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:

2.0.0-1,  2.0.0-0

depends blast:

>=2.2.31

depends libsvm:

>=3.16

depends python:

>3.6

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install psytrans

and update with::

   mamba update psytrans

To create a new environment, run:

mamba create --name myenvname psytrans

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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