Basic awk & sed

Extract fields 2, 4, and 5 from file.txt:

awk '{print $2,$4,$5}' input.txt

Print each line where the 5th field is equal to ‘abc123’:

awk '$5 == "abc123"' file.txt

Print each line where the 5th field is not equal to ‘abc123’:

awk '$5 != "abc123"' file.txt

Print each line whose 7th field matches the regular expression:

awk '$7  ~ /^[a-f]/' file.txt

Print each line whose 7th field does not match the regular expression:

awk '$7 !~ /^[a-f]/' file.txt

Get unique entries in file.txt based on column 2 (takes only the first instance):

awk '!arr[$2]++' file.txt

Print rows where column 3 is larger than column 5 in file.txt:

awk '$3>$5' file.txt

Sum column 1 of file.txt:

awk '{sum+=$1} END {print sum}' file.txt

Compute the mean of column 2:

awk '{x+=$2}END{print x/NR}' file.txt

Replace all occurances of foo with bar in file.txt:

sed 's/foo/bar/g' file.txt

Trim leading whitespaces and tabulations in file.txt:

sed 's/^[ \t]*//' file.txt

Trim trailing whitespaces and tabulations in file.txt:

sed 's/[ \t]*$//' file.txt

Trim leading and trailing whitespaces and tabulations in file.txt:

sed 's/^[ \t]*//;s/[ \t]*$//' file.txt

Delete blank lines in file.txt:

sed '/^$/d' file.txt

Delete everything after and including a line containing EndOfUsefulData:

sed -n '/EndOfUsefulData/,$!p' file.txt

awk & sed for bioinformatics

Returns all lines on Chr 1 between 1MB and 2MB in file.txt. (assumes) chromosome in column 1 and position in column 3 (this same concept can be used to return only variants that above specific allele frequencies):

cat file.txt | awk '$1=="1"' | awk '$3>=1000000' | awk '$3<=2000000'

Basic sequence statistics. Print total number of reads, total number unique reads, percentage of unique reads, most abundant sequence, its frequency, and percentage of total in file.fq:

cat myfile.fq | awk '((NR-2)%4==0){read=$1;total++;count[read]++}END{for(read in count){if(!max||count[read]>max) {max=count[read];maxRead=read};if(count[read]==1){unique++}};print total,unique,unique*100/total,maxRead,count[maxRead],count[maxRead]*100/total}'

Convert .bam back to .fastq:

samtools view file.bam | awk 'BEGIN {FS="\t"} {print "@" $1 "\n" $10 "\n+\n" $11}' > file.fq

Keep only top bit scores in blast hits (best bit score only):

awk '{ if(!x[$1]++) {print $0; bitscore=($14-1)} else { if($14>bitscore) print $0} }' blastout.txt

Keep only top bit scores in blast hits (5 less than the top):

awk '{ if(!x[$1]++) {print $0; bitscore=($14-6)} else { if($14>bitscore) print $0} }' blastout.txt

Split a multi-FASTA file into individual FASTA files:

awk '/^>/{s=++d".fa"} {print > s}' multi.fa

Output sequence name and its length for every sequence within a fasta file:

cat file.fa | awk '$0 ~ ">" {print c; c=0;printf substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END { print c; }'

Convert a FASTQ file to FASTA:

sed -n '1~4s/^@/>/p;2~4p' file.fq > file.fa

Extract every 4th line starting at the second line (extract the sequence from FASTQ file):

sed -n '2~4p' file.fq

Print everything except the first line

awk 'NR>1' input.txt

Print rows 20-80:

awk 'NR>=20&&NR<=80' input.txt

Calculate the sum of column 2 and 3 and put it at the end of a row:

awk '{print $0,$2+$3}' input.txt

Calculate the mean length of reads in a fastq file:

awk 'NR%4==2{sum+=length($0)}END{print sum/(NR/4)}' input.fastq

Convert a VCF file to a BED file

sed -e 's/chr//' file.vcf | awk '{OFS="\t"; if (!/^#/){print $1,$2-1,$2,$4"/"$5,"+"}}'

Create a tab-delimited transcript-to-gene mapping table from a GENCODE GFF. The substr(x,s,n) returns n characters from string x starting from position s. This gets rid of the quotes and semicolon.

bioawk -c gff '$feature=="transcript" {print $group}' gencode.v28.annotation.gtf | awk -F ' ' '{print substr($4,2,length($4)-3) "\t" substr($2,2,length($2)-3)}' > txp2gene.tsv

extract specific reads from fastq file according to reads name :

zcat a.fastq.gz | awk 'BEGIN{RS="@";FS="\n"}; $1~/readsName/{print $2; exit}'

count missing sample in vcf file per line:

bcftools query -f '[%GT\t]\n' a.bcf |  awk '{miss=0};{for (x=1; x<=NF; x++) if ($x=="./.") {miss+=1}};{print miss}' > nmiss.count

sort, uniq, cut, etc.

Number each line in file.txt:

cat -n file.txt

Count the number of unique lines in file.txt

cat file.txt | sort -u | wc -l

Find lines shared by 2 files (assumes lines within file1 and file2 are unique; pipe to wd -l to count the number of lines shared):

sort file1 file2 | uniq -d

# Safer

sort -u file1 > a

sort -u file2 > b

sort a b | uniq -d

# Use comm

comm -12 file1 file2

Sort numerically (with logs) (g) by column (k) 9:

sort -gk9 file.txt

Find the most common strings in column 2:

cut -f2 file.txt | sort | uniq -c | sort -k1nr | head

Pick 10 random lines from a file:

shuf file.txt | head -n 10

Print all possible 3mer DNA sequence combinations:

echo {A,C,T,G}{A,C,T,G}{A,C,T,G}

Untangle an interleaved paired-end FASTQ file. If a FASTQ file has paired-end reads intermingled, and you want to separate them into separate /1 and /2 files, and assuming the /1 reads precede the /2 reads:

cat interleaved.fq |paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" > deinterleaved_1.fq) | cut -f 5-8 | tr "\t" "\n" > deinterleaved_2.fq

Take a fasta file with a bunch of short scaffolds, e.g., labeled >Scaffold12345, remove them, and write a new fasta without them:

samtools faidx genome.fa && grep -v Scaffold genome.fa.fai | cut -f1 | xargs -n1 samtools faidx genome.fa > genome.noscaffolds.fa

Display hidden control characters:

python -c "f = open('file.txt', 'r'); f.seek(0); file = f.readlines(); print file" 

find, xargs, and GNU parallel

Download GNU parallel at https://www.gnu.org/software/parallel/.

Search for .bam files anywhere in the current directory recursively:

find . -name "*.bam"

Delete all .bam files (Irreversible: use with caution! Confirm list BEFORE deleting):

find . -name "*.bam" | xargs rm

Rename all .txt files to .bak (backup *.txt before doing something else to them, for example):

find . -name "*.txt" | sed "s/\.txt$//" | xargs -i echo mv {}.txt {}.bak | sh

Chastity filter raw Illumina data (grep reads containing :N:, append (-A) the three lines after the match containing the sequence and quality info, and write a new filtered fastq file):

find *fq | parallel "cat {} | grep -A 3 '^@.*[^:]*:N:[^:]*:' | grep -v '^\-\-$' > {}.filt.fq"

Run FASTQC in parallel 12 jobs at a time:

find *.fq | parallel -j 12 "fastqc {} --outdir ."

Index your bam files in parallel, but only echo the commands (--dry-run) rather than actually running them:

find *.bam | parallel --dry-run 'samtools index {}'

seqtk

Download seqtk at https://github.com/lh3/seqtk. Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.

Convert FASTQ to FASTA:

seqtk seq -a in.fq.gz > out.fa

Convert ILLUMINA 1.3+ FASTQ to FASTA and mask bases with quality lower than 20 to lowercases (the 1st command line) or to N (the 2nd):

seqtk seq -aQ64 -q20 in.fq > out.fa

seqtk seq -aQ64 -q20 -n N in.fq > out.fa

Fold long FASTA/Q lines and remove FASTA/Q comments:

seqtk seq -Cl60 in.fa > out.fa

Convert multi-line FASTQ to 4-line FASTQ:

seqtk seq -l0 in.fq > out.fq

Reverse complement FASTA/Q:

seqtk seq -r in.fq > out.fq

Extract sequences with names in file name.lst, one sequence name per line:

seqtk subseq in.fq name.lst > out.fq

Extract sequences in regions contained in file reg.bed:

seqtk subseq in.fa reg.bed > out.fa

Mask regions in reg.bed to lowercases:

seqtk seq -M reg.bed in.fa > out.fa

Subsample 10000 read pairs from two large paired FASTQ files (remember to use the same random seed to keep pairing):

seqtk sample -s100 read1.fq 10000 > sub1.fq

seqtk sample -s100 read2.fq 10000 > sub2.fq

Trim low-quality bases from both ends using the Phred algorithm:

seqtk trimfq in.fq > out.fq

Trim 5bp from the left end of each read and 10bp from the right end:

seqtk trimfq -b 5 -e 10 in.fa > out.fa

Untangle an interleaved paired-end FASTQ file. If a FASTQ file has paired-end reads intermingled, and you want to separate them into separate /1 and /2 files, and assuming the /1 reads precede the /2 reads:

seqtk seq -l0 -1 interleaved.fq > deinterleaved_1.fq

seqtk seq -l0 -2 interleaved.fq > deinterleaved_2.fq

GFF3 Annotations

Print all sequences annotated in a GFF3 file.

cut -s -f 1,9 yourannots.gff3 | grep $'\t' | cut -f 1 | sort | uniq

Determine all feature types annotated in a GFF3 file.

grep -v '^#' yourannots.gff3 | cut -s -f 3 | sort | uniq

Determine the number of genes annotated in a GFF3 file.

grep -c $'\tgene\t' yourannots.gff3

Extract all gene IDs from a GFF3 file.

grep $'\tgene\t' yourannots.gff3 | perl -ne '/ID=([^;]+)/ and printf("%s\n", $1)'

Print length of each gene in a GFF3 file.

grep $'\tgene\t' yourannots.gff3 | cut -s -f 4,5 | perl -ne '@v = split(/\t/); printf("%d\n", $v[1] - $v[0] + 1)'

FASTA header lines to GFF format (assuming the length is in the header as an appended "_length" as in Velvet assembled transcripts):

grep '>' file.fasta | awk -F "_" 'BEGIN{i=1; print "##gff-version 3"}{ print $0"\t BLAT\tEXON\t1\t"$10"\t95\t+\t.\tgene_id="$0";transcript_id=Transcript_"i;i++ }' > file.gff

Other generally useful aliases for your .bashrc

Get a prompt that looks like user@hostname:/full/path/cwd/:$

export PS1="\u@\h:\w\\$ "

Never type cd ../../.. again (or use autojump, which enables you to navigate the filesystem faster):

alias ..='cd ..'

alias ...='cd ../../'

alias ....='cd ../../../'

alias .....='cd ../../../../'

alias ......='cd ../../../../../'

Browse 'up' and 'down'

alias u='clear; cd ../; pwd; ls -lhGgo'

alias d='clear; cd -; ls -lhGgo'

Ask before removing or overwriting files:

alias mv="mv -i"

alias cp="cp -i"  

alias rm="rm -i"

My favorite ls aliases:

alias ls="ls -1p --color=auto"

alias l="ls -lhGgo"

alias ll="ls -lh"

alias la="ls -lhGgoA"

alias lt="ls -lhGgotr"

alias lS="ls -lhGgoSr"

alias l.="ls -lhGgod .*"

alias lhead="ls -lhGgo | head"

alias ltail="ls -lhGgo | tail"

alias lmore='ls -lhGgo | more'

Use cut on space- or comma- delimited files:

alias cuts="cut -d \" \""

alias cutc="cut -d \",\""

Pack and unpack tar.gz files:

alias tarup="tar -zcf"

alias tardown="tar -zxf"

Or use a generalized extract function:

# as suggested by Mendel Cooper in "Advanced Bash Scripting Guide"

extract () {

   if [ -f $1 ] ; then

       case $1 in

        *.tar.bz2)      tar xvjf $1 ;;

        *.tar.gz)       tar xvzf $1 ;;

        *.tar.xz)       tar Jxvf $1 ;;

        *.bz2)          bunzip2 $1 ;;

        *.rar)          unrar x $1 ;;

        *.gz)           gunzip $1 ;;

        *.tar)          tar xvf $1 ;;

        *.tbz2)         tar xvjf $1 ;;

        *.tgz)          tar xvzf $1 ;;

        *.zip)          unzip $1 ;;

        *.Z)            uncompress $1 ;;

        *.7z)           7z x $1 ;;

        *)              echo "don't know how to extract '$1'..." ;;

       esac

   else

       echo "'$1' is not a valid file!"

   fi

}

Use mcd to create a directory and cd to it simultaneously:

function mcd { mkdir -p "$1" && cd "$1";}

Go up to the parent directory and list it's contents:

alias u="cd ..;ls"

Make grep pretty:

alias grep="grep --color=auto"

Refresh your .bashrc:

alias refresh="source ~/.bashrc"

Edit your .bashrc:

alias eb="vi ~/.bashrc"

Common typos:

alias mf="mv -i"

alias mroe="more"

alias c='clear'

alias emacs='vim'

Show your $PATH in a prettier format:

alias showpath='echo $PATH | tr ":" "\n" | nl'

Use pandoc to convert a markdown file to PDF:

# USAGE: mdpdf document.md document.md.pdf

alias mdpdf="pandoc -s -V geometry:margin=1in -V documentclass:article -V fontsize=12pt"

Find text in any file (ft "mytext" *.txt):

function ft { find . -name "$2" -exec grep -il "$1" {} \;; }

Etc

Run the last command as root:

sudo !!

Place the argument of the most recent command on the shell:

'ALT+.' or '<ESC> .'

Type partial command, kill this command, check something you forgot, yank the command, resume typing:

<CTRL+u> [...] <CTRL+y>

Jump to a directory, execute a command, and jump back to the current directory:

(cd /tmp && ls)

Stopwatch (Enter or ctrl-d to stop):

time read

Create a script of the last executed command:

echo "!!" > foo.sh

Reuse all parameter of the previous command line:

!*

List or delete all files in a folder that don't match a certain file extension (e.g., list things that are not compressed; remove anything that is not a .foo or .bar file):

ls !(*.gz)

rm !(*.foo|*.bar)

Insert the last command without the last argument:

!:- <new_last_argument>

Rapidly invoke an editor to write a long, complex, or tricky command:

fc

Print a specific line (e.g. line 42) from a file:

sed -n 42p <file>

Terminate a frozen SSH session (enter a new line, type the ~ key then the . key):

[ENTER]~.

Remove blank lines from a file using grep and save output to new file:

grep . filename > newfilename

Find large files (e.g., >500M):

find . -type f -size +500M

Exclude a column with cut (e.g., all but the 5th field in a tab-delimited file):

cut -f5 --complement

Find files containing text (-l outputs only the file names, -i ignores the case -r descends into subdirectories)

grep -lir "some text" *