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 . SCRIPT_NAME: PepStats_Tables_v1.0.1.sh SCRIPT_VERSION: 1.0.1 USAGE: PepStats_Tables_v1.0.1.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_v1.0.1.sh -p Homo_sapiens.GRCh38.pep.all.fa -r PepStats_Tables 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: Required (see: 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/

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