The primary objective behind creating this script was to facilitate the generation of 'pdf' or 'png' image files depicting the size distribution of transcripts or proteins, excluding genomes, from fasta files.
###########################################################################
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: Fasta_Seq_Plot_v1.0.5.sh
SCRIPT_VERSION: 1.0.5
USAGE: Fasta_Seq_Plot_v1.0.5.sh
-p Proteins_Fasta_File.fa # REQUIRED (Proteins File)
(if '-t' Not Provided)
-t Transcripts_Fasta_File.fa # REQUIRED (Transcripts File)
(if '-p' Not Provided)
-n 'Homo sapiens' # REQUIRED (Species Name)
-k 0 # OPTIONAL (default=0='Do Not Print')
-z TMPDIR Location # OPTIONAL (default=0='TMPDIR Run')
TYPICAL COMMANDS:
Fasta_Seq_Plot_v1.0.5.sh -p Proteins_Fasta_File.fa -n 'Homo sapiens'
Fasta_Seq_Plot_v1.0.5.sh -t Transcripts_Fasta_File.fa -n 'Homo sapiens'
INPUT01: -p FLAG REQUIRED input
ONLY if the '-t' flag associated file
is not provided
INPUT01_FORMAT: Proteome Fasta File
INPUT01_DEFAULT: No default
INPUT02: -t FLAG REQUIRED input
ONLY if the '-p' flag associated file
is not provided
INPUT02_FORMAT: Transcriptome Fasta File
INPUT02_DEFAULT: No default
INPUT03: -n FLAG REQUIRED input
INPUT03_FORMAT: Text
INPUT03_DEFAULT: None
INPUT03_NOTES:
The text should correspond to the species name whose fasta file is being
analyzed.
If the text provided is composed on more than one word (e.g.,
Genus species), then the text must be enclosed by single or double quotes.
INPUT04: -k FLAG OPTIONAL input
INPUT04_FORMAT: Numeric: '0' == 'Do Not Print' | '1' == 'Print'
INPUT04_DEFAULT: '0' == 'Do Not Print'
INPUT04_NOTES:
If this flag is activated (i.e., set to '1'), then, in addition to the
sequence plots generated, a copy of the R Script files that were used to
generate those figures will also be printed to the output directory.
In theory, these files could be modified (or not) and re-run in R, to
re-generate the sequence plots.
INPUT05: -z FLAG OPTIONAL input
INPUT05_FORMAT: Numeric: '0' == TMPDIR Run | '1' == Local Run
INPUT05_DEFAULT: '0' == TMPDIR Run
INPUT05_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:
GNU AWK: Required (https://www.gnu.org/software/gawk/)
GNU COREUTILS: Required (https://www.gnu.org/software/coreutils/)
datamash: Required (http://www.gnu.org/software/datamash)
R: Required (https://www.r-project.org/)
Assumes that the packages tidyverse, ggplot2, and ggeasy
are already installed
R - ggplot2: Required (https://github.com/tidyverse/ggplot2)
R - ggeasy: Required (https://github.com/jonocarroll/ggeasy)
Author: Rodolfo Aramayo
WORK_EMAIL: raramayo@tamu.edu
PERSONAL_EMAIL: rodolfo@aramayo.org
###########################################################################
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
GNU COREUTILS (https://www.gnu.org/software/coreutils/)
(GNU coreutils) 9.4
Copyright (C) 2023 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Written by Richard M. Stallman and David MacKenzie.
GNU AWK (https://www.gnu.org/software/gawk/)
GNU Awk 5.3.0, API 4.0
Copyright (C) 1989, 1991-2023 Free Software Foundation.
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 http://www.gnu.org/licenses/.
DATAMASH ( (http://www.gnu.org/software/datamash)
datamash (GNU datamash) 1.8-dirty
Copyright (C) 2022 Assaf Gordon and Tim Rice
License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Written by Assaf Gordon, Tim Rice, Shawn Wagner, Erik Auerswald.
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.
R - ggplot2 (https://github.com/tidyverse/ggplot2)
Package: ggplot2
Version: 3.5.0
Title: Create Elegant Data Visualisations Using the Grammar of Graphics
R - ggeasy (https://github.com/jonocarroll/ggeasy)
Package: ggeasy
Title: Easy Access to 'ggplot2' Commands
Version: 0.1.4