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_v1.0.4.sh
SCRIPT_VERSION:                 1.0.4

USAGE: PepStats_Tables_v1.0.4.sh
 -p Proteins_Fasta_File.fa      # REQUIRED (Proteins File)
 -r PepStats_Tables             # OPTIONAL (Run Name)
 -z TMPDIR Location             # OPTIONAL (default='0'='TMPDIR Run')

TYPICAL COMMANDS:
 PepStats_Tables_v1.0.4.sh -p Proteins_Fasta_File.fa

INPUT01:          -p FLAG       REQUIRED - Proteins 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' == Local 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.

 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.

 '1' Processes the data in the same directory where the script is being run.

DEPENDENCIES:
 EMBOSS: Required (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/