dynamotable 0.3.0

Read and write Dynamo table files as pandas dataframes

dynamotable

dynamotable is a Python package to facilitate reading and writing of table files from the Dynamo subtomogram averaging package

Features

• Read table files created by Dynamo as pandas DataFrames
• Write table files compatible with Dynamo subtomogram averaging from minimal data
• Supports reading and writing of table map files with tables to keep track of tomogram files
• clean API

Installation

Installation is available directly from the Python package index

pip install dynamotable

Usage

Reading table files

Simple

import dynamotable
df = dynamotable.read('t_double.tbl')

>>> df = dynamotable.read('t_double.tbl')
>>> df
     tag  aligned_value  averaged_value        dx  ...  npar  undefined1  ref  sref
0      1              1               0  2.517800  ...     0           0    0     5
1      2              1               0  3.246300  ...     0           0    0     4
2      3              1               0 -2.984100  ...     0           0    0     4
3      4              1               0  3.307000  ...     0           0    0     4
4      5              1               0  1.058900  ...     0           0    0     2
..   ...            ...             ...       ...  ...   ...         ...  ...   ...
295  296              1               0 -2.656600  ...     0           0    0     5
296  297              1               0  3.829400  ...     0           0    0     1
297  298              1               0  1.701600  ...     0           0    0     5
298  299              1               0  0.003773  ...     0           0    0     2
299  300              1               0 -0.231290  ...     0           0    0     3

[300 rows x 35 columns]

With table map file

table map files are two column text files containing the tomogram index (found in column 20 of a table file) and the file path of the tomogram.

>>> df = dynamotable.read('t_complex.tbl', 'tmap_complex.doc')
>>> df

>>> df
        tag  aligned_value  ...  eig1                   tomo_file
0         2              1  ...     0  tomo_ts01.mrc_15.00Apx.mrc
1         4              1  ...     0  tomo_ts01.mrc_15.00Apx.mrc
2         6              1  ...     0  tomo_ts01.mrc_15.00Apx.mrc
3         8              1  ...     0  tomo_ts01.mrc_15.00Apx.mrc
4        10              1  ...     0  tomo_ts01.mrc_15.00Apx.mrc
     ...            ...  ...   ...                         ...
8737  18064              1  ...     0  tomo_ts99.mrc_15.00Apx.mrc
8738  18066              1  ...     0  tomo_ts99.mrc_15.00Apx.mrc
8739  18068              1  ...     0  tomo_ts99.mrc_15.00Apx.mrc
8740  18070              1  ...     0  tomo_ts99.mrc_15.00Apx.mrc
8741  18072              1  ...     0  tomo_ts99.mrc_15.00Apx.mrc

[8742 rows x 42 columns]

An extra column called tomo_file is added to the dataframe which contains the filepath of the tomogram you wish the particle to be linked to

Writing table files

Table files are written with dynamotable.write

>>> dynamotable.write(df, 'table_out.tbl')

Note that

• if tag is not a column in the dataframet then tags will be generated automatically
• if tomo_file is a column in the dataframe then a corresponding table map file will be generated
• if tomo_file is provided but no tomogram table indices are present these will be generated automatically
• if the aligned_value column is not present it will be set to 1 to mark particles for alignment in subtomogram averaging projects

License

The project is released under the BSD 3-Clause License