topcons: parse TOPCONS output

In gogleva/SecretSanta: flexible pipelines for secretome prediction

Description

This function parses results of TOPCONS method, used to predict transmembrane domains. The parser is restricted to 'piper'-like behaviour.

Usage

topcons(input_obj, parse_dir, topcons_mode = c("API", "WEB-server",
  "stand-alone"), TM, SP = FALSE)

Arguments

input_obj	an instance of CBSResult class, produced by previous step;
parse_dir	dir with archived topcons output (for WSDL-API or WEB outputs) or dir with output produced by stand-alone version.
topcons_mode	WEB - output from TOPCOS2 web-server http://topcons.net/ WSDL-API - output returned by WSDL API script http://topcons.net/pred/help-wsdl-api/ stand-alone - results of TOPCONS stand-alone version https://github.com/ElofssonLab/TOPCONS2
TM	allowed number of TM domains in mature peptides, recommended value <= 1; use TM = 0 for strict filtering
SP	filter according to TOPCONS prediction of signal peptides. TRUE - keep only proteins containg signal peptides according to TOPCONS; FALSE - disable filtering for TOPCONS-based predictions of signal peptides. Deafault = FALSE.

Value

TopconsResult object

Examples

aa <- readAAStringSet(system.file("extdata", "sample_prot_100.fasta",
           package = "SecretSanta"), use.names = TRUE)
inp <- CBSResult(in_fasta = aa)
# predict signal peptides:
sp <- signalp(inp, version = 2, organism = 'euk', run_mode = "starter",
legacy_method = 'hmm')
# integrate topcons predictions
p_dir <- system.file("extdata", "rst_SVw4hG.zip", package = "SecretSanta")
tpc <- topcons(input_obj = sp, parse_dir = p_dir, topcons_mode = "WEB-server",
              TM = 0, SP = TRUE)

gogleva/SecretSanta documentation built on May 30, 2019, 8:02 a.m.