Bash script to split multifasta file !
#Using awk, we can easily split a file (multi.fa) into chunks of size N (here, N=500), by using the following one-liner: awk 'BEGIN {n=0;} /^>/ {if(n%500==0){file=spr...837 days ago
Command line to print disk usage on Linux terminal !
#Print disk usage - perl du -h |perl -e'%h=map{/.\s/;99**(ord$&&7)-$`,$_}`du -h`;die@h{sort%h}' #Bash du -k * | sort -nr | cut -f2 | xargs -d '\n' du -sh #Base du -scBM | sort -n #More du -s * | sort -rn | cut -f2- | xargs -d "\n" du -sh828 days ago
Bash script to transfer files to server !
# rsync options source destination rsync -azvh --progress PacBio_clean.fa xxx@xxx.xxx.res.in:/home/ # scp source_file_name username@destination_host:destination_folder scp –rpv /datafile xxx@192.168.1.100:/home/me817 days ago
808 days ago
Bash command to count reads in fastq file !
#ref fastq file #ref1_1.fq) echo $(( $(wc -l806 days ago
Bash script to find difference between two files !
#lines which are exist only in file2: grep -Fxvf file1 file2 > file3 #lines which are exist only in file1: grep -Fxvf file2 file1 > file3 #lines which are exist in both files: grep -Fxf file1 file2 > file3786 days ago
Bash command to explore assembly summary genbank !
wget https://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt pip3 install csvkit csvcut -t -K 1 -c 'excluded_from_refseq' assembly_summary_genbank.txt \ | tail -n +2 | tr ";" "\n" \ | sed -e 's/^ //' -e 's/ $//' | grep -v '""' \ | sort | uniq -c | sort -nr782 days ago
Bash script to convert multiline fasta to single line fasta !
#file.fa is multiline fasta awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa780 days ago
731 days ago
Bash script to convert Multi-line Fasta to Single-line Fasta !
#!/bin/bash input_filename="multi_line.fasta" output_filename="single_line.fasta" awk '/^>/ {printf("\n%s\n", $0);next; } { printf("%s", $0);} END {printf("\n");}...109 days ago