non-parsing FCS file (and a fix)
- Dominant language
- Python
- Stars
- 84
- Forks
- 51
- PR merge metrics
- No merged PRs in 30d
Description
Hi, flow cytometry files from Apogee don't parse with fcs parser.
They (inexplicably) have a bunch of spaces before $P1N in the header, this can be remedied without too much trouble though.
An example of an FCS file with the issue:
https://bitbucket.org/mwfcomp/incubation_experiment/raw/a6ef3685428f6e373442ab0e04b553b36bbcdd48/sample_data/2015-07-08/THP-1%20-%20235%20nm%20Capsule%2016%20hr.fcs
And a (slightly hacky) script to fix this per file:
https://bitbucket.org/mwfcomp/incubation_experiment/raw/a6ef3685428f6e373442ab0e04b553b36bbcdd48/fcs_file_fixer.py
This could be dealt with more elegantly in the parser, I would be happy to put together a solution for it if this is acceptable and this project is still being maintained?
Contributor guide
Research direction
Download the linked Apogee FCS sample and reproduce the parsing failure before reading the workaround in fcs_file_fixer.py. Trace how the parser reads the header around the padded $P1N field; done means the example parses directly without the per-file fixer and existing FCS parsing remains unaffected.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100