aspring

From Thoraxe outputs for a single query gene to its Alternative Splicing Repetitive Units

usage: __main__.py [-h] --gene GENENAME [--path_data PATH_DATA]
                   [--path_hhsuite_scripts PATH_HHSUITE_SCRIPTS] [--len LEN]
                   [--id ID] [--norealign NOREALIGN] [--glo_loc GLO_LOC]
                   [--mact MACT] [--id_pair ID_PAIR]
                   [--idCons_pair IDCONS_PAIR] [--pval PVAL] [--nbSpe NBSPE]
                   [--cov COV] [--version]

Named Arguments

--gene

name of queried gene

--path_data

path to dir containing ThorAxe outputs (default: “/home/docs/checkouts/readthedocs.org/user_builds/aspring/checkouts/latest/docs”)

Default: “/home/docs/checkouts/readthedocs.org/user_builds/aspring/checkouts/latest/docs”

--path_hhsuite_scripts

path to the folder containing the scripts of hhsuite, by default it uses the value of the environment variable HHSUITE_SCRIPTS if it exists

Default: “”

--len

don’t create profiles for msas in which sequences are of length < len aa (default: 5)

Default: 5

--id

[0.0,100.0] maximum pairwise sequence identity (%) (default: 100.0)

Default: 100.0

--norealign

bool, 1 if norealign else 0, do NOT realign displayed hits with Maximum Accuracy algorithm (MAC) (default: 1)

Default: 1

--glo_loc

bool, 1 if global else 0, use global/local alignment mode for searching/ranking (default: 1)

Default: 1

--mact

[0.0,1.0] posterior prob threshold for MAC realignment controlling greediness at alignment ends: 0:global >0.1:local (default: 0.0)

Default: 0.0

--id_pair

[0.0,100.0] Identity percentage threshold between first sequence in msa of s-exon for each s-exon in a pair (default: 50.0)

Default: 50.0

--idCons_pair

[0.0,100.0] Identity percentage threshold between consensus sequence of msa of s-exon for each s-exon in a pair (should be equal to id_pair) (default: 50.0)

Default: 50.0

--pval

[0.0,1.0] p-value threshold for HMM-HMM alignment of a s-exons pair (default: 0.001)

Default: 0.001

--nbSpe

[1,10] minimum number of species in msa for s-exons in the pair (default: 2)

Default: 2

--cov

[0.0,1.0] Threshold for coverage of s-exon A and B in alignment of A and B (default: 0.8)

Default: 0.8

--version

show program’s version number and exit