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drgirasol / FSAnalyzer

DNA Fragment Analysis using Matlab
GNU General Public License v3.0
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Experimental Management #1

Open drgirasol opened 8 years ago

drgirasol commented 8 years ago

At the moment too many things have to be defined manually by the user. When starting an analysis one has to chose the size-standard, a mapping file and the FSA files. To change this and to start working on a by-project or by-experiment basis, we should do the following: The user chooses an analysis folder (e.g. "arnica montana ssr analysis 1"). The program then looks for the necessary files in that directory:

  1. The size standard file: "sizeStandard.txt"
  2. A mapping file (if alternative names instead of the FSA filenames are required): "fileSampleMap.txt"
  3. The raw data (FSA): subdirectory "rawData"

If any of the files are not found, the user will be asked to locate them, and they will be moved to the locations inside the analysis folder.

Further settings (e.g. threshold for peak detection, peak modifications) and the subsequent results are also stored inside this folder. When a folder is selected, that contains settings and results, these are considered and loaded. So by opening am analysis it will reflect to current state of the experiment.

ufcyg commented 8 years ago

Experimental Management improvement

The whole process in selecting data, saving and loading has been reworked.

In the previous version the user had to define every single input such as FSA-Files, a txt-file containing information about the samples and the used marker. This has been replaced by a (possible) single click load. When the user clicks on 'Select Data' he will be asked to define a folder. This folder will be scanned for .fsa, .txt *.mat and a folder which last 4 letters are DATA

If the FSA-files are found in root they will be moved to a newly created folder 'rawDATA' when a folder is found, only the .fsa files in this folder will be read and not moved or copied. If no .fsa files are detected the user will be prompted to select some on its own. These files will then be copied to 'rawDATA' folder in root.

An iteration over the filenames of .txt files detects a file named SizeStandard * .txt ( \ = possible user modification like ' - LIZ1200). If not detected the user will be asked to localize a fitting file which will then copied to root.

Same for SampleIDs*.txt, but if SSR Mode is activated this will be skipped totally.

Last step is looking for *.mat files, if one is found it will be loaded without a new preanalysis and the user can continue where he stopped last. If more than one or none is found the user will be asked to select a proper save. Is this process aborted by user a preanalysis will be done.

Furthermore the newly created save function improves the bugreport function by a more selective dataset to be transmitted; resulting in smaller files and faster transmission.

Files affected by this change: FSAnalyzerGUIv3.m saloDataset.m (new!) callplotM.m callplotC.m scanfolder.m (new!) updatereset.m createDIR.m sendbugreport.m calchash.m

drgirasol commented 8 years ago

So much for the planning part :-/ ... (see wiki) Please don't mix different issues (like the bugreport), create an issue for an issue...