protParamWrap

A wrapper to submit multiple sequences to calculate protein parameter.

Requirements

• Julia
  • module protParam (the package has to be included into julia)
  • module BioSequences@2.0.5 (the package has to be included into julia)
• Installation of Julia and modules can be found here.

Workflow

• .fasta files are seperated into single files
• .protParam.jl files are generated for each sequence
• .jl files are processed by julia and protParam
• results are saved in the summary.txt file

Citation

Breslmayr, E. (2021). protParamWrap - A tool for submission and calculation of multiple protein sequence parameters (Version v1.0). Zenodo. http://doi.org/10.5281/zenodo.4770671

Installation

• Bash script, just make it executable and run.
• Download this repo and copy the protParamWrap file into a folder you prefer.
• Make it executable: chmod +x protParamWrap
• Test it: ./protParamWrap or ./protParamWrap -h

SourceCode compiling with Argbash - argument parser generator

template file can be changed and converted to executable code (tested with argbash_2.10; Ubuntu_16.04, 20.04)

argbash protParamWrap_template -o protParamWrap

Problems

• Fasta file must look like this:

• Amino acid sequence in the .fasta file can only include standard amino acids like 'RHKDESTNQCGPAVILMFYW'; otherwise protParam crashes!
• If sequence names have a space in between (e.g. >seq1 name), everything after the first space will be ignored. Best is to connect the words (e.g. >seq1_name).