pathoscope2biom
A script to convert multiple PathoScope2 output files to BIOM format
Requisites
- R (tested in R v3.3.2)
- R libraries:
- phyloseq
- taxize
- plyr
- dplyr
- biomformat
Usage
Rscript pathoscope2biom.R [path to pathoscope output] [matching pattern to files]
Rscript pathoscope2biom.R example *.tsv
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.