From facfafe4b50cdab2e04a8fde5d58cbdfc8f102c2 Mon Sep 17 00:00:00 2001 From: Guoyi Zhang Date: Fri, 5 Jul 2024 15:14:53 +1000 Subject: [PATCH] polish: fix the pwd dir --- RGBEPP.sh | 33 ++++++++++++++++----------------- 1 file changed, 16 insertions(+), 17 deletions(-) diff --git a/RGBEPP.sh b/RGBEPP.sh index 6c5e87e..80ab2d0 100644 --- a/RGBEPP.sh +++ b/RGBEPP.sh @@ -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