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Parse settings #101

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merged 23 commits into from
Nov 22, 2023
Merged

Parse settings #101

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8fc4166
:art: format code (max-line-length=120!)
Sep 25, 2023
f5445a7
Merge branch 'main' of https://github.com/Proteobench/ProteoBench int…
Sep 25, 2023
f05c2a9
Merge branch 'main' into parse_settings
Sep 25, 2023
56e846f
:sparkles: parse mqpar.xml to dictionary
Sep 25, 2023
b8a56b1
Merge main into parse_settings
Sep 25, 2023
d7e38b7
:bug: add support for newer annotations in py38
Sep 26, 2023
532157f
:sparkles: DataFrame and csv format for MQ parameters
Sep 26, 2023
9b69350
Merge branch 'main' into parse_settings
Oct 12, 2023
be17263
:art: format merged file
Oct 12, 2023
27079ef
Merge branch 'main' into parse_settings
Oct 21, 2023
fcce49f
:sparkles: Parse MSFragger parameter files
Oct 21, 2023
dc1233e
:sparkles: Proline params + mapping params to our names
Oct 21, 2023
07ff672
Merge branch 'main' into parse_settings
Nov 9, 2023
8ab896a
:art: correct spelling mistake fragmnent -> fragment
Nov 10, 2023
a83dbcf
:construction: Prepare renaming according to SDRF
Nov 10, 2023
030eb20
:sparkles: SDRF extended naming
Nov 11, 2023
682825d
:construction: start extracting MQ params
Nov 13, 2023
33aebf4
Merge branch 'main' into parse_settings
Nov 13, 2023
df208d2
:bug: update test ("fragmnent" -> "fragment")
Nov 13, 2023
5a95fa0
:sparkles: Add parsing of attributes for MaxQuant 1.5
Nov 19, 2023
f47c6fc
:sparkles: extract ms2 parameter based on specified method
Nov 19, 2023
769624a
:construction_worker:
Nov 19, 2023
27f8f1f
Merge branch 'main' into parse_settings
Nov 22, 2023
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41 changes: 21 additions & 20 deletions proteobench/io/params/__init__.py
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There are two parameters missing, and I did not find the correspondance in the SDRF doc. But maybe I missed it:
'software_name' for the software tool (that combines a search engine and some algorithms for quantification)
'search_engine_version'

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yes, me neither. I guess this is something SDRF does intend to have.

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Could you check with Veit? Or anybody else? I think that we don't take any risk any way if we name them this way, No?

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no, we can decide the name for parameters specific to our needs. SDRF is independent of software tools, so it would not make sense to have this kind of information there.

Original file line number Diff line number Diff line change
Expand Up @@ -2,29 +2,30 @@
from typing import Optional


# Reference for parameter names
# https://github.com/bigbio/proteomics-sample-metadata/blob/master/sdrf-proteomics/assets/param2sdrf.yml
# new name as comment
@dataclass
class ProteoBenchParameters:
search_engine: Optional[str] = None
software_version: Optional[str] = None
fdr_psm: Optional[str] = None
fdr_peptide: Optional[str] = None
fdr_protein: Optional[str] = None
MBR: Optional[str] = None
precursor_tol: Optional[str] = None
fdr_psm: Optional[str] = None # ident_fdr_psm
fdr_peptide: Optional[str] = None # ident_fdr_peptide
fdr_protein: Optional[str] = None # ident_fdr_protein
MBR: Optional[str] = None # enable_match_between_runs
precursor_tol: Optional[
str
] = None # precursor_mass_tolerance, value and unit not separated
precursor_tol_unit: Optional[str] = None
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fragment_tol: Optional[str] = None
fragment_tol: Optional[
str
] = None # fragment_mass_tolerance, value and unit not separated
fragment_tol_unit: Optional[str] = None
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enzyme_name: Optional[str] = None
missed_cleavages: Optional[str] = None
min_pep_length: Optional[str] = None
max_pep_length: Optional[str] = None
fixed_modifications: Optional[str] = None
variable_modifications: Optional[str] = None
max_num_modifications: Optional[str] = None
precursor_charge: Optional[str] = None


# params = ProteoBenchParameters()
# params.search_engine = "MaxQuant"
# params
# %%
enzyme_name: Optional[str] = None # enzyme
missed_cleavages: Optional[str] = None # allowed_miscleavages
min_pep_length: Optional[str] = None # min_peptide_length
max_pep_length: Optional[str] = None # max_peptide_length
fixed_modifications: Optional[str] = None # fixex_mods
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should be 'fixed_mods'

variable_modifications: Optional[str] = None # variable_mods
max_num_modifications: Optional[str] = None # max_mods
precursor_charge: Optional[str] = None # min_precursor_charge
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if we don't enter all the possible precursor charges, then we should have min_ and max_precursor_charge

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But the maximum can be unlimited in some tools?

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I am not sure. I guess that if this happens, we'll have a missing value there.
What I meant was more that in cases like in MQ, where they give all the charges that they consider, we need to get the min. and max. No?

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MQ specifies a range of min. and max. charge. We only have a problem if a tools would e.g. allow peptides with charges 2,3 and 5, but excludes charges with 4. But I guess this is quite uncommon?

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Yep, you are absolutely right. There could be an issue in this case. I don't like this.
Do you think that it is/was/should be discussed for the SDRF-extended format? Because this problem can also arise for them.

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In that case yes, as we should not diverge from SDRF-extended.

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