malacology/RGBEPP
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polish: fix the pwd dir

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kuoi 2024-07-05 15:14:53 +10:00
parent 32c423a283
commit facfafe4b5
1 changed files with 16 additions and 17 deletions
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33
RGBEPP.sh
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@ -3,24 +3,23 @@
### Environment Setting
pkgver=0.0.1
DirRaw=00_raw
DirQcTrim=01_fastp
DirAssembly=02_spades
DirFasta=03_assemblied
DirMap=04_diamond
DirPre=05_pre
DirSplit=06_split
DirMerge=07_merge
DirAlign=08_macse
PathSplitfsata=~/Downloads/PhD/wes/splitfasta-cpp
DirHome=$(pwd)
DirRaw=$DirHome/00_raw
DirQcTrim=$DirHome/01_fastp
DirAssembly=$DirHome/02_spades
DirFasta=$DirHome/03_assemblied
DirMap=$DirHome/04_diamond
DirPre=$DirHome/05_pre
DirSplit=$DirHome/06_split
DirMerge=$DirHome/07_merge
DirAlign=$DirHome/08_macse
PathSplitfsata=/usr/bin/splitfasta-cpp
PathMacse=/usr/share/java/macse.jar
PathSortdiamond=/home/guoyi/Downloads/PhD/wes/sortdiamond
HELP=false
PathSortdiamond=/usr/bin/sortdiamond
ARG_C='scaffolds'
#ARG_F='all'
ARG_M=16
ARG_T=8
@ -45,7 +44,7 @@ show_help(){
\t--sortdiamond\tsortdiamond file path\n \
\t--splitfasta\tsplitfasta file path\n \
for example: bash $0 -c scaffolds -f all -l list -g genes \ \n \
\t -r Reference.exons.aa.fas \n"
\t -r reference.aa.fas \n"
}
if [ $# -eq 0 ]; then
@ -282,11 +281,11 @@ if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "map" ]; then
#10: send: End of alignment in subject
#11: evalue: Expect value
#12: bitscore: Bit score
#13: qlen: Query sequence length 比对序列长度
#13: qlen: Query sequence length
#14: slen: Subject sequence length
#15: gaps: Total number of gaps
#16: ppos: Percentage of positive - scoring matches
#17: qframe: Query frame (frames in ECPP.sh)
#17: qframe: Query frame (frames in blast?)
#18: qseq: Aligned part of query sequence
done