STAR file I/O in Python

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Project description

starfile

starfile is a package for reading and writing STAR files in Python.

starfile can be used interactively to inspect/explore files or in scripts and larger software packages to provide basic STAR file I/O functions. Data is exposed as simple python dictionaries or pandas dataframes.

This package was designed principally for compatibility with files generated by RELION.

For more information on working with dataframes, please see the pandas docs.

For starfile specific documentation, see teamtomo.org/starfile

Quickstart

For the following file particles.star with a single data block

data_particles

loop_
_rlnCoordinateX #1
_rlnCoordinateY #2
_rlnCoordinateZ #3
_rlnAngleRot #4
_rlnAngleTilt #5
_rlnAnglePsi #6
_rlnMicrographName #7
91.798700	83.622600	203.341030	-51.740000	173.930000	32.971000	01_10.00Apx.mrc
97.635800	80.437000	203.136160	141.500000	171.760000	-134.680000	01_10.00Apx.mrc
92.415200	88.842700	210.663900	-78.750000	173.930000	87.263200	01_10.00Apx.mrc
94.607830	93.135410	205.425960	-85.215000	167.170000	85.632200	01_10.00Apx.mrc
86.187800	80.125400	204.558750	14.910000	163.260000	-16.030000	01_10.00Apx.mrc
91.824240	76.738300	203.794280	39.740000	168.410000	-57.250000	01_10.00Apx.mrc
98.253300	73.530100	203.856030	73.950000	166.380000	-84.640000	01_10.00Apx.mrc
101.303500	80.290800	194.790400	-178.878000	166.090000	73.181000	01_10.00Apx.mrc

Read the file

import starfile

df = starfile.read('particles.star')

Interact with the data

df['rlnCoordinateX'] += 10
df.head()

   rlnCoordinateX  rlnCoordinateY  rlnCoordinateZ  rlnAngleRot  rlnAngleTilt  rlnAnglePsi rlnMicrographName
0       101.79870        83.62260       203.34103      -51.740        173.93      32.9710   01_10.00Apx.mrc
1       107.63580        80.43700       203.13616      141.500        171.76    -134.6800   01_10.00Apx.mrc
2       102.41520        88.84270       210.66390      -78.750        173.93      87.2632   01_10.00Apx.mrc
3       104.60783        93.13541       205.42596      -85.215        167.17      85.6322   01_10.00Apx.mrc
4        96.18780        80.12540       204.55875       14.910        163.26     -16.0300   01_10.00Apx.mrc

Save the (modified) data to file

starfile.write(df, 'modified_particles.star')

For more advanced usage please check out the examples.

Installation

pip install starfile

Project details

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Release history Release notifications | RSS feed

0.111 yanked

Jun 18, 2020

0.12 yanked

Jun 27, 2020

0.11 yanked

Jun 18, 2020

0.5.8

May 21, 2024

0.5.7

Apr 29, 2024

0.5.6

Feb 22, 2024

0.5.5

Feb 22, 2024

This version

0.5.4

Jan 16, 2024

0.5.3

Jan 15, 2024

0.5.2

Dec 5, 2023

0.5.1

Oct 26, 2023

0.5.0

Oct 11, 2023

0.4.12

Apr 11, 2023

0.4.11

Jan 6, 2022

0.4.10

Dec 18, 2021

0.4.9

Oct 8, 2021

0.4.7

Sep 14, 2021

0.4.6

Sep 8, 2021

0.4.5

Apr 18, 2021

0.4.4

Dec 11, 2020

0.4.2

Dec 11, 2020

0.4.1

Dec 8, 2020

0.4.0 yanked

Dec 1, 2020

Reason this release was yanked:

significant performance regression

0.3.3

Nov 24, 2020

0.3.2

Nov 9, 2020

0.3.1 yanked

Oct 15, 2020

Reason this release was yanked:

bug in reading simple star files (fixed in 0.3.2)

0.3.0 yanked

Oct 15, 2020

Reason this release was yanked:

bug in reading simple star files (fixed in 0.3.2)

0.2.3

Oct 13, 2020

0.2.2

Oct 3, 2020

0.2.1

Oct 3, 2020

0.2.0

Oct 3, 2020

0.1.3

Sep 28, 2020

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