pepstats_tables_python - PepStats_Tables

AramayoLab

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:

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 ```

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/.

SCRIPTNAME: PepStatsTablesv1.0.0.py SCRIPTVERSION: 1.0.0

USAGE: PepStatsTablesv1.0.0.py -p Homosapiens.GRCh38.pep.all.fa # REQUIRED (Proteins File - Proteome) -r PepStatsTables # OPTIONAL (Run Name) -z TMPDIR Location # OPTIONAL (default=0='TMP TMPDIR Run')

TYPICAL COMMANDS: PepStatsTablesv1.0.0.py -p Homosapiens.GRCh38.pep.all.fa -r PepStatsTables

INPUT01: -p FLAG REQUIRED - Protein File INPUT01FORMAT: Fasta Format INPUT01DEFAULT: No default

INPUT02: -r FLAG OPTIONAL - Run Name INPUT02FORMAT: Text INPUT02DEFAULT: PepStats_Tables

INPUT03: -z FLAG OPTIONAL input INPUT03FORMAT: Numeric: 0 == TMP TMPDIR Run | 1 == Local TMP Run INPUT03DEFAULT: 0 == TMP TMPDIR Run INPUT03NOTES: 0 Processes the data in the TMP $TMPDIR directory of the computer used or of the node assigned by the SuperComputer scheduler INPUT03NOTES: 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 WORKEMAIL: raramayo@tamu.edu PERSONALEMAIL: rodolfo@aramayo.org

```

Development/Testing Environment:

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

Required Script Dependencies:

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

Version Number: 6.6.0.0

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

- Python
Published by raramayo almost 2 years ago