iSanXoT-0.2.9

DATE: 2021_03

Highlights

• The Basic PTM workflow is optimised.

Changes in the Graphical User Interface

• Open correctly the dialog to load the input files in a PTM workflow.

• Style changes.

• Load correctly the "input file" table.

Changes in the Code Workflow

• The createRels program admits the ':' delimter for the join of columns.

• The REPORT program shows the level without relationship with the high-level. For example, it shows the protein without descriptions or it shows the protein without genes.

• Filtering correctly the file used by SANSON program.

iSanXoT-0.2.8

DATE: 2021_03

Highlights

• Pre-release of PTM workflow.

Changes in the Graphical User Interface

• PTM workflow has been included. It is a preliminar version.

• The interface accepts the input files for the PTM workflow.

• Add an auto overflow for worlflow log table.

• The identifier of HTML elements for the inputs have changed.

Changes in the Code Workflow

• Scan Id column has been added in the ID.tsv files. The value is "[Spectrum_File]-[Scan]-[Charge]" for the search engines: PD, MSFragger and Commet.
  Therefore, the WSPP_SBT will accept that column values.

• The samples files will have a version prefix.

• The keys for the inputs: indir, outdir, catfile, etc. have changed.

• The Default parameters for the "createSansonLevel" are included in the "tpl_commands".

• "stats" file in "sanxot" program: Fix the bug when the given list is empty.

iSanXoT-0.2.7

DATE: 2021_03

Highlights

• Improvements in the REPORT command.

• The installation module has been improved.

• The image of Sanson diagram is reported.

Changes in the Graphical User Interface

• The appareance of worked-out examples has changed.

• The structure of workflow config file has changed.

• The Mar. 2021 database has been added.

• Improvements in the log tables of processes.

• The REPORT command has new colummns.

Changes in the Code Workflow

• Improvements in the REPORT program:

  • New way to propvide the "description" info for the given level.
  • There is a new parameter 'show_leves' that allows us to say which levels we want in the report file.
  • Merge the given intermediate report using the union of keys from both frames.

• The installation module has been improved. Now, it install another programas like "java", "dot", etc. The installation of forced modules has been disabled.

• The image of Sanson diagram is reported.

• Bug fixed: In some cases, the report program needed the files "gene2description" and "category2description". Now, these files are created in the Database table.

iSanXoT-0.2.6

DATE: 2021_02

Highlights

• We have started to include some documentation.

• Due we have included a "force" column for each tasktable. For this reason, this version is not compatible with projects executed by iSanXoT's with lower versions.

Changes in the Graphical User Interface

• There is some documentation.

• Gramatical changes.

• The internal files of the application have been restructured.

• We have included the "force" column that is a flag for the forced execution of command.

• We have included the "gene2description" relationship file in the table.

• Bug fixed: exporting the tasktable of databases section.

Changes in the Code Workflow

• Bug fixed - createRels:

  • There were a problem reporting the category2categoryall files when the input database came from two or more species. In the reindex of dataframe.
  • there were empty cells.

• Now, the table "Select input files" accepts a filename and the path of file for the column "Infile".

• The NextCloud url where the databases and samples are saved, have changed.

• report:

  • We include the 'gene' column to the correct report.
  • we delete the all columns correctly.

• installer: Now, we force the installation of some parts of requirements.

iSanXoT-0.2.5

0.2.5

DATE: 2021_02

Highlights

• We have changed the visualization of Log panels of GUI.

Changes in the Graphical User Interface

• We have fixed the filter of REPORT command.

• Bug fixed: When you create a workflow from the scratch, there is a conflict with the relationship tables (CatDB and CatFile). Both tables are created. Then, two processes create the same relationship file.

• The table of sanson command needs another Norm column: Lower norm and Higher norm.

• If at least one cell of optinal parameters is filled, then the "advanced parameters" is shown.

Changes in the Code Workflow

• Bug fixed: The filter function was not working correctly in the REPORT command. The pandas "eval" function did not filter correctly.

iSanXoT-0.2.4

0.2.4

DATE: 2021_01

Highlights

• We have changed the workflow managment system. Now we have developed "mysnake"

Changes in the Graphical User Interface

• The GUI executes the new workflow managment system (MySnake).

• The validation menu has been deprecated.

Changes in the Code Workflow

• We have created "mysnake" workflow managment system but we still use "snakemake" to know the list of processes for the workflow.

• We have changed the config file of workflow. Now, the rows of tables represents the commands.
  For that, there are a list of commands and each command is composed by list of rules (programs).

• We have changed some internal programs of workflow. First, they save the results in temporal file and then, they rename to the final file name.

iSanXoT-0.2.3

0.2.3

DATE: 2021_01

Highlights

• We have included a new condition for sanxot program.

Changes in the Graphical User Interface

• tpl_commands.yaml: The "-m 600" parameter has been added into all the firsts comands of sanxot.

Changes in the Code Workflow

• sanxot: The "emergencyvariance" has been changed.
  In the case the maximum iterations are reached (see -m), force the provided variance by the user. Default 0.0

iSanXoT-0.2.2

DATE: 2021_01

Highlights

• We have included the WSPPG-SBT command in the basic workflow.

Changes in the Graphical User Interface

• We have included the WSPPG-SBT command in the basic workflow.
• We include the commands only by the configuration file (workflow.json)
• We merge common functions for the programs: table2cfg, ratios, create_id

iSanXoT-0.2.1

• Database from UniProt
  ...

iSanXoT-0.2.0

First draft of alpha version