BIOINFORMATICS IN ONE LINE

In biology, there are many ways to solve a task. However, biologists sometimes need simple ways to get easy tasks done quick - without actually compromising efficiency and accuracy. If that is what you need, the following list might help you. Below I have gathered some commands which I did wrote or find useful to solve different bioinformatics problems. Be aware that some of these scripts are perhaps a bit too specific, so bear that in mind when using them for your own work.

Fasta / FASTQ

Convert multiple-line Fasta To single-line Fasta

awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);}  END {printf("\n");}' < INPUT.fasta | tail -n +2 > OUTPUT.fasta 

Count bases (A, C, G, T) and missing (N, ?) per sample in single-line Fasta (slow for long files!)

while read line; do echo $line | grep -v '>' | grep -o "[ACGT]" | sort | uniq -c | paste - - - - | tr "\n" "\t" ;  echo $line | grep -v '>' | grep -o "[?N]" | sort | uniq -c | sort -k2r | paste - - ; echo $line | grep '>' | tr "\n" "\t" ; done < INPUT.fasta

Count total number of bases in Fasta (across all sequences)

grep -v ">" INPUT.fasta | wc | awk '{print $3-$1}'

Count number of sequences in FASTQ.gz file

parallel “echo {} && gunzip -c {} | wc -l | awk ‘{d=\$1; print d/4;}’” ::: INPUT.gz

Using a list of identifiers (one sequence name per line), extract sequences from Fasta/FASTQ files (needs seqtk)

seqtk subseq INPUT.fq name.list > out.fq

Parse a Fasta (useful to modify identifiers)

awk '/^>/{printf $0"\n",++i; next}{print}' INPUT.fasta

Sequence length from Fasta

cat INPUT.fasta|awk '$0 ~ ">" {if (NR > 1) {print c;} c=0;printf substr($0,2,200) "\t"; } $0 !~ ">" {c+=length($0);} END { print c; }'

Alignments

For a particular sample in a phylip alignment, count occurrences of a single character (eg. "A")

grep "SAMPLE" ALIGNMENT.phylip | awk '{print $2}' | awk -F"A" '{print NF-1}' 

Phylogenetic trees

Fast way to display a tree in newick format (needs 'ete3')

ete3 view --text -t TREE.nw

Compare topology of a list of trees vs reference tree (needs 'ete3')

ete3 compare --src_tree_list TREES.list -r REFERENCE.nw

Reroot newick tree (needs 'newick_utils')

nw_reroot -l INPUT.tree OUTGROUP

SNPs

Count heterozygous SNPs in a beagle file

echo $(awk ‘{if ($3 != $4) print $3, $4 }’ INPUT.bgl | wc -l )/$total*100 | bc -l

Others

General use:

Compare two unsorted lists

comm -13 <(sort file1) <(sort file2)

Delete all files with size 0 in current directory

find . -type f -empty -delete

Add extension (e.g. ".tre") to multiple files

find . -type f -print0 | xargs -0 -I{} mv "{}" "{}".tre

Remove extension (e.g. ".txt") for multiple files

find -type f -name '*.txt' | while read f; do mv "$f" "${f%.txt}"; done

Fast way (multi-core) to compress or decompress big files (using pigz)

tar cf - paths-to-archive | pigz -9 -p 32 > archive.tar.gz

pigz -dc target.tar.gz | tar xf -

Sum a column of numbers

<cmd> | paste -sd+ | bc

Specific use:

Count the number of a specific character (e.g. "NA") in each line (prints also the 1st word, delimited by space)

paste <(while read LINE ; do echo -n "$LINE" | awk -F" " '{print $1}' ; done < INPUT.file) <(awk -F\NA '{print NF-1}' INPUT.file)