Mit expression #5

OmidOftadeh · 2020-02-13T11:28:47Z

Mitochondrial expression system

OmidOftadeh · 2020-02-13T16:11:53Z

Hi Pierre,
Indeed, I have changed 3 files to implement mitochondrial RNAP and ribosome.
Here is a description of changes in each file:

genes.py: the setters for transcribed_by and translated_by attributes are changed so they can be set if either the gene is not connected to a model or it is connected to a model, but synthesis constraint is not created yet.
memodel.py: two functions, add_translation_by and add_transcription_by were added to assign the corresponding RNAP and ribosome to each gene, respectively. Moreover, _populate_ribosome and _populate_rnap were modified to define a total capacity constraint per each ribosome and RNAP.
dict.py: it was modified so that regardless of type of transcribe_by and translated_by (either enzyme object or string) it can be converted to JSON file.

Cheer,
Omid

EDIT (by Pierre): formatting

psalvy · 2020-02-24T08:23:59Z

etfl/core/genes.py

@@ -14,6 +14,7 @@
 from cobra import Gene
 from Bio.Seq import Seq
 from Bio.Alphabet import DNAAlphabet, RNAAlphabet, ProteinAlphabet
+from etfl.optim.constraints import SynthesisConstraint


change to
from ..optim.constraints import SynthesisConstraint

psalvy · 2020-02-24T08:24:58Z

etfl/core/genes.py

+            else:
+                # We need to make the model change the corresponding cstr
+                mod_id = self.id + '_transcription'
+                Cstr = self.model.get_constraints_of_type(SynthesisConstraint)


please respect the conventions and use Uppercas names only for classes. variables are lowercase most of the time.

psalvy · 2020-02-24T08:26:08Z

etfl/core/genes.py

+                try:
+                    Cstr.get_by_id(mod_id)
+                except KeyError:
+                    cstr_exist = 0


Please use True and False instead of 1 and 0

Also please add comments as to why you are doing this: checking that the genes are not transcribed yet.

psalvy · 2020-02-24T08:29:55Z

etfl/core/genes.py

+                self._transcribed_by = value
+            else:
+                # We need to make the model change the corresponding cstr
+                mod_id = self.id + '_transcription'


Please replace by get_transcription_reaction_name

You mean I should write a new function to do this?

There is already a function for this here

psalvy · 2020-02-24T08:30:39Z

etfl/core/genes.py

+                    cstr_exist = 0
+                if cstr_exist:
+                    # trancription constraint already exists
+                    raise NotImplementedError()


Please add #TODO with instructions

psalvy · 2020-02-24T08:30:52Z

etfl/core/genes.py

@@ -86,7 +107,27 @@ def translated_by(self):
    @translated_by.setter
    def translated_by(self,value):
        # TODO: Make this a setter that rewrites the adequate constraints
-        raise NotImplementedError()
+        if value != self._translated_by:


Same comments as before

psalvy · 2020-02-24T08:31:50Z

etfl/core/memodel.py

@@ -259,24 +259,54 @@ def add_nucleotide_sequences(self, sequences):
        :param sequences:
        :return:
        """
-
+        


can you please remove these empty lines containing only spaces

psalvy · 2020-02-24T08:32:34Z

etfl/core/memodel.py

+
+    def add_transcription_by(self, transcription_dict):
+
+        for gene_id, transcripted_by in transcription_dict.items():


Please rename transcripted_by into transcribed_by

psalvy · 2020-02-24T08:33:12Z

etfl/core/memodel.py

+            # transcripted_by is a list of rnap(s)
+            try:
+                self.genes.get_by_id(gene_id).transcribed_by = transcripted_by
+            except KeyError:


Please add a comment explaining in which case this error would happen

psalvy · 2020-02-24T08:35:06Z

etfl/core/memodel.py


    def _make_peptide_from_gene(self, gene_id):
        free_pep = Peptide(id=gene_id,
                           name='Peptide, {}'.format(gene_id),
                           gene_id=gene_id)
        free_pep._model = self
        self.peptides += [free_pep]
+
+    def add_peptide_sequences(self, aa_sequences):


Can you remind me for which case you had to add this ?

This is a function that I have to add my peptide sequences. It's not related to mitochondrial expression. You can neglect it.

psalvy · 2020-02-24T08:38:31Z

etfl/core/memodel.py

-                     for x in self.rnap]
+        # only for genes trascribed by this rnap
+        sum_RMs = symbol_sum([x.unscaled for x in all_rnap_usage \
+                             if x.hook.transcribed_by is None \


Add a comment explaining why we include the None as well

psalvy · 2020-02-24T08:39:15Z

etfl/core/memodel.py

-                - sum([x.concentration for x in self.rnap.values()])
-        usage /= min([x.scaling_factor for x in self.rnap.values()])
+                - sum([self.rnap[rnap_id].concentration])
+        usage /= min([self.rnap[rnap_id].scaling_factor])


You can remove the min here, we do not have an iterable anymore

psalvy · 2020-02-24T08:39:56Z

etfl/core/memodel.py

        # The total RNAP capacity constraint looks like
        # ΣRMi + Σ(free RNAPj) = Σ(Total RNAPj)
        usage = sum_RMs \
                + sum([x.unscaled for x in free_rnap]) \
-                - sum([x.concentration for x in self.rnap.values()])
-        usage /= min([x.scaling_factor for x in self.rnap.values()])
+                - sum([self.rnap[rnap_id].concentration])


You can remove the sum here, we do not have a list anymore

psalvy · 2020-02-24T08:40:25Z

etfl/core/memodel.py

-        sum_RPs = symbol_sum([x.unscaled for x in all_ribosome_usage])
+        # only for genes traslated by this ribosome
+        sum_RPs = symbol_sum([x.unscaled for x in all_ribosome_usage \
+                              if x.hook.translated_by is None \


same as before

psalvy · 2020-02-24T08:54:34Z

etfl/io/dict.py

+            if gene.translated_by is not None else None
+    except AttributeError:
+        obj['translated_by'] = [x for x in gene.translated_by] \
+            if gene.translated_by is not None else None            


I see no method to read that back from the dictionary ?

I will do this later ;)

psalvy · 2020-02-24T08:54:42Z

etfl/io/dict.py

                g._rna            = Seq(gene_dict['rna'], alphabet=RNAAlphabet())
                g._peptide        = Seq(gene_dict['peptide'], alphabet=ProteinAlphabet())
                g._copy_number    = int(gene_dict['copy_number'])
-
+                


psalvy

Please go through the comments and implement the requested fixes. In particular:

You need to comment more your code
There is no method to read the transcribed_by / translated_by back from the dictionary upon serialization

…is solved

ENH: implement mitochondrial expression system

d5f94c2

OmidOftadeh force-pushed the mit_expression branch from 185af82 to d5f94c2 Compare February 13, 2020 15:42

psalvy added the enhancement New feature or request label Feb 13, 2020

psalvy self-assigned this Feb 13, 2020

psalvy self-requested a review February 13, 2020 16:30

psalvy reviewed Feb 24, 2020

View reviewed changes

psalvy requested changes Feb 24, 2020

View reviewed changes

FIX: implemented the comments

605c00b

OmidOftadeh force-pushed the mit_expression branch from 8717f82 to 605c00b Compare February 28, 2020 18:54

FIX: the issue for the genes with several assigned ribosome and rnap …

2cd0619

…is solved

OmidOftadeh force-pushed the mit_expression branch from 80dcb00 to 2cd0619 Compare March 3, 2020 18:26

psalvy force-pushed the dev branch from a78593e to 5e5d8e8 Compare June 29, 2020 14:30

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Mit expression #5

Mit expression #5

OmidOftadeh commented Feb 13, 2020

OmidOftadeh commented Feb 13, 2020 •

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		def add_transcription_by(self, transcription_dict):

		for gene_id, transcripted_by in transcription_dict.items():

Mit expression #5

Are you sure you want to change the base?

Mit expression #5

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OmidOftadeh commented Feb 13, 2020

OmidOftadeh commented Feb 13, 2020 • edited by psalvy Loading

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OmidOftadeh commented Feb 13, 2020 •

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