recipe psytrans

psytrans.py - Parasite & Symbiont Transcriptome Separation

Homepage:

https://github.com/rivera10/psytrans

License:

GPLv3

Recipe:

/psytrans/meta.yaml

psytrans.py separates the sequences of a host species from those of its main symbiont(s) or parasite(s) based on Support Vector Machine classification. The program takes as input a file in fasta format with the sequences to be classified. The program also requires a file with sequences of a species related to the host, and a file with sequences related to the symbiont (or parasite). The queries will be compared to these two files using BLASTX. Alternatively, the user can provide the output of pre-computed BLASTX searches (in tabular format: -outfmt 6 or 7). The classification is then carried out using the command line tools from libsvm.

package psytrans

(downloads) docker_psytrans

Versions:

2.0.0-12.0.0-0

Depends:
Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install psytrans

and update with:

conda update psytrans

or use the docker container:

docker pull quay.io/biocontainers/psytrans:<tag>

(see psytrans/tags for valid values for <tag>)

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