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eyurtsev / fcsparser

A python parser for reading fcs files supporting FCS 2.0, 3.0, 3.1
MIT License
74 stars 45 forks source link

non-parsing FCS file (and a fix) #25

Open matt-faria opened 3 years ago

matt-faria commented 3 years ago

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?

eyurtsev commented 3 years ago

PRs will be very welcome. I'm happy to merge as long as you include unit-tests.

For style if possible follow PEP-8 conventions and google style doc-strings (I don't have any linters that check for that, so if that's difficult I can follow up with appropriate linting).