README

What's this?

It is software for fragment analysis (MLPA, QF-PCR etc.) data processing.

Features

FragalyseQt version 0.3.1+ supports assays with up to 8 different dyes used simultaneously, selective channel hiding, non-Latin run names, can correctly handle damaged files, exports peaks locations, areas, FWHM's and channel names in CSV for any *.FSA or *.HID files and exports in CSV internal analysis data for *.FSA of *.HID files generated by ABI 3500 and SeqStudio series equipment. Peaks areas are calculated assuming they are Gaussian peaks. For noisy runs denoising and baseline correction options is available. All the things are done without rewriting any data inside files FragalyseQt works with!

What file formats are supported?

Currently, only *.FSA and *.HID files are supported. I've tried to add SCF files support, but SCF supports only 4 fluorescence channels and can't store information about size standard used for current assay. This renders SCF file format quite obsolete and unusable for modern assays and thus, this program won't support it.

But, anyway, if you wish to add support for any file format, you may help to implement it by sending patches.

What FragalyseQt is useful for?

Currently it is helpful for capillary electrophoresis troubleshooting and not so complex analysis of sized data obtained using 3500 or SeqStudio family analyzers. If you know precisely your peaks positions and no sizong is required - you mayuse FragalyseQt for these data analysis too.

Because FragalyseQt analyses raw capillary electrophoresis data, you may obtain peak areas different from true ones if your peaks are crowded (like in TP-PCR). In this case you MUST use baseline correction and denoising option.

FragalyseQt makes no changes in analysed files, sou if you wish to save analysis results - you must export them in CSV.

What features are planned for FragalyseQt?

Well, first of all - sizing (a bit laborous work). In future I plan to add bining support to allow automated genotyping usin FragalyseQt.

How can I support you?

You may either provide run files from machines I haven't tested FragalyseQt with, provide patches or support me financially. Either case, contact me by email ( dorif11 AT gmail DOT com ), Telegram ( t.me/nurgle ) or here, at GitHub. Every help is important!

What's the license of FragalyseQt?

GNU General Public License version 3 for versions prior to 0.4.x. GNU Affero General Public License version 3 for versions from 0.4 and up.

How to get it working at *ubuntu/Debian/SUSE/macOS?

Install python 3.8+, git and PyQt5/PyQt6/PySide6 (only these Python bindings for Qt are supported) in any way that is comfortable to you. After this, clone FragalyseQt from Git repository and install remaining requirements. I propose you to do this using pip:

git clone https://github.com/Dorif/fragalyseqt && cd fragalyseqt && pip install -r requirements.txt && python3 main.py

If you are using something RHEL-based - read next chapters and may the luck be with you.

How to get it working at AltLinux?

Prepare enviroment to run FragalyseQt (GCC and python3-dev are needed to build BioPython):

su -c "apt-get install -y git gcc python3-module-pip python3-module-scipy python3-module-numpy-testing python3-dev"

Download and run FragalyseQt:

git clone https://github.com/Dorif/fragalyseqt && cd fragalyseqt && pip install -r requirements.txt && python3 main.py

How to get it working at RHEL/Oracle 8+?

Prepare enviroment to run FragalyseQt:

sudo yum install python-qt5 git

Download and run FragalyseQt:

git clone https://github.com/Dorif/fragalyseqt && cd fragalyseqt && pip install -r requirements.txt && python3 main.py

How to get it working at RHEL/CentOS/Oracle/Scientific 7?

These systems have no PyQt5 in their repos, nor you can install PyQt5 at these systems freshly installed. To install PyQt5 you should first update pip and clean pip cache:

sudo pip3 install --upgrade pip && rm -rf .pip/cache

After that install packages needed for FragalyseQt to work:

pip3 install pyqt5 && sudo yum install git

Download and run FragalyseQt:

git clone https://github.com/Dorif/fragalyseqt && cd fragalyseqt && pip install -r requirements.txt && python3 main.py

How to get it working at FreeBSD?

First, install Git and libraries needed to run FragalyseQt (assuming you have Python 3.9):

pkg install git graphics/py-pyqtgraph biology/py-biopython textproc/py-charset-normalizer py39-pip && pip-3.9 install pybaselines

Now, download FragalyseQt and run it:

git clone https://github.com/Dorif/fragalyseqt && cd fragalyseqt && python3.9 main.py

Or, if you wish to install all python libraries from PIP (but make sure they are not installed as native packages):

pkg install git py39-pip && git clone https://github.com/Dorif/fragalyseqt && cd fragalyseqt && pip-3.9 install -r requirements.txt && python3.9 main.py

How to get it working at OpenBSD?

First, install Git and libraries needed to run FragalyseQt:

pkg_add git py3-pip py3-qt5 py3-pyqtgraph py3-biopython py3-charset-normalizer py3-scipy && pip3 install pybaselines

Now, download FragalyseQt and run it:

git clone https://github.com/Dorif/fragalyseqt && cd fragalyseqt && python3 main.py

Or, if you wish to install all python libraries from PIP (but make sure they are not installed as native packages):

pkg_add git py3-pip && git clone https://github.com/Dorif/fragalyseqt && cd fragalyseqt && pip3 install -r requirements.txt && python3 main.py

How to get it working at NetBSD?

First, install Git and libraries needed to run FragalyseQt. In this case it is essential to install pyqtgraph by pip, because native NetBSD package seems to be broken in some way (assuming you have quite recent version of NetBSD and python 3.11):

pkg_add git py311-pip py311-qt5 py311-biopython py311-charset-normalizer py311-scipy && pip3.11 install pyqtgraph pybaselines

Now, download FragalyseQt and run it:

git clone https://github.com/Dorif/fragalyseqt && cd fragalyseqt && python3.11 main.py

Or, if you wish to install all python libraries from PIP (but make sure they are not installed as native packages):

pkg_add git py311-pip && git clone https://github.com/Dorif/fragalyseqt && cd fragalyseqt && pip3.11 install -r requirements.txt && python3.11 main.py

Will it run at non-x86 machines?

Yes, it will, because it is cross-platform not only in terms of OS, but also in terms of hardware. At least it was run at RISC-V and ARM based machines.

Known bad systems.

OpenVMS - has no Qt, no stable Python at least for x86_64 version, forget it. Solaris/Illumos - SciPy cannot be built and installed. Haiku - pyqtgraph package seems to be broken (resolves with installation by pip), SciPy package is compiled without ndimage module and fails to install by pip, maybe this will be fixed in future.

How can I further speed-up FragalyseQt?

If you are using Linux or macOS, you may install Pyston (a performance-optimizing JIT for Python) for this purpose, it will speed up Python 3.7 - 3.10 compatible applications, not only FragalyseQt:

pip3 install pyston_lite_autoload

About test files origin.

FSA files from ABI 3100 and HID files from ABI 3500 are from NCBI OSIRIS test file set. NCBI OSIRIS is public domain software.
NCBI OSIRIS source is available at: https://github.com/ncbi/osiris
NCBI OSIRIS home page: https://www.ncbi.nlm.nih.gov/osiris/

Files from ABI 310 are from MLPAinter project, licensed under GNU GPL v3.
MLPAinter source code is available at: https://code.google.com/archive/p/mlpainter/
MLPAinter publication full text is available at: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-67

SeqStudio for GlobalFiler and RapidHIT ID v1.x files are obtained by myself and contain no other persons data.

COrDis Plus files for Nanophore-05 and SeqStudio were provided by Dmitrii Romaniuk, ISB, Moscow and contain no personal data.

Superyears Honor 1616 files were provided by Vadim Ponkratov, "Litolab", Berdsk, Russia and contain no personal data.