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:
Molecular_weight
Isoelectric_Point
Mole%_Ala
Mole%_Cys
Mole%_Asp
Mole%_Glu
Mole%_Phe
Mole%_Gly
Mole%_His
Mole%_Ile
Mole%_Lys
Mole%_Leu
Mole%_Met
Mole%_Asn
Mole%_Pro
Mole%_Gln
Mole%_Arg
Mole%_Ser
Mole%_Thr
Mole%_Val
Mole%_Trp
Mole%_Tyr
Mole%_Tiny
Mole%_Small
Mole%_Aliphatic
Mole%_Aromatic
Mole%_Non-polar
Mole%_Polar
Mole%_Charged
Mole%_Basic
Mole%_Acidic
Protein_ID
In theory, thie script could be easily modified to extract other protein properties calculated by PepStats, but not extracted by the current script
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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_v1.0.0.py
SCRIPT_VERSION: 1.0.0
USAGE: PepStats_Tables_v1.0.0.py
-p Homo_sapiens.GRCh38.pep.all.fa # REQUIRED (Proteins File - Proteome)
-r PepStats_Tables # OPTIONAL (Run Name)
-z TMPDIR Location # OPTIONAL (default=0='TMP TMPDIR Run')
TYPICAL COMMANDS:
PepStats_Tables_v1.0.0.py -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 == TMP TMPDIR Run | 1 == Local TMP Run
INPUT03_DEFAULT: 0 == TMP TMPDIR Run
INPUT03_NOTES: 0 Processes the data in the TMP $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: [email protected]
PERSONAL_EMAIL: [email protected]
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Distributor ID: Apple, Inc.
Description: Apple M1 Max
Release: 14.4.1
Codename: Sonoma
Distributor ID: Ubuntu
Description: Ubuntu 22.04.3 LTS
Release: 22.04
Codename: jammy