,149 " style="fill:orange;stroke:black;stroke-width:0;opacity:0.5"/></g>
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<tspan>ref start-end -> NC_017659.1:1-1898</tspan></title>
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<polygon id="pO83_CORR.NC_017659.1.1.1898.1.+" points="130.138101983003,149 130.138101983003,151 392.25566572238,151 392.25566572238,149 " style="fill:orange;stroke:black;stroke-width:0;opacity:0.5"/></g>
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<g class='myth'><title><tspan>feature_id -> pO83_CORR.indel.NC_017659.1.fake.1.1898.1.+</tspan>
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<g class='myth'><title><tspan>feature_id -> pO83_CORR.indel.NC_017659.1.fake.1.1898.1.+</tspan>
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<tspan>track name -> pO83_CORR.indel</tspan>
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<tspan>ref start-end -> NC_017659.1.fake:1-1898</tspan></title><path id="pO83_CORR.indel.NC_017659.1.fake.1.1898.1.+" path d="M-104.49716713881 349 L-104.49716713881 351 L157.620396600567 351 L157.620396600567 349 Z" clip-path="url(#cut-pO83_CORR.indel-NC_017659.1.fake-1)" style="fill:orange;stroke:black;stroke-width:0;opacity:0.5"/></g>
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<tspan>ref start-end -> NC_017659.1.fake:1-1898</tspan></title>
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<path id="pO83_CORR.indel.NC_017659.1.fake.1.1898.1.+" d="M-104.49716713881 349 L-104.49716713881 351 L157.620396600567 351 L157.620396600567 349 Z" clip-path="url(#cut-pO83_CORR.indel-NC_017659.1.fake-1)" style="fill:orange;stroke:black;stroke-width:0;opacity:0.5"/></g>
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<g class='myth'><title><tspan>pO83_CORR.NC_017659.1.1.1898.1.+ -> pO83_CORR.indel.NC_017659.1.fake.1.1898.1.+</tspan>
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<tspan>query -> NC_017659.1.fake:1:1898</tspan>
@@ -2086,13 +2092,15 @@ <h1>./out1, you can zoom in/out or drag, thanks https://github.com/ariutta/svg-p
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<g class='myth'><title><tspan>feature_id -> pO83_CORR.NC_017659.1.1891.2100.1.+</tspan>
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<g class='myth'><title><tspan>feature_id -> pO83_CORR.NC_017659.1.1891.2100.1.+</tspan>
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<tspan>track name -> pO83_CORR</tspan>
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<tspan>ref start-end -> NC_017659.1:1891-2100</tspan></title><polygon id="pO83_CORR.NC_017659.1.1891.2100.1.+" points="391.150849858357,149 391.150849858357,151 420.152266288952,151 420.152266288952,149 " style="fill:orange;stroke:black;stroke-width:0;opacity:0.5"/></g>
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<tspan>ref start-end -> NC_017659.1:1891-2100</tspan></title>
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<polygon id="pO83_CORR.NC_017659.1.1891.2100.1.+" points="391.150849858357,149 391.150849858357,151 420.152266288952,151 420.152266288952,149 " style="fill:orange;stroke:black;stroke-width:0;opacity:0.5"/></g>
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<g class='myth'><title><tspan>feature_id -> pO83_CORR.indel.NC_017659.1.fake.5251.5460.1.+</tspan>
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<g class='myth'><title><tspan>feature_id -> pO83_CORR.indel.NC_017659.1.fake.5251.5460.1.+</tspan>
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<tspan>track name -> pO83_CORR.indel</tspan>
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<tspan>ref start-end -> NC_017659.1.fake:5251-5460</tspan></title><polygon id="pO83_CORR.indel.NC_017659.1.fake.5251.5460.1.+" points="620.538243626062,349 620.538243626062,351 649.539660056657,351 649.539660056657,349 " style="fill:orange;stroke:black;stroke-width:0;opacity:0.5"/></g>
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<tspan>ref start-end -> NC_017659.1.fake:5251-5460</tspan></title>
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<polygon id="pO83_CORR.indel.NC_017659.1.fake.5251.5460.1.+" points="620.538243626062,349 620.538243626062,351 649.539660056657,351 649.539660056657,349 " style="fill:orange;stroke:black;stroke-width:0;opacity:0.5"/></g>
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<g class='myth'><title><tspan>pO83_CORR.NC_017659.1.1891.2100.1.+ -> pO83_CORR.indel.NC_017659.1.fake.5251.5460.1.+</tspan>
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<tspan>query -> NC_017659.1.fake:5251:5460</tspan>

‎example/out1.notitle.svg‎

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‎example/out1.plot.log‎

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Original file line numberDiff line numberDiff line change
@@ -110,6 +110,10 @@ draw feature_id = pO83_CORR.indel.NC_017659.1.fake.5460.147060.1.+
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plot crosslink pair pO83_CORR.indel.NC_017659.1.fake.5251.5460.1.+,pO83_CORR.NC_017659.1.1891.2100.1.+, 1th -> 4
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plot crosslink pair pO83_CORR.indel.NC_017659.1.fake.1891.5257.1.+,pO83_CORR.NC_017659.1.2101.5468.1.+, 2th -> 4
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plot crosslink pair pO83_CORR.indel.NC_017659.1.fake.5460.147060.1.+,pO83_CORR.NC_017659.1.5460.147060.1.+, 3th -> 4
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plot crosslink pair pO83_CORR.indel.NC_017659.1.fake.1.1898.1.+,pO83_CORR.NC_017659.1.1.1898.1.+, 4th -> 4
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lengend start
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scale_display is yes
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disply scale

‎example/out1.prepare.data.error.tmp‎

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Original file line numberDiff line numberDiff line change
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+ cat out1.synteny.setting.conf
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+ cat out1.synteny.crosslink
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+ cat out1.pO83_CORR.out1.synteny.gff out1.pO83_CORR.indel.out1.synteny.gff
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+ sort -u
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+ awk -F ' ' '{print $3}'
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+ sort -u
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+ sed -r 's/^(pO83_CORR\s.*\.gff)\s/\1,out1.pO83_CORR.out1.synteny.gff\t/' tracks.1.list
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+ cp tracks.1.list.out1 tracks.1.list.out1.tmp
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+ sed -r 's/^(pO83_CORR.indel\s.*\.gff)\s/\1,out1.pO83_CORR.indel.out1.synteny.gff\t/' tracks.1.list.out1.tmp

‎example/out1.svg‎

Lines changed: 24 additions & 16 deletions
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