Multiline fasta to single line fasta !
perl -pe '$. > 1 and /^>/ ? print "\n" : chomp' in.fasta > out.fasta859 days ago
858 days ago
Bash command to count reads in fastq file !
#ref fastq file #ref1_1.fq) echo $(( $(wc -l855 days ago
849 days ago
Commands to Find and replace in file(s0) !
#Use SED sed -i 's/my/your/g' test.txt test2.txt test3.txt #Use FIND and SED find . -name *.txt -exec sed -i 's/my/your/g' {} \; #Use AWK awk '{sub(/{OLD_TERM}/,{NEW_TERM}); print}' {file} awk '{sub(/my/,your); print}' test.txt awk '{gsub(/i/,"a"); print}' test.txt833 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.fa830 days ago
Command line to move all files from a directory !
find ~/Downloads/ -type f -print0 | xargs -0 mv -t ~/Videos782 days ago
781 days ago
728 days ago
Conda command to install checkV
...lecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ##...30 KB conda-forge kcounter-0.1.1 | py36h...ta-4.2.0-py36h5fab9bb_0 kcounter bioconda/linux-64...################# | 100% kcounter-0.1.1 | 871 KB | #...699 days ago