cdienem
commented
6 years ago Hi Sara,
sorry for my late reply but I was busy with my dissertation. I have checked my local version (which I just committed again) with your star file and also the -h option and it works. Are you sure you use the latest version? Because you also miss some other functions that I implemented later (like --debug).
Best, Chris
_Hello again! First, please accept my thanks for sharing this script. It's saved me a ton of time. I'm interested in writing pseudo Autopicking output files so that I can display my good particles on the original micrographs and look for trends. so I want to use --splitby {underscore}rlnMicrographName to split up my particles file that has ~50k particles into star files representing each micrograph in the dataset.
My input file particles3.star looks like this:
data_
loop_ _rlnCoordinateX #1 _rlnCoordinateY #2 _rlnClassNumber #3 _rlnAutopickFigureOfMerit #4 _rlnAnglePsi #5 _rlnMicrographName #6 1925.0 1531.0 49.0 0.484168 48.399981 movies/FoilHole_19688228_Data_19688973_19688974_20171219_1300_frames1to20.mrc
I'm trying to run it this way:
python /path/_git/StarTool/startool.py particles3.star --split_by _rlnMicrographName usage: startool [-h] [--info [INFO]] [--show [SHOW]] [--use USE] [--select SELECT] [--select_regex SELECT_REGEX] [--select_star SELECT_STAR] [--select_fancy SELECT_FANCY] [--release [RELEASE]] [--deselect [DESELECT]] [--sort SORT] [--tros TROS] [--subset SUBSET] [--add_col ADD_COL] [--delete_col DELETE_COL] [--rename_col RENAME_COL] [--delete_table DELETE_TABLE] [--rename_table RENAME_TABLE] [--replace REPLACE] [--replace_regex REPLACE_REGEX] [--replace_star REPLACE_STAR] [--delete [DELETE]] [--merge MERGE] [--query QUERY] [--write_selection WRITE_SELECTION] [--write WRITE] i startool: error: unrecognized arguments: --split_by _rlnMicrographName
_also, as an aside, when I call -h I don't see --splitby in the list of functions.
python /path/_git/StarTool/startool.py -h usage: startool [-h] [--info [INFO]] [--show [SHOW]] [--use USE] [--select SELECT] [--select_regex SELECT_REGEX] [--select_star SELECT_STAR] [--select_fancy SELECT_FANCY] [--release [RELEASE]] [--deselect [DESELECT]] [--sort SORT] [--tros TROS] [--subset SUBSET] [--add_col ADD_COL] [--delete_col DELETE_COL] [--rename_col RENAME_COL] [--delete_table DELETE_TABLE] [--rename_table RENAME_TABLE] [--replace REPLACE] [--replace_regex REPLACE_REGEX] [--replace_star REPLACE_STAR] [--delete [DELETE]] [--merge MERGE] [--query QUERY] [--write_selection WRITE_SELECTION] [--write WRITE] i
Swiss army knife for editing star files
positional arguments: i
optional arguments: -h, --help show this help message and exit --info [INFO] --show [SHOW] --use USE --select SELECT --select_regex SELECT_REGEX --select_star SELECT_STAR --select_fancy SELECT_FANCY --release [RELEASE] --deselect [DESELECT] --sort SORT --tros TROS --subset SUBSET --add_col ADD_COL --delete_col DELETE_COL --rename_col RENAME_COL --delete_table DELETE_TABLE --rename_table RENAME_TABLE --replace REPLACE --replace_regex REPLACE_REGEX --replace_star REPLACE_STAR --delete [DELETE] --merge MERGE --query QUERY --write_selection WRITE_SELECTION --write WRITE