AddedDocNoteForLookupTables #2
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Merge preprocessing branch w/ master
Modified clustersubseq to perform over 4 different flag seqs, which are keys to scaled syn/rep
Updates: MASS-PRF was written in the standard C++ programming language. The software package is accompanied by a manual document, example data, source codes, and compiled executable commands for Windows/Linux/Mac. Source codes are released to GPLv3, and can be downloaded from https://github.com/Townsend-Lab-Yale/MASSPRF_10July2016/.
-SCL 0 for no scaling -SCL 1 for automatic scaling -SCL <num> for user defined scaling
The thresholds of gamma thresholds for positive and negative selections.
Updated compiling command without 'make'; put the C++ version and thread details in.
Added the information for MASSPRF pipeline folder, and simulation folder.
Update PRFCluster.cpp
Update PRFCluster.h
Change 1800 to 2700 to adjust to a min_scale_length of 900
…-values of the 2x2 contingency tables.
added under the session 'How to run MASS-PRF?': - "Note: The program requires the four LookupTables in the working directory to run successfully, for more details about the LookupTables, please refer to the session ‘Gamma calculation using four Lookup Tables’ below."
Silent clustering -s 1 is the default option.
-s 1 is the default, the default is clustering silent sites.
Revised README.md to include detailed installation and setup instructions This update improves the README file by integrating comprehensive installation steps, usage guidance, and symlink setup for the MASS-PRF pipeline. It consolidates information from existing documentation to ensure users have a streamlined and clear setup process.
1. Update Time Output Format to Include Leading Zeros
Original Code:
int h = t / 3600, m = (t % 3600) / 60, s = t % 60;
if (h) cout << h << ":" << m << ":" << s << endl;
else cout << m << ":" << s << endl;
Modified Code:
int h = t / 3600, m = (t % 3600) / 60, s = t % 60;
if (h)
cout << setw(2) << setfill('0') << h << ":"
<< setw(2) << setfill('0') << m << ":"
<< setw(2) << setfill('0') << s << endl;
else
cout << setw(2) << setfill('0') << m << ":"
<< setw(2) << setfill('0') << s << endl;
These scripts were originally developed by Prof. Nic Fisk, Associate Professor at URI and a friend of the lab, to map selection pressures onto 3D protein structures. They were added to MASSPRF, with his permission, to facilitate 3D visualization of selection mapping.
These scripts were originally developed by Prof. Nic Fisk, Associate Professor at URI and a friend of the lab, to map selection pressures onto 3D protein structures. They were added to MASSPRF, with his permission, to facilitate 3D visualization of selection mapping.
These examples were provided by Prof. Nic Fisk to map selection pressures onto 3D protein structures. They were later incorporated into MASSPRF to enhance its 3D visualization capabilities.
These scripts were originally developed by Prof. Nic Fisk, Associate Professor at URI and a friend of the lab, to map selection pressures onto 3D protein structures. They were added to MASSPRF, with his permission, to facilitate 3D visualization of selection mapping.
The .txt files used in this script are examples of MASS-PRF output files. They serve as input for processing and analysis, demonstrating how to extract and visualize selection coefficients (Gamma values) to generate the 2D plots.
We would like to thank Dr. Hayley Hassler for her contribution as the author of the 2D scripts used to process the *.txt files and generate the 2D plots shown in Figure 4. These Python scripts were specifically designed to take the MASS-PRF output as input and create the visualizations depicted in the figure.
Update void PRFCluster::showHelpInfo()
Update VERSION and LASTUPDATE
Modified the readFasta and readFastaConsensus functions in base.cpp to improve the detection of missing end-of-line characters in FASTA files. Changes: Updated the condition checking for the end of the file. Changed: cpp if (is.eof() == true && temp == "") to cpp if (is.eof() == true && temp != "") This ensures that if the file ends without a newline and the last line is not empty, a warning is triggered. Enhances error detection for improperly formatted FASTA files. This update improves the robustness of the format validation process.
Return . former update crush the program
Change
name = entry.split('_')
gene_name = name[0] + '_' + name[1]
To:
name = entry.split('_')
gene_name = os.path.splitext(entry)[0]
To solve file name needs to have an underscroll
In this way, regardless of whether the file name contains underscores, the file name without the extension can be correctly extracted as the gene_name.
How to modify the output text (without changing the code) so that the user is not confused when seeing the message - even though the program continues to run normally
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added under the session 'How to run MASS-PRF?'
'Note: The program requires the four LookupTables in the working directory to run successfully, for more details about the LookupTables, please refer to the session ‘Gamma calculation using four Lookup Tables’ below.'