parse_signalp: convert output of Signalp-2.0 and Signalp-3.0 to...
In gogleva/SecretSanta: flexible pipelines for secretome prediction

Description Usage Arguments Value See Also Examples

This function parses the output of the command line tools signalp2 and signalp3 to standardize outputs for data analysis.

Alternatively, parse_signalp can be called independently on outputs of signalp2 and signalp3 and captured in a system call or stored in a file.

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parse_signalp(input, input_type = c("path", "system_call"), method = c("nn",
  "hmm"), pred_filter = "Signal peptide", version = c(2, 3),
  source_fasta = NULL)

`input`	output of the command line tools `signalp2` or `signalp3`/
`input_type`	a character string with the following options: `input_type = "path"` - path to a file with text output from `signalp2` or `signalp3` `input_type = "system_call"` - output from the `signalp2` or `signalp3` system call
`method`	which prediction method to use. Options are: `method = "hmm"` - for HMM-based predictions `method = "nn"` - for prediction based on neural networks
`pred_filter`	filter for the type of prediction. Options are: `pred_filter = "Signal peptide"` `pred_filter = "Signal anchor"` `pred_filter = "Non-secretory protein"` `pred_filter = "all"` - in case all three filter options shall be included
`version`	version of SignalP used: 2.0 or 3.0
`source_fasta`	source fasta file, required to rescue names when signalp2, nn method is used

parsed signalp2 or signalp3 output, organised in a tibble object.

signalp

# Example 1: parse signalp2 output, stored in a file:
s_path <- system.file("extdata", "sample_prot_sp2_hmm_out",
package = "SecretSanta")
parse_signalp(input = s_path, input_type = "path", 
pred_filter = "Signal peptide", version = 3, method = 'hmm')

# alternatively users can select for all prediction filters
parse_signalp(input = s_path, input_type = "path", pred_filter = "all", method = 'hmm', version = 2)

# Example2: parse signalp2 output
# captured in a system call. Note, here we assume that
# signalp2 is accessible via $PATH.
s_fasta <- system.file("extdata", "small_prot.fasta",
package = "SecretSanta")
# capture system call:
con_hmm <- system(paste('signalp2 -t euk -f short -m hmm -trunc 70', s_fasta), intern = TRUE)
con_nn <- system(paste('signalp3 -t euk -f short -m nn -trunc 70', s_fasta), intern = TRUE)
# parse captured system call:
parse_signalp(input = con_hmm, input_type = "system_call", method = 'hmm', version = 2)
parse_signalp(input = con_nn, input_type = "system_call",
method = 'nn', version = 3, pred_filter = 'all')