eyurtsev / eyurtsev/fcsparser

non-parsing FCS file (and a fix)

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#25 1 comment 0 reactions 0 assignees View on GitHub
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

Open the contributing 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

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