alphadia 1.9.3.dev2__tar.gz → 1.10.3__tar.gz

{alphadia-1.9.3.dev2/alphadia.egg-info → alphadia-1.10.3}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: alphadia
-Version: 1.9.3.dev2
+Version: 1.10.3
 Summary: A novel proteomics search engine for DIA data based on end-to-end transfer learning.
 Author-email: Mann Labs <wallmann@biochem.mpg.de>
 License:                                  Apache License
@@ -219,49 +219,110 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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 Requires-Dist: peptdeep>=1.3.0
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@@ -273,14 +334,11 @@ Requires-Dist: pandoc; extra == "docs"
 Provides-Extra: development
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@@ -288,6 +346,7 @@ Requires-Dist: myst_parser; extra == "development"
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 Requires-Dist: pandoc; extra == "development"
+Dynamic: license-file
 
 ![GitHub Release](https://img.shields.io/github/v/release/mannlabs/alphadia?logoColor=green&color=brightgreen)
 ![Versions](https://img.shields.io/badge/python-3.10_%7C_3.11_%7C_3.12-brightgreen)
@@ -365,15 +424,34 @@ AlphaDIA can be installed on Windows, macOS and Linux. Please choose the preferr
 * [**Slurm installation:**](docs/installation.md#slurm-cluster-installation) Choose this for running alphaDIA on a research cluster with Slurm.
 
 ### One-click GUI installation
-Currently available for **MacOS** and **Windows**.
 You can download the latest release of alphaDIA [here](https://github.com/Mannlabs/alphadia/releases/latest).
 
-* **Windows:** Download the latest `alphadia-X.Y.Z-windows-amd64.exe` build and double click it to install. If you receive a warning during installation click *Run anyway*.
-* **MacOS:** Download the latest build suitable for your chip architecture
+
+#### Windows
+Download the latest `alphadia-X.Y.Z-windows-amd64.exe` build and double click it to install. If you receive a warning during installation click *Run anyway*.
+Important note: always install AlphaDIA into a new folder, as the installer will not properly overwrite existing installations.
+
+#### Linux
+If you want to use `.raw` files from Thermo instruments AlphaRaw is required, which depends on Mono.
+A detailed guide to installing AlphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
+
+Download the latest `alphadia-X.Y.Z-linux-x64.deb` build and install it via `dpkg -i alphadia-X.Y.Z-linux-x64.deb`.
+
+#### MacOS
+If you want to use `.raw` files from Thermo instruments AlphaRaw is required, which depends on Mono.
+A detailed guide to installing AlphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
+
+Download the latest build suitable for your chip architecture
 (can be looked up by clicking on the Apple Symbol > *About this Mac* > *Chip* ("M1", "M2", "M3" -> `arm64`, "Intel" -> `x64`),
 `alphadia-X.Y.Z-macos-darwin-arm64.pkg` or `alphadia-X.Y.Z-macos-darwin-x64.pkg`. Open the parent folder of the downloaded file in Finder,
-right-click and select *open*. If you receive a warning during installation click *Open*. If you want to use `.raw` files on Thermo instruments alphaRaw is required, which depends on Mono. A detailed guide to installing alphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
-* **Linux:** Download the latest `alphadia-X.Y.Z-linux-x64.deb` build and install it via `dpkg -i alphadia-X.Y.Z-linux-x64.deb`.
+right-click and select *open*. If you receive a warning during installation click *Open*.
+
+In newer MacOS versions, additional steps are required to enable installation of unverified software.
+This is indicated by a dialog telling you `“alphadia. ... .pkg” Not Opened`.
+1. Close this dialog by clicking `Done`.
+2. Choose `Apple menu` > `System Settings`, then `Privacy & Security` in the sidebar. (You may need to scroll down.)
+3. Go to `Security`, locate the line "alphadia.pkg was blocked to protect your Mac" then click `Open Anyway`.
+4. In the dialog windows, click `Open Anyway`.
 
 
 As of now, **Linux** users need follow the steps for the
@@ -387,10 +465,10 @@ you can install alphaDIA via `pip`.
 Please make sure you have a valid installation of conda or miniconda.
 We recommend setting up miniconda as described on their [website](https://docs.conda.io/projects/miniconda/en/latest/).
 
-If you want to use `.raw` files on Thermo instruments alphaRaw is required, which depends on Mono. A detailed guide to installing alphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
+If you want to use `.raw` files on Thermo instruments alphaRaw is required, which depends on Mono. A detailed guide to installing AlphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
 
 #### 2. Setting up the environment
-For any Python package, it is highly recommended to use a separate, as otherwise dependancy conflicts can occur with already existing packages. We generally recommend [miniconda](https://docs.anaconda.com/free/miniconda/).
+For any Python package, it is highly recommended to use a separate, as otherwise dependency conflicts can occur with already existing packages. We generally recommend [miniconda](https://docs.anaconda.com/free/miniconda/).
 
 Finally, alphaDIA and all its dependencies can be installed by
 ```bash

{alphadia-1.9.3.dev2 → alphadia-1.10.3}/README.md

@@ -74,15 +74,34 @@ AlphaDIA can be installed on Windows, macOS and Linux. Please choose the preferr
 * [**Slurm installation:**](docs/installation.md#slurm-cluster-installation) Choose this for running alphaDIA on a research cluster with Slurm.
 
 ### One-click GUI installation
-Currently available for **MacOS** and **Windows**.
 You can download the latest release of alphaDIA [here](https://github.com/Mannlabs/alphadia/releases/latest).
 
-* **Windows:** Download the latest `alphadia-X.Y.Z-windows-amd64.exe` build and double click it to install. If you receive a warning during installation click *Run anyway*.
-* **MacOS:** Download the latest build suitable for your chip architecture
+
+#### Windows
+Download the latest `alphadia-X.Y.Z-windows-amd64.exe` build and double click it to install. If you receive a warning during installation click *Run anyway*.
+Important note: always install AlphaDIA into a new folder, as the installer will not properly overwrite existing installations.
+
+#### Linux
+If you want to use `.raw` files from Thermo instruments AlphaRaw is required, which depends on Mono.
+A detailed guide to installing AlphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
+
+Download the latest `alphadia-X.Y.Z-linux-x64.deb` build and install it via `dpkg -i alphadia-X.Y.Z-linux-x64.deb`.
+
+#### MacOS
+If you want to use `.raw` files from Thermo instruments AlphaRaw is required, which depends on Mono.
+A detailed guide to installing AlphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
+
+Download the latest build suitable for your chip architecture
 (can be looked up by clicking on the Apple Symbol > *About this Mac* > *Chip* ("M1", "M2", "M3" -> `arm64`, "Intel" -> `x64`),
 `alphadia-X.Y.Z-macos-darwin-arm64.pkg` or `alphadia-X.Y.Z-macos-darwin-x64.pkg`. Open the parent folder of the downloaded file in Finder,
-right-click and select *open*. If you receive a warning during installation click *Open*. If you want to use `.raw` files on Thermo instruments alphaRaw is required, which depends on Mono. A detailed guide to installing alphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
-* **Linux:** Download the latest `alphadia-X.Y.Z-linux-x64.deb` build and install it via `dpkg -i alphadia-X.Y.Z-linux-x64.deb`.
+right-click and select *open*. If you receive a warning during installation click *Open*.
+
+In newer MacOS versions, additional steps are required to enable installation of unverified software.
+This is indicated by a dialog telling you `“alphadia. ... .pkg” Not Opened`.
+1. Close this dialog by clicking `Done`.
+2. Choose `Apple menu` > `System Settings`, then `Privacy & Security` in the sidebar. (You may need to scroll down.)
+3. Go to `Security`, locate the line "alphadia.pkg was blocked to protect your Mac" then click `Open Anyway`.
+4. In the dialog windows, click `Open Anyway`.
 
 
 As of now, **Linux** users need follow the steps for the
@@ -96,10 +115,10 @@ you can install alphaDIA via `pip`.
 Please make sure you have a valid installation of conda or miniconda.
 We recommend setting up miniconda as described on their [website](https://docs.conda.io/projects/miniconda/en/latest/).
 
-If you want to use `.raw` files on Thermo instruments alphaRaw is required, which depends on Mono. A detailed guide to installing alphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
+If you want to use `.raw` files on Thermo instruments alphaRaw is required, which depends on Mono. A detailed guide to installing AlphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
 
 #### 2. Setting up the environment
-For any Python package, it is highly recommended to use a separate, as otherwise dependancy conflicts can occur with already existing packages. We generally recommend [miniconda](https://docs.anaconda.com/free/miniconda/).
+For any Python package, it is highly recommended to use a separate, as otherwise dependency conflicts can occur with already existing packages. We generally recommend [miniconda](https://docs.anaconda.com/free/miniconda/).
 
 Finally, alphaDIA and all its dependencies can be installed by
 ```bash

alphadia-1.10.3/alphadia/__init__.py

@@ -0,0 +1,9 @@
+#!python
+
+import warnings
+
+__version__ = "1.10.3"
+
+warnings.filterwarnings(
+    "ignore", message="Dependency 'dask' not installed.", module="directlfq"
+)

{alphadia-1.9.3.dev2 → alphadia-1.10.3}/alphadia/cli.py

@@ -3,6 +3,7 @@
 
 Ideally the CLI module should have as little logic as possible so that the search behaves the same from the CLI or a jupyter notebook.
 """
+# ruff: noqa: E402 # Module level import not at top of file
 
 import argparse
 import json
@@ -11,9 +12,11 @@ import os
 import re
 import sys
 
-import matplotlib
 import yaml
 
+logging.getLogger("matplotlib.font_manager").setLevel(logging.ERROR)
+import matplotlib  # noqa: E402
+
 import alphadia
 from alphadia import utils
 from alphadia.constants.keys import ConfigKeys

{alphadia-1.9.3.dev2 → alphadia-1.10.3}/alphadia/constants/default.yaml

@@ -10,13 +10,26 @@ fasta_paths: []
 quant_directory: null
 
 general:
+
   thread_count: 10
-  # maximum number of threads or processes to use per raw file
+  # Enables separate transfer learning step
+  transfer_step_enabled: false
+
+  # Enables separate MBR step
+  mbr_step_enabled: true
+
+  # === advanced settings ===
+  # whether to reuse previously calculated calibration data
   reuse_calibration: false
+  # whether to reuse previously calculated quantification data
   reuse_quant: false
+  # whether to use Astral MS1 feature detection
   astral_ms1: false
+  # logging verbosity level (DEBUG, INFO, PROGRESS, WARNING, ERROR)
   log_level: 'INFO'
+  # whether to memory map detector events for improved performance
   mmap_detector_events: false
+  # whether to use GPU acceleration for library prediction and scoring
   use_gpu: true
   # whether to save the libraries to the output directory
   save_library: True       # input library
@@ -27,25 +40,44 @@ library_loading:
   # if retention times are reported in absolute units, the rt_heuristic defines rt is interpreted as minutes or seconds
 
 library_prediction:
-  predict: False
+  # Basic parameters
+  # whether to use alphaPeptDeep to predict peptide properties
+  enabled: false
+  # enzyme used for in-silico digest
   enzyme: trypsin
+  # fixed modifications for in-silico digest
+  # Format: Modification@AminoAcid
+  # Example: Carbamidomethyl@C
   fixed_modifications: 'Carbamidomethyl@C'
+  # variable modifications for in-silico digest. Semicolon separated list
+  # See https://github.com/MannLabs/alphabase/blob/c99c1ec7eb482745f6dae58a324658d6b6c4abf0/alphabase/constants/const_files/modification.tsv
+  # Format: Modification@AminoAcid
+  # Example: Oxidation@M;Acetyl@Protein_N-term
   variable_modifications: 'Oxidation@M;Acetyl@Protein_N-term'
+  # maximum number of variable modifications per peptide
   max_var_mod_num: 2
+  # number of missed cleavages allowed for in-silico digest
   missed_cleavages: 1
   # using tuples here as it makes interaction with the GUI easier
+  # minimum and maximum number of amino acids for generated precursors
   precursor_len:
     - 7
     - 35
+  # minimum and maximum charge states for generated precursors
   precursor_charge:
     - 2
     - 4
+  # minimum and maximum m/z values for generated precursors
   precursor_mz:
     - 400
     - 1200
+  # minimum and maximum m/z values for generated fragments
   fragment_mz:
     - 200
     - 2000
+
+  # === advanced settings ===
+  # normalized collision energy for fragment generation
   nce: 25.0
 
   # list of fragment types (see alphabase.peptide.fragment.FRAGMENT_TYPES for supported types)
@@ -56,13 +88,15 @@ library_prediction:
 
   # maximum charge state for predicted fragments
   max_fragment_charge: 2
+
+  # instrument types as supported by peptdeep. Leave this as Lumos if you are not 100% sure you know what you are changing
   instrument: Lumos
 
   # set path for custom peptdeep model. If set to null, the default model will be used
   peptdeep_model_path: null
 
-  # set peptdeep model type. Possible values are 'generic', 'phospho', 'digly'. If set to null, the generic model will be used
-  peptdeep_model_type: null
+  # set peptdeep model type. Possible values are 'generic', 'phospho', 'digly'.
+  peptdeep_model_type: 'generic'
 
 # define custom alphabase modifications not part of unimod or alphabase
 # also used for decoy channels
@@ -96,25 +130,27 @@ custom_modifications:
     composition: C(12)
 
 search:
-  channel_filter: '0'
-  exclude_shared_ions: True
-  compete_for_fragments: True
-
-  target_num_candidates: 2
   # target ms1 tolerance in ppm
   target_ms1_tolerance: 5
   # target ms2 tolerance in ppm
   target_ms2_tolerance: 10
-  # target ion mobility tolerance in 1/K_0
-  target_mobility_tolerance: 0.0 # default is to optimize automatically
-  # target retention time tolerance in seconds if > 1, or a proportion of the total gradient length if < 1
+  # target retention time tolerance in seconds if > 1, or a proportion of the total gradient length if < 1. 0.0 means to optimize automatically
   target_rt_tolerance: 0.0 # default is to optimize automatically
+    # target ion mobility tolerance in 1/K_0
+  target_mobility_tolerance: 0.0 # default is to optimize automatically
 
+  # === advanced settings ===
   quant_window: 3
+  target_num_candidates: 3
+  # filter to apply to the channels. If set to "", all channels will be used.
+  channel_filter: ""
+  exclude_shared_ions: True
+  compete_for_fragments: True
+  # target retention time tolerance in seconds if > 1, or a proportion of the total gradient length if < 1
   quant_all: True
-
-search_advanced:
   top_k_fragments: 12
+  experimental_xic: True
+
 
 calibration:
 
@@ -235,10 +271,14 @@ multiplexing:
 fdr:
   fdr: 0.01
   group_level: 'proteins'
+  inference_strategy: "heuristic"
+
+
+  # === advanced settings ===
   competetive_scoring: true
   keep_decoys: false
   channel_wise_fdr: false
-  inference_strategy: "heuristic"
+
   # (Experimental)
   # uses a two-step classifier consisting of a logistic regression and a neural network, with a default maximum of 5 iterations per fitting call
   enable_two_step_classifier: false
@@ -248,15 +288,27 @@ fdr:
   enable_nn_hyperparameter_tuning: false
 
 search_output:
+  # Output file format for search results. Can be either "tsv" or "parquet"
+  file_format: "tsv"
+  # Enable label-free quantification at peptide level and generate peptide matrix
   peptide_level_lfq: false
+  # Enable label-free quantification at precursor level and generate precursor matrix
   precursor_level_lfq: false
+
+  # === advanced settings ===
+  # Minimum number of fragments required for quantification
   min_k_fragments: 12
+  # Minimum correlation required between fragment XICs for quantification
   min_correlation: 0.9
+  # Number of samples used for quadratic fit in retention time alignment
   num_samples_quadratic: 50
+  # Minimum number of non-missing values required for quantification
   min_nonnan: 3
+  # Enable normalization of label-free quantification values
   normalize_lfq: True
-  # can be either "parquet" or "tsv"
-  file_format: "tsv"
+
+  # Save fragment quant matrix for advanced users
+  save_fragment_quant_matrix: False
 
 # Configuration for the optimization of search parameters. These parameters should not normally be adjusted and are for the use of experienced users only.
 optimization:
@@ -334,6 +386,8 @@ transfer_library:
   # if true, the library is created for transfer learning
   enabled: False
 
+  # === advanced settings ===
+
   # list of fragment types (see alphabase.peptide.fragment.FRAGMENT_TYPES for supported types)
   # Supported types are: a, b, c, x, y, z, b_modloss, y_modloss, b_H2O, y_H2O, b_NH3, y_NH3, c_lossH, z_addH
   fragment_types: ['b', 'y']
@@ -361,6 +415,8 @@ transfer_learning:
   # if true, a custom peptdeep model will be created using the transfer learned library
   enabled: False
 
+  # === advanced settings ===
+
   # number of precursors per batch
   batch_size: 2000
 
@@ -394,9 +450,3 @@ transfer_learning:
 
   # instrument type encoded during training
   instrument: 'Lumos'
-
-
-# scope of default yaml should be one search step
-multistep_search:
-  transfer_step_enabled: False
-  mbr_step_enabled: False

{alphadia-1.9.3.dev2 → alphadia-1.10.3}/alphadia/constants/keys.py

@@ -32,3 +32,9 @@ class ConfigKeys(metaclass=ConstantsClass):
     RAW_PATHS = "raw_paths"
     FASTA_PATHS = "fasta_paths"
     QUANT_DIRECTORY = "quant_directory"
+
+
+class SearchStepFiles(metaclass=ConstantsClass):
+    PSM_FILE_NAME = "psm.parquet"
+    FRAG_FILE_NAME = "frag.parquet"
+    FRAG_TRANSFER_FILE_NAME = "frag.transfer.parquet"

{alphadia-1.9.3.dev2 → alphadia-1.10.3}/alphadia/constants/multistep.yaml

@@ -34,6 +34,7 @@ library:
     enabled: False
 
 mbr:
+  fasta_paths: []
   fdr:
     inference_strategy: library
   search:
@@ -43,7 +44,7 @@ mbr:
   general:
     reuse_quant: False
   library_prediction:
-    predict: False
+    enabled: False
   transfer_library:
     enabled: False
   transfer_learning:

{alphadia-1.9.3.dev2 → alphadia-1.10.3}/alphadia/exceptions.py

@@ -40,6 +40,16 @@ class UserError(CustomError):
     """
 
 
+class GenericUserError(UserError):
+    """Raise when something is wrong with the user."""
+
+    _error_code = "USER_ERROR"
+
+    def __init__(self, msg: str, detail_msg: str = ""):
+        self._msg = msg
+        self._detail_msg = detail_msg
+
+
 class NoPsmFoundError(BusinessError):
     """Raise when no PSMs are found in the search results."""