Merging annotations

This page contains usage information for pytom_merge_stars.py.

Merging starfiles

After running template matching and candidate extraction on multiple tomograms, each tomogram will have an individual starfile with particle annotations. Each starfile will contain the MicrographName column which refers back to the tomogram name. Multiple starfiles can therefore be appended to results in a large list which can be used in other software (such as RELION, WarpM) to load annotations. These software will link the annotations to specific tilt-series using the MicrographName column.

Usage

pytom_merge_stars.py merges multiple starfiles into a single starfile. Basic usage of the script is:

pytom_merge_star.py 
  [-h] 
  [-i INPUT_DIR] 
  [-o OUTPUT_FILE] 
  [--log LOG]

Without providing any parameters the script will try to merge all the starfiles in the current working directory and save them to a new file particles.star.

Parameters

The following options are available:

• -h, --help

  Show a help message and exit.

• -i INPUT_DIR, --input-dir INPUT_DIR

  Provide a path to a directory of starfiles. The script will try to merge all files that end in '.star', it is up to the user to ensure that they are mergeable.

• -o OUTPUT_FILE, --output-file OUTPUT_FILE

  Path for writing the output starfile.

• --log LOG

  Can be switched from default info to debug mode to be more verbose.