Sanrrone / fetchMyLineage

Giving genus and specie name, the script give you a complete lineage

fetchMyLineage

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fetchMyLineage is a script that fetch a complete lineage (Kingdom, Phylum, Class, Order, Family, Genus, Species). Save yourself headaches :D, you only need a genus and species name and the script will do the work.

Requisites

• bash version >= 4.0

• Mac OSX
• (for linux user, replace "tail -r" for "tac" command in the script)

Usage

bash fetchMyLineage.bash [genus] [specie]

where [genus] and [specie] is a genus and specie name

Output

Example:

bash fetchMyLineage.bash Escherichia Coli

Output:

Superkingdom: Bacteria
Phylum: Proteobacteria
Class: Gammaproteobacteria
Order: Enterobacterales
Family: Enterobacteriaceae
Genus: Escherichia
Specie: Coli

External useful tools

check for these tools to extract some useful information from your data:

• multiGenomicContext: Check the genomic context of several genomes or sequence just providing the GBK files.

• fetchMyLineage: Return the complete lineage of your organism just providing the genus and species names.

• extractSeq: Extract and size defined sequence from and specific contig, from and specific genome.

• plotMyGBK: Plot your GBK in a circular graph with COG categories.

• pasteTaxID: fetch the taxonomic IDs to your fastas.

• GGisy: Plot synteny of two sequence (you can use two genomes), and see the identity of the matched regions.

• getS2: obtain the order parameter to each residue of your simulation.