SHEso

SHell scripts of Esoteric value

dist_between.sh

Find the distance between pairs of genomic elements on contigs. E.g. CRISPR arrays and Cas operons. Two inputs are needed each containing the positions of the elements. E.g. first could contain position of CRISPR arrays, the other positions of Cas operons. Both inputs should be whitespace-delimited with four columns: Contig, Element name, start, end. Start has to be lower than end.

More info is in the script.

./dist_between.sh File1 File2

dist_nearest.sh

Find the nearest distance between pairs of genomic elements on contigs. E.g. CRISPR arrays and Cas operons. Two inputs are needed each containing the positions of the elements. E.g. first could contain position of CRISPR arrays, the other positions of Cas operons. Both inputs should be whitespace-delimited with four columns: Contig, Element name, start, end. Start has to be lower than end.

Unique elements in File1 is kept. For example, if File1 contains CRISPR arrays and File2 contains Cas operons, then the output contains the nearest Cas operon to each CRISPR array. Cas operons might therefore be duplicated.

More info is in the script

./dist_nearest.sh File1 File2

wavg_by_group.sh

Weighted average by group. Input is a whitespace-delimted file with three columns: Grouping factor, value to average, weight. Output is the weighted average of the second column for each unique value in the first column

./wavg_by_group.sh File.tab

mult2single.sh

Multiline fasta to single line fasta

./mult2single.sh File.fasta

fastabyid.sh

Extract sequences from multi fasta with a list of IDs

./fastabyid.sh File.fasta IDs.txt

split_multifasta.sh

Split a multi-fasta into single fasta files. Names will correspond to fasta headers with .fa extension

./split_multifasta.sh File.fasta

split_multifasta2.sh

Split a multi-fasta into chunks with a set number of sequences in each. Names will be 3rd argument followed by a number with .fna extension

./split_multifasta2.sh File.fasta 1000 chunk

Russel88/SHEso