Include additional subcommands - Githubissues

cnobles / iGUIDE

Bioinformatic pipeline for identifying dsDNA breaks by marker based incorporation, such as breaks induced by designer nucleases like Cas9.

https://iguide.readthedocs.io/en/latest/

GNU General Public License v3.0

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Include additional subcommands #23

Open cnobles opened 5 years ago

cnobles commented 5 years ago

Complete the functionality of the additional subcommands:

config : modify / update / create config files for running iGUIDE
- subsubcommand style, possibly include a python-base command line tutorial / guide to create a config file.

cnobles commented 5 years ago

Implemented the 'list_samples' subcommand in latest release 2f44a19897cb2c591301308f096687fbdb14b968.

cnobles commented 5 years ago

Implemented 'report' and 'clean' in v0.9.4 update (33b558e393ae7c5a8584d8e59122f2dba5fc6ec9).

cnobles commented 5 years ago

Implemented 'eval' and modified 'report' in v0.9.6 update (5a15cdf64b0966fdd4d4a3e324194825e01a0961).

Evaluating an assimilated dataset or datasets groups the data and applies the same references. This workflow (Processing sequence data to alignments -> assimilating data -> evaluation -> report) allows for easy branching analysis from the evaluation.

cnobles commented 5 years ago

Implemented the 'summary' subcommand in v0.9.8 merge (28cc071fb4243c0bf34b3210ae6b6ec00498b8f4).

summary : prints a short text-based report given a config or eval file
- output in a text-based format, broken up by specimen or condition, similar to the report
- supply option to filter by MESL and/or top N off-target sites with coord and gene_id