Interact with sequences

Get statistics on sequences:

• awk command to get the size of all lectures in a file : awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' unique.fasta |paste - -
• samtools command to index a file (useful for pggb): samtools faidx myfile.fasta
• Replace string in file: sed -i "s/thing_to_replace/thing_replacing/g" file > out and replace spaces sed 's/[[:space:]]/_/g' file.fa > out.fa
• Replace within file: sed -i 's/>chr7/>newname/g' fasta.fa Split a multifasta file:
• awk -F '>' '/^>/ {F=sprintf("%s.fasta", $2); print > F;next;} {print F; close(F)}' < file.fasta

Get fast stats on a GFA file:

• Print all number of lines types: <graph.gfa sed 's/^\(.\).*/\1/' | sort | uniq -c
• Get all P-lines from file: grep '^P' input_file.gfa | awk '{print $2}'
• Get global graph size: grep '^S' mgc_human_1.gfa | awk '{sum+=length($3)} END{print sum}'

Extract subparts of a VCF file : `grep ’^#[^#]|^chr1:blank:’ file

Schedule jobs on SLURM cluster:

• See here to chain jobs

Extract entries from multifasta file:

• samtools faidx (with examples)