PepStats_Tables_Bash

Motivation

This script was generated with the objective of constructing a table summarizing the main physical-chemical properties associated with each protein present in a given proteome.

The script uses PepStats, an EMBOSS program to extract and construct a table displaying the following protein properties:

Protein_ID
Molecular_weight
No_Residues
Average_Residue_Weight
Isoelectric_Point
Mole%_Tiny
Mole%_Small
Mole%_Aliphatic
Mole%_Aromatic
Mole%_Non-polar
Mole%_Polar
Mole%_Charged
Mole%_Basic
Mole%_Acidic

In theory, thie script could be easily modified to extract other protein properties calculated by PepStats, but not extracted by the current script

Documentation

####################################################################################################
ARAMAYO_LAB

This program is free software: you can redistribute it and/or modify it under the terms of the GNU
General Public License as published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not,
see <https://www.gnu.org/licenses/>.

SCRIPT_NAME:                       PepStats_Tables_v1.0.2.sh
SCRIPT_VERSION:                    1.0.2

USAGE: PepStats_Tables_v1.0.2.sh
       -p Homo_sapiens.GRCh38.pep.all.fa               # REQUIRED (Proteins File - Proteome)
       -r PepStats_Tables                              # OPTIONAL (Run Name)
       -z TMPDIR Location                              # OPTIONAL (default=0='TMPDIR Run')

TYPICAL COMMANDS:
                                   PepStats_Tables_v1.0.2.sh -p Homo_sapiens.GRCh38.pep.all.fa

INPUT01:          -p FLAG          REQUIRED - Protein File
INPUT01_FORMAT:                    Fasta Format
INPUT01_DEFAULT:                   No default

INPUT02:          -r FLAG          OPTIONAL - Run Name
INPUT02_FORMAT:                    Text
INPUT02_DEFAULT:                   PepStats_Tables

INPUT03:          -z FLAG          OPTIONAL input
INPUT03_FORMAT:                    Numeric: 0 == TMPDIR Run | 1 == Normal Run
INPUT03_DEFAULT:                   0 == TMPDIR Run
INPUT03_NOTES:                     0 Processes the data in the $TMPDIR directory of the computer
                                     used or of the node assigned by the SuperComputer scheduler
INPUT03_NOTES:                     Processing the data in the $TMPDIR directory of the node
                                     assigned by the SuperComputer scheduler reduces the possibility
                                     of file error generation due to network traffic
INPUT03_NOTES:                     1 Processes the data in the same directory where the script is
                                     being run

DEPENDENCIES:                      EMBOSS PepStats (http://emboss.open-bio.org/html/adm/ch01s01.html)

Author:                            Rodolfo Aramayo
WORK_EMAIL:                        raramayo@tamu.edu
PERSONAL_EMAIL:                    rodolfo@aramayo.org
####################################################################################################

Development/Testing Environment:

Distributor ID:       Ubuntu
Description:	      Ubuntu 22.04.3 LTS
Release:	          22.04
Codename:	          jammy

Distributor ID:       Apple, Inc.
Description:          Apple M1 Max
Release:              14.4.1
Codename:             Sonoma

Required Script Dependencies:

EMBOSS (https://emboss.sourceforge.net/download/)

Version Number: 6.6.0.0

Credits: https://emboss.sourceforge.net/credits/