1# get dir size
2du -hs dirname
3# get disk space
4df -h
5

1find /where/to/find/ -type f -name "*.sh"

1# get the nth line from a file, print a specific line from a file
2head -n filename | tail -1
3sed 'NUMq;d' filename

 1# create a tar.gz archive from a dir
 2tar -zcvf tar-archive-name.tar.gz source-folder-name
 3# preserve permissions
 4tar -pcvzf tar-archive-name.tar.gz source-folder-name
 5
 6
 7# extract a tar.gz compressed archive, switch the ‘c’ flag to an ‘x’ to extract
 8tar -zxvf tar-archive-name.tar.gz
 9# permission preserving condition
10tar -pxvzf tar-archive-name.tar.gz

1ls -la . | grep "\->" | awk '{print $9}' | xargs rm

1shopt -s nullglob # set the counting start from 1 instead of 0
2num_files=(*)
3num_files=${#num_files[@]}
4echo #num_files

1export PATH=$PATH:/place/with/the/file

 1
 2# add something to end of all header lines
 3sed 's/>.*/&SUFFIX/' file.fa > outfile.fa
 4
 5#clean up a fasta file so only first column of the header remain
 6awk '{print $1}' file.fa > output.fa
 7
 8# count the number of sequences in fasta file
 9grep -c '>' file.fa
10grep '>' file.fa | wc -l
11

 1#!/usr/bin/env bash
 2
 3genomeList='ppopv1 p717main p717alt pPtriNisquallyV4 pPdelWV94 pPtriStettler pSpurV5 pSpurFC pAtha pGmax pMtru pEgra pPper pSlyc pVvin pSbic pSita pOsat'
 4
 5ppopv1='/work/cjtlab/popv1/Poptr1_1_GeneModels_GeneCatalog_frozen20080522_aa.fasta'
 6p717main='/work/cjtlab/717genomeV2/annotation/main.prelim.v2.1/PtremulaxPopulusalbav2.1p.primaryTrs.pep.fa'
 7p717alt='/work/cjtlab/717genomeV2/annotation/alt.prelim.v2.1/PtremulaxPopulusalbaaltv2.1.primaryTrs.pep.fa'
 8pPtriNisquallyV4='/work/cjtlab/NisquallyV4/annotation/Ptrichocarpav4.1g.primaryTrs.pep.fa'
 9pPdelWV94='/work/cjtlab/Pdelt/PdeltoidesWV94_445_v2.1/PdeltoidesWV94_445_v2.1.protein_primaryTranscriptOnly.fa'
10pPtriStettler='/work/cjtlab/Database/Ptri_stettlerV1.1/annotation/PtrichocarpaStettler14_532_v1.1.protein.fa'
11pSpurV5='/work/cjtlab/Spurpurea94006/Spurpurea_519_v5.1.protein.fa'
12pSpurFC='/work/cjtlab/SpurpureaFC/annotation/SpurpureaFishCreek_518_v3.1.protein.fa'
13pAtha='/work/cjtlab/Database/Atha/annotation/Athaliana_447_Araport11.protein.fa'
14pGmax='/work/cjtlab/Database/Gmax/annotation/Gmax_275_Wm82.a2.v1.protein.fa'
15pMtru='/work/cjtlab/Database/Mtru/annotation/Mtruncatula_285_Mt4.0v1.protein.fa'
16pEgra='/work/cjtlab/Database/Egrandis/v2.0/annotation/Egrandis_297_v2.0.protein.fa'
17pPper='/work/cjtlab/Database/Pper/annotation/Ppersica_298_v2.1.protein.fa'
18pSlyc='/work/cjtlab/Database/Slycopersicum/ITAG3.2/annotation/Slycopersicum_514_ITAG3.2.protein.fa'
19pVvin='/work/cjtlab/Database/Vvinifera/v2.1/annotation/Vvinifera_457_v2.1.protein.fa'
20pSbic='/work/cjtlab/Database/Sbicolor/v3.1.1/annotation/Sbicolor_454_v3.1.1.protein.fa'
21pSita='/work/cjtlab/Database/Sitalica/v2.2/annotation/Sitalica_312_v2.2.protein.fa'
22pOsat='/work/cjtlab/Database/Osativa/v7.0/annotation/Osativa_323_v7.0.protein.fa'
23
24echo 'genome path loaded'
25

 1#!/usr/bin/env bash
 2source /work/cjtlab/scripts/bash/genome_path_var.sh
 3
 4
 5
 6for species in $genomeList
 7do
 8	eval 'cp $'{$species}' fastaFiles'
 9	eval 'hmmscan --tblout $species-tbl.tab --domtblout $species-domtbl.tab --pfamtblout $species-pfamtbl.tab /db/pfam/27.0-3.1b1/Pfam-A.hmm $'{$species}
10
11done

 1#!/bin/bash
 2# only if you have bash 4 in your CentOS system
 3shopt -s globstar
 4for file in **/*
 5do
 6    slash=${file//[^\/]}
 7    case "${#slash}" in
 8        0) echo "|-- ${file}";;
 9        1) echo "|   |--  ${file}";;
10        2) echo "|   |   |--  ${file}";;
11    esac
12done

1#!/bin/bash
2for filename in /Data/*.txt; do
3    for ((i=0; i<=3; i++)); do
4        ./MyProgram.exe "$filename" "Logs/$(basename "$filename" .txt)_Log$i.txt"
5    done
6done

 1
 2# extract fasta file id
 3grep -o -E "^>\w+" file.fasta | tr -d ">"
 4
 5# Return the lengths of all the sequences in a multifasta
 6
 7falens(){
 8awk '/^>/ {if (seqlen){print seqlen}; print ;seqlen=0;next; } { seqlen += length($0)}END{print seqlen}' $1
 9}
10
11# Remove duplicated fastas in a multifasta:
12
13dedupe(){
14cat $1 | awk '!_[$0]++'
15}
16
17# Merge a multifasta into a single fasta sequence (remove all but the first header, and deal with newlines):
18
19fastcat(){
20cat $1 | sed -e '1!{/^>.*/d;}' | sed  ':a;N;$!ba;s/\n//2g'
21}
22
23# split a multifasta into separate files
24splitfa(){
25i=1;
26while read line ; do
27  if [ ${line:0:1} == ">" ] ; then
28    header="$line"
29    echo "$header" >> seq"${i}".fasta
30  else
31    seq="$line"
32    echo "$seq" >> seq"${i}".fasta
33    ((i++))
34  fi
35done < $1
36}
37
38# get the nucleotide count for all sequences in a multi sequence file
39echo -e "seq_id\tA\tU\tG\tC"; while read line; do echo $line | grep ">" | sed 's/>//g'; for i in A U G C;do echo $line | grep -v ">" | grep -o $i | wc -l | grep -v "^0"; done; done < your_fasta_file.fa | paste - - - - -
40
41# linearize the complete fasta file
42while read line; do
43  if [ "${line:0:1}" == ">" ]; then 
44    echo -e "\n"$line;
45  else 
46    echo $line | tr -d '\n' ; 
47  fi; 
48done < input.fasta | sed '/^--$/d' > output.fasta
49
50# or 
51awk '{if(NR==1) {print $0} else {if($0 ~ /^>/) {print "\n"$0} else {printf $0}}}' input.fasta > output.fasta
52
53# and then pick up certain id with the following cmd
54grep -A1 'Q15049' output.fasta
55