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2024
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| Online Access: | https://doi.org/10.5281/zenodo.10889792 |
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| _version_ | 1866902017360789504 |
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| author | Aramayo, Rodolfo |
| author_facet | Aramayo, Rodolfo |
| contents | <h1><strong>AramayoLab</strong></h1> <h2><strong>Motivation</strong></h2> <pre><code>This script was generated with the objective of constructing a table summarizing the main physical-chemical properties <br>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 <br>by the current script </code></pre> <h2>Documentation</h2> <pre><code>######################################################################################################################################################################################################## 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: raramayo@tamu.edu PERSONAL_EMAIL: rodolfo@aramayo.org ######################################################################################################################################################################################################## </code></pre> <h2>Development/Testing Environment:</h2> <pre><code>Distributor ID: Apple, Inc. Description: Apple M1 Max Release: 14.4.1 Codename: Sonoma </code></pre> <pre><code>Distributor ID: Ubuntu Description: Ubuntu 22.04.3 LTS Release: 22.04 Codename: jammy </code></pre> <h2>Required Script Dependencies:</h2> <h3>EMBOSS (https://emboss.sourceforge.net/download/)</h3> <h4>Version Number: 6.6.0.0</h4> <h4>Credits: https://emboss.sourceforge.net/credits/</h4> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_10889792 |
| institution | Zenodo |
| language | |
| publishDate | 2024 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | PepStats_Tables_Python Aramayo, Rodolfo <h1><strong>AramayoLab</strong></h1> <h2><strong>Motivation</strong></h2> <pre><code>This script was generated with the objective of constructing a table summarizing the main physical-chemical properties <br>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 <br>by the current script </code></pre> <h2>Documentation</h2> <pre><code>######################################################################################################################################################################################################## 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: raramayo@tamu.edu PERSONAL_EMAIL: rodolfo@aramayo.org ######################################################################################################################################################################################################## </code></pre> <h2>Development/Testing Environment:</h2> <pre><code>Distributor ID: Apple, Inc. Description: Apple M1 Max Release: 14.4.1 Codename: Sonoma </code></pre> <pre><code>Distributor ID: Ubuntu Description: Ubuntu 22.04.3 LTS Release: 22.04 Codename: jammy </code></pre> <h2>Required Script Dependencies:</h2> <h3>EMBOSS (https://emboss.sourceforge.net/download/)</h3> <h4>Version Number: 6.6.0.0</h4> <h4>Credits: https://emboss.sourceforge.net/credits/</h4> |
| title | PepStats_Tables_Python |
| url | https://doi.org/10.5281/zenodo.10889792 |