polish: fix the pwd dir
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1 changed files with 16 additions and 17 deletions
33
RGBEPP.sh
33
RGBEPP.sh
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@ -3,24 +3,23 @@
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### Environment Setting
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### Environment Setting
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pkgver=0.0.1
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pkgver=0.0.1
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DirRaw=00_raw
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DirQcTrim=01_fastp
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DirAssembly=02_spades
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DirFasta=03_assemblied
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DirMap=04_diamond
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DirPre=05_pre
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DirSplit=06_split
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DirMerge=07_merge
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DirAlign=08_macse
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PathSplitfsata=~/Downloads/PhD/wes/splitfasta-cpp
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DirHome=$(pwd)
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DirRaw=$DirHome/00_raw
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DirQcTrim=$DirHome/01_fastp
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DirAssembly=$DirHome/02_spades
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DirFasta=$DirHome/03_assemblied
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DirMap=$DirHome/04_diamond
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DirPre=$DirHome/05_pre
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DirSplit=$DirHome/06_split
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DirMerge=$DirHome/07_merge
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DirAlign=$DirHome/08_macse
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PathSplitfsata=/usr/bin/splitfasta-cpp
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PathMacse=/usr/share/java/macse.jar
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PathMacse=/usr/share/java/macse.jar
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PathSortdiamond=/home/guoyi/Downloads/PhD/wes/sortdiamond
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PathSortdiamond=/usr/bin/sortdiamond
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HELP=false
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ARG_C='scaffolds'
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ARG_C='scaffolds'
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#ARG_F='all'
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ARG_M=16
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ARG_M=16
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ARG_T=8
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ARG_T=8
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@ -45,7 +44,7 @@ show_help(){
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\t--sortdiamond\tsortdiamond file path\n \
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\t--sortdiamond\tsortdiamond file path\n \
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\t--splitfasta\tsplitfasta file path\n \
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\t--splitfasta\tsplitfasta file path\n \
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for example: bash $0 -c scaffolds -f all -l list -g genes \ \n \
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for example: bash $0 -c scaffolds -f all -l list -g genes \ \n \
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\t -r Reference.exons.aa.fas \n"
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\t -r reference.aa.fas \n"
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}
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}
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if [ $# -eq 0 ]; then
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if [ $# -eq 0 ]; then
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@ -282,11 +281,11 @@ if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "map" ]; then
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#10: send: End of alignment in subject
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#10: send: End of alignment in subject
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#11: evalue: Expect value
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#11: evalue: Expect value
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#12: bitscore: Bit score
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#12: bitscore: Bit score
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#13: qlen: Query sequence length 比对序列长度
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#13: qlen: Query sequence length
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#14: slen: Subject sequence length
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#14: slen: Subject sequence length
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#15: gaps: Total number of gaps
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#15: gaps: Total number of gaps
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#16: ppos: Percentage of positive - scoring matches
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#16: ppos: Percentage of positive - scoring matches
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#17: qframe: Query frame (frames in ECPP.sh)
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#17: qframe: Query frame (frames in blast?)
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#18: qseq: Aligned part of query sequence
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#18: qseq: Aligned part of query sequence
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done
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done
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