Bioinformatics one-liners

A collection of bioinformatics one-liners that I used quite often.

Reverse complement sequence

echo <SEQUENCE> | perl -nle 'print map{$_ =~ tr/ACGT/TGCA/; $_} reverse split("",$_)'

Combine multiple rows based on the same column value

awk '$1!=p{if(p)print s; p=$1; s=$0; next}{sub(p,x); s=s $0} END{print s}'

Split multiple columns into two columns with common first column

awk -v OFS='\t' '{for (i=2;i<=NF;i++) print $1,$i}'

Get a range of text

awk '/START-WORD/, /END-WORD/' input > output
sed -n "/START-WORD-HERE/,/END-WORD-HERE/p" input > output
sed "/START-WORD-HERE/,/END-WORD-HERE/!d" input > output

Get a specific sequence from a fasta file

sed '/>Smp_000020.1/,/>/!d' <fasta file>| awk '/>/{i++}i==1'
sed -n '/Smp_000020/,/>/p' <fasta file> | sed '$d' 

Convert pdf to png

mogrify -verbose -density 300 -resize 800 -format png *.pdf

Remove blank lines

grep -v -e '^$'    
sed '/^$/d'

Call Artemis

bsub -q yesterday -n2 -o o -e e -R "span[hosts=1]" -M 2000 -R 'select[mem>2000] rusage[mem=2000]' -I art -Dshow_cov_plot <FILE>

Sum and Mean of column 1

awk '{sum+=$1} END {print sum}'
awk '{x+=$1}END{print x/NR}'

Print lines whose 5th field does not match the regular expression

awk '$5 !~ /^Smp_[0-9\{6\}]/'
awk '$5 != "STRING"'
awk 'substr($5,1,10) == "STRING"' 

Trim leading and trailing whitespaces and tabulations

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

Output sequence name and length

cat seq.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

Sort gff file for tabix

sort -k1,1 -k4,4 -V

Number each line

cat -n FILE 
less -N FILE

Print file name and content

grep . *.txt

Extract all gene IDs from a GFF3 file

cat <GFF3 FILE> | grep $'\tgene\t' | perl -ne '/ID=([^;]+)/ and printf("%s\n", $1)'

Print line 20 content

sed -n 20p FILE
awk '(NR==20){print $0}' FILE

Omit 1st line and print lines with 4 columns

awk 'NR > 1 && NF == 4' FILE

NCBI Blast+

blastp -query <> -db <> -num_alignments 5 -num_descriptions 10 -out <>

Search for any string in all txt files

grep -r 'STRING1\|STRING2\|STRING3' ./*.txt

Conditions based on column values

awk '{for (i=2; i<=8; i++) if ($i<-0.2){print $0; next}}'
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