transcript_query

transcript_query download from Ensembl the transcript and exon information needed for thoraxe.

usage: transcript_query [-h] [-s SPECIES] [-o ORTHOLOGY] [-l SPECIESLIST] [-v]
                        [--version]
                        genename

Positional Arguments

genename

gene name in Ensembl (e.g. MAPK8) or the Ensembl Stable ID (e.g ENSG00000107643). Note that the Stable ID can not include a version number at the end.

Named Arguments

-s, --species

species to look for the gene name

Default: “homo_sapiens”

-o, --orthology

Orthology relationship to use; 1:1, 1:n or m:n

Default: “1:1”

-l, --specieslist

It could be a list of more than one species separated by commas and without spaces, e.g. homo_sapiens,mus_musculus, or a single file with the species list (one species per line). If nothing is indicated, all the available species are used.

Default: “”

-v, --verbose

Print detailed progress.

Default: False

--version

show program’s version number and exit

It has been developed at LCQB (Laboratory of Computational and Quantitative Biology), UMR 7238 CNRS, Sorbonne Université.

Caution

It is possible to get more transcripts and genes by allowing 1:n or n:m orthology using the –orthology argument. However, thoraxe can not ensure that the s-exons contain orthologous exonic regions under that setup.