=======
emtable
=======
Emtable is a STAR file parser originally developed to simplify and speed up metadata conversion between Scipion and Relion. It is available as a small self-contained Python module (https://pypi.org/project/emtable/) and can be used to manipulate STAR files independently from Scipion.
How to cite
-----------
Please cite the code repository DOI: `10.5281/zenodo.4303966 <https://zenodo.org/record/4303966>`_
Authors
-------
* Jose Miguel de la Rosa-Trevín, Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
* Grigory Sharov, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, England
Testing
-------
``python3 -m unittest discover emtable/tests``
Examples
--------
To start using the package, simply do:
.. code-block:: python
from emtable import Table
Each table in STAR file usually has a *data\_* prefix. You only need to specify the remaining table name:
``Table(fileName=modelStar, tableName='perframe_bfactors')``
Be aware that from Relion 3.1 particles table name has been changed from "data_Particles" to "data_particles".
Reading
#######
For example, we want to read the whole *rlnMovieFrameNumber* column from modelStar file, table *data_perframe_bfactors*.
The code below will return a list of column values from all rows:
.. code-block:: python
table = Table(fileName=modelStar, tableName='perframe_bfactors')
frame = table.getColumnValues('rlnMovieFrameNumber')
We can also iterate over rows from "data_particles" Table:
.. code-block:: python
table = Table(fileName=dataStar, tableName='particles')
for row in table:
print(row.rlnRandomSubset, row.rlnClassNumber)
Alternatively, you can use **iterRows** method which also supports sorting by a column:
.. code-block:: python
mdIter = Table.iterRows('particles@' + fnStar, key='rlnImageId')
If for some reason you need to clear all rows and keep just the Table structure, use **clearRows()** method on any table.
Writing
#######
If we want to create a new table with 3 pre-defined columns, add rows to it and save as a new file:
.. code-block:: python
tableShifts = Table(columns=['rlnCoordinateX',
'rlnCoordinateY',
'rlnAutopickFigureOfMerit',
'rlnClassNumber'])
tableShifts.addRow(1024.54, 2944.54, 0.234, 3)
tableShifts.addRow(445.45, 2345.54, 0.266, 3)
tableShifts.write(f, tableName="test", singleRow=False)
*singleRow* is **False** by default. If *singleRow* is **True**, we don't write a *loop_*, just label-value pairs. This is used for "one-column" tables, such as below:
.. code-block:: bash
data_general
_rlnImageSizeX 3710
_rlnImageSizeY 3838
_rlnImageSizeZ 24
_rlnMicrographMovieName Movies/20170629_00026_frameImage.tiff
_rlnMicrographGainName Movies/gain.mrc
_rlnMicrographBinning 1.000000
_rlnMicrographOriginalPixelSize 0.885000
_rlnMicrographDoseRate 1.277000
_rlnMicrographPreExposure 0.000000
_rlnVoltage 200.000000
_rlnMicrographStartFrame 1
_rlnMotionModelVersion 1
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"description": "=======\nemtable\n=======\n\nEmtable is a STAR file parser originally developed to simplify and speed up metadata conversion between Scipion and Relion. It is available as a small self-contained Python module (https://pypi.org/project/emtable/) and can be used to manipulate STAR files independently from Scipion.\n\nHow to cite\n-----------\n\nPlease cite the code repository DOI: `10.5281/zenodo.4303966 <https://zenodo.org/record/4303966>`_\n\nAuthors\n-------\n\n * Jose Miguel de la Rosa-Trev\u00edn, Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden\n * Grigory Sharov, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, England\n\nTesting\n-------\n\n``python3 -m unittest discover emtable/tests``\n\nExamples\n--------\n\nTo start using the package, simply do:\n\n.. code-block:: python\n\n from emtable import Table\n\nEach table in STAR file usually has a *data\\_* prefix. You only need to specify the remaining table name:\n\n``Table(fileName=modelStar, tableName='perframe_bfactors')``\n\nBe aware that from Relion 3.1 particles table name has been changed from \"data_Particles\" to \"data_particles\".\n\nReading\n#######\n\nFor example, we want to read the whole *rlnMovieFrameNumber* column from modelStar file, table *data_perframe_bfactors*.\n\nThe code below will return a list of column values from all rows:\n\n.. code-block:: python\n\n table = Table(fileName=modelStar, tableName='perframe_bfactors')\n frame = table.getColumnValues('rlnMovieFrameNumber')\n\nWe can also iterate over rows from \"data_particles\" Table:\n\n.. code-block:: python\n\n table = Table(fileName=dataStar, tableName='particles')\n for row in table:\n print(row.rlnRandomSubset, row.rlnClassNumber)\n\nAlternatively, you can use **iterRows** method which also supports sorting by a column:\n\n.. code-block:: python\n\n mdIter = Table.iterRows('particles@' + fnStar, key='rlnImageId')\n\nIf for some reason you need to clear all rows and keep just the Table structure, use **clearRows()** method on any table.\n\n\nWriting\n#######\n\nIf we want to create a new table with 3 pre-defined columns, add rows to it and save as a new file:\n\n.. code-block:: python\n\n tableShifts = Table(columns=['rlnCoordinateX',\n 'rlnCoordinateY',\n 'rlnAutopickFigureOfMerit',\n 'rlnClassNumber'])\n tableShifts.addRow(1024.54, 2944.54, 0.234, 3)\n tableShifts.addRow(445.45, 2345.54, 0.266, 3)\n\n tableShifts.write(f, tableName=\"test\", singleRow=False)\n\n*singleRow* is **False** by default. If *singleRow* is **True**, we don't write a *loop_*, just label-value pairs. This is used for \"one-column\" tables, such as below:\n\n\n.. code-block:: bash\n\n data_general\n\n _rlnImageSizeX 3710\n _rlnImageSizeY 3838\n _rlnImageSizeZ 24\n _rlnMicrographMovieName Movies/20170629_00026_frameImage.tiff\n _rlnMicrographGainName Movies/gain.mrc\n _rlnMicrographBinning 1.000000\n _rlnMicrographOriginalPixelSize 0.885000\n _rlnMicrographDoseRate 1.277000\n _rlnMicrographPreExposure 0.000000\n _rlnVoltage 200.000000\n _rlnMicrographStartFrame 1\n _rlnMotionModelVersion 1\n\n\n",
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