Command_Line_Tricks

Setting a global variable (makes large chunks of data slightly more readable)

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export variable=/Full/path
cd $variable

export mgs=/home/mpavia/Tres_Rios/qc_metagenomes
cd $mgs

Convert csv to tsv

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perl -pe "s/,/\t/g;" CSV_file.csv > output_TSV_file.tsv

Count number of specific file types in a directory

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find *fa -type f | wc -l

Clean up gene names from prodigal output

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awk 'BEGIN{FS="#"}{if(/^>/){print ">"$1}else{print $0}}' prodiga_output.faa > clean_prodiga_output.faa`

MOD to bash profile which allows you to search history (paste in .bash_profile

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bind '"\e[A": history-search-backward'

bind '"\e[B": history-search-forward'

Generate a contig to bin file

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for i in bin_directory/*.fa; do 
      bid=$(basename ${i%.fa});
      cat $i | grep ^'>' | cut -f1 -d' ' | tr -d '>' | sed 's/$/\t'$bid'/' >> output_name.map;
done

Filter contigs by length

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awk -v RS='>[^\n]+\n' 'length() >= 2000 {printf "%s", prt $0} {prt = RT}' contig_file.fasta > output.fa

Rename file extensions

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for f in *.fasta; do
    mv -- "$f" "${f%.fasta}.fa"
done

Batch renames files from a csv (oldfilename,newfilename)

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awk -F',' 'system("mv " $1 " " $2)' old_2_new_filenames.csv