VER: 0.9 - RedGEM is Here! #26
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FIX: Catch None type in formulas
…the deprected variable GREP_OPTIONS='--color=auto'
…queue, better relaxation with in_place option and queueing of the constraints
…rement to have better UI
reactions/metabolites
… for less clutter
…edure by using pyTFA VA instead of cobra's, prepared the code for other lumping methods
…ment by medium override definition
…s not know it is being run on Travis
…test to skip while working on a solution
Codecov Report
@@ Coverage Diff @@
## master #26 +/- ##
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- Coverage 65.41% 56.13% -9.29%
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Files 38 44 +6
Lines 2539 3235 +696
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+ Hits 1661 1816 +155
- Misses 878 1419 +541
Continue to review full report at Codecov.
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…dding a home-made function for reaction summing to try to avoid gpr eval memory issues
…ing to models in favor of a lightweight dict_based method.
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This release includes (finally!) a Python implementation of our redGEM[1] and lumpGEM[2] papers for systematic genome-scale metabolic model reduction.
The code is still in development, so any feedback is welcome :)
This version also features:
[1] Ataman, Meric, et al. "redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models." PLoS computational biology 13.7 (2017): e1005444.
https://doi.org/10.1371/journal.pcbi.1005444
[2] Ataman, Meric, and Vassily Hatzimanikatis. "lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites." PLoS computational biology 13.7 (2017): e1005513.
https://doi.org/10.1371/journal.pcbi.1005513