Merge pull request #27 from MannLabs/development

Development

.gitignore

@@ -193,3 +193,5 @@ _proc/
 
 sandbox/
 test_data/unit_tests/input_table_formats/spectronaut.frgions.large.tsv.tmp.longformat.columnfilt.tsv
+test_data/unit_tests/input_table_formats/diann.tsv.diann_protein.aq_reformat.tsv
+test_data/unit_tests/input_table_formats/mq_peptides.txt.maxquant_peptides_leading_razor_protein.aq_reformat.tsv

directlfq/__init__.py

@@ -2,7 +2,7 @@
 
 
 __project__ = "directlfq"
-__version__ = "0.2.16"
+__version__ = "0.2.17"
 __license__ = "Apache"
 __description__ = "An open-source Python package of the AlphaPept ecosystem"
 __author__ = "Mann Labs"
@@ -15,11 +15,11 @@
 ]
 __python_version__ = ">=3.8,<3.10"
 __classifiers__ = [
-    "Development Status :: 1 - Planning",
+    # "Development Status :: 1 - Planning",
     # "Development Status :: 2 - Pre-Alpha",
     # "Development Status :: 3 - Alpha",
     # "Development Status :: 4 - Beta",
-    # "Development Status :: 5 - Production/Stable",
+     "Development Status :: 5 - Production/Stable",
     # "Development Status :: 6 - Mature",
     # "Development Status :: 7 - Inactive"
     "Intended Audience :: Science/Research",

directlfq/protein_intensity_estimation.py

@@ -31,18 +31,18 @@ def estimate_protein_intensities(normed_df, min_nonan, num_samples_quadratic, nu
     allprots = list(normed_df.index.get_level_values(0).unique())
     LOGGER.info(f"{len(allprots)} lfq-groups total")
 
-    list_of_tuple_w_protein_profiles_and_shifted_peptides = get_list_of_tuple_w_protein_profiles_and_shifted_peptides(allprots, normed_df, num_samples_quadratic, min_nonan, num_cores)
-    protein_df = get_protein_dataframe_from_list_of_protein_profiles(allprots=allprots, list_of_tuple_w_protein_profiles_and_shifted_peptides=list_of_tuple_w_protein_profiles_and_shifted_peptides, normed_df= normed_df)
+    list_of_tuple_w_protein_profiles_and_shifted_peptides = get_list_of_tuple_w_protein_profiles_and_shifted_peptides(normed_df, num_samples_quadratic, min_nonan, num_cores)
+    protein_df = get_protein_dataframe_from_list_of_protein_profiles(list_of_tuple_w_protein_profiles_and_shifted_peptides=list_of_tuple_w_protein_profiles_and_shifted_peptides, normed_df= normed_df)
     if config.COMPILE_NORMALIZED_ION_TABLE:
-        ion_df = get_ion_intensity_dataframe_from_list_of_shifted_peptides(list_of_tuple_w_protein_profiles_and_shifted_peptides, allprots)
+        ion_df = get_ion_intensity_dataframe_from_list_of_shifted_peptides(list_of_tuple_w_protein_profiles_and_shifted_peptides, column_names = normed_df.columns)
     else:
         ion_df = None
 
     return protein_df, ion_df
 
 
-def get_list_of_tuple_w_protein_profiles_and_shifted_peptides(allprots, normed_df, num_samples_quadratic, min_nonan, num_cores):
-    input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan = get_input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan(normed_df, allprots, num_samples_quadratic, min_nonan)
+def get_list_of_tuple_w_protein_profiles_and_shifted_peptides(normed_df, num_samples_quadratic, min_nonan, num_cores):
+    input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan = get_input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan(normed_df, num_samples_quadratic, min_nonan)
 
     if num_cores is not None and num_cores <=1:
         list_of_tuple_w_protein_profiles_and_shifted_peptides = get_list_with_sequential_processing(input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan)
@@ -51,7 +51,7 @@ def get_list_of_tuple_w_protein_profiles_and_shifted_peptides(allprots, normed_d
     return list_of_tuple_w_protein_profiles_and_shifted_peptides
 
 
-def get_input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan(normed_df, allprots, num_samples_quadratic, min_nonan):
+def get_input_specification_tuplelist_idx__df__num_samples_quadratic__min_nonan(normed_df, num_samples_quadratic, min_nonan):
     list_of_normed_dfs = get_normed_dfs(normed_df)
     return zip(range(len(list_of_normed_dfs)),list_of_normed_dfs, itertools.repeat(num_samples_quadratic), itertools.repeat(min_nonan))
 
@@ -197,15 +197,14 @@ def _get_shortened_dataframe(self):
 
 
 
-def get_ion_intensity_dataframe_from_list_of_shifted_peptides(list_of_tuple_w_protein_profiles_and_shifted_peptides, allprots):
+def get_ion_intensity_dataframe_from_list_of_shifted_peptides(list_of_tuple_w_protein_profiles_and_shifted_peptides, column_names):
     ion_names = []
     ion_vals = []
     protein_names = []
-    column_names = list_of_tuple_w_protein_profiles_and_shifted_peptides[0][1].columns.tolist()
     for idx in range(len(list_of_tuple_w_protein_profiles_and_shifted_peptides)):
-        protein_name = allprots[idx]
         ion_df = list_of_tuple_w_protein_profiles_and_shifted_peptides[idx][1]
-        ion_names += ion_df.index.values.tolist()
+        protein_name = ion_df.index.get_level_values(0)[0]
+        ion_names += ion_df.index.get_level_values(1).tolist()
         ion_vals.append(ion_df.to_numpy())
         protein_names.extend([protein_name]*len(ion_df.index))
     merged_ions = 2**np.concatenate(ion_vals)
@@ -229,11 +228,12 @@ def add_protein_name_to_ion_df(ion_df, protein):
     return ion_df
 
 
-def get_protein_dataframe_from_list_of_protein_profiles(allprots, list_of_tuple_w_protein_profiles_and_shifted_peptides, normed_df):
+def get_protein_dataframe_from_list_of_protein_profiles(list_of_tuple_w_protein_profiles_and_shifted_peptides, normed_df):
     index_list = []
     profile_list = []
 
     list_of_protein_profiles = [x[0] for x in list_of_tuple_w_protein_profiles_and_shifted_peptides]
+    allprots = [x[1].index.get_level_values(0)[0] for x in list_of_tuple_w_protein_profiles_and_shifted_peptides]
 
     for idx in range(len(allprots)):
         if list_of_protein_profiles[idx] is None:

misc/bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.16
+current_version = 0.2.17
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

release/one_click_linux_gui/control

@@ -1,5 +1,5 @@
 Package: directlfq
-Version: 0.2.16
+Version: 0.2.17
 Architecture: all
 Maintainer: Mann Labs <opensource@alphapept.com>
 Description: directlfq

release/one_click_linux_gui/create_installer_linux.sh

@@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel
 # Setting up the local package
 cd release/one_click_linux_gui
 # Make sure you include the required extra packages and always use the stable or very-stable options!
-pip install "../../dist/directlfq-0.2.16-py3-none-any.whl[stable, gui]"
+pip install "../../dist/directlfq-0.2.17-py3-none-any.whl[stable, gui]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller==4.10

release/one_click_macos_gui/Info.plist

@@ -9,9 +9,9 @@
 	<key>CFBundleIconFile</key>
 	<string>alpha_logo.icns</string>
 	<key>CFBundleIdentifier</key>
-	<string>directlfq.0.2.16</string>
+	<string>directlfq.0.2.17</string>
 	<key>CFBundleShortVersionString</key>
-	<string>0.2.16</string>
+	<string>0.2.17</string>
 	<key>CFBundleInfoDictionaryVersion</key>
 	<string>6.0</string>
 	<key>CFBundleName</key>

release/one_click_macos_gui/create_installer_macos.sh

@@ -20,7 +20,7 @@ python setup.py sdist bdist_wheel
 
 # Setting up the local package
 cd release/one_click_macos_gui
-pip install "../../dist/directlfq-0.2.16-py3-none-any.whl[stable, gui]"
+pip install "../../dist/directlfq-0.2.17-py3-none-any.whl[stable, gui]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller==4.10
@@ -40,5 +40,5 @@ cp ../../LICENSE Resources/LICENSE
 cp ../logos/alpha_logo.png Resources/alpha_logo.png
 chmod 777 scripts/*
 
-pkgbuild --root dist/directlfq --identifier de.mpg.biochem.directlfq.app --version 0.2.16 --install-location /Applications/directlfq.app --scripts scripts directlfq.pkg
+pkgbuild --root dist/directlfq --identifier de.mpg.biochem.directlfq.app --version 0.2.17 --install-location /Applications/directlfq.app --scripts scripts directlfq.pkg
 productbuild --distribution distribution.xml --resources Resources --package-path directlfq.pkg dist/directlfq_gui_installer_macos.pkg

release/one_click_macos_gui/distribution.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8" standalone="no"?>
 <installer-script minSpecVersion="1.000000">
-    <title>directlfq 0.2.16</title>
+    <title>directlfq 0.2.17</title>
     <background mime-type="image/png" file="alpha_logo.png" scaling="proportional"/>
     <welcome file="welcome.html" mime-type="text/html" />
     <conclusion file="conclusion.html" mime-type="text/html" />

release/one_click_windows_gui/create_installer_windows.sh

@@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel
 # Setting up the local package
 cd release/one_click_windows_gui
 # Make sure you include the required extra packages and always use the stable or very-stable options!
-pip install "../../dist/directlfq-0.2.16-py3-none-any.whl[stable, gui]"
+pip install "../../dist/directlfq-0.2.17-py3-none-any.whl[stable, gui]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller==4.10

release/one_click_windows_gui/directlfq_innoinstaller.iss

@@ -2,7 +2,7 @@
 ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
 
 #define MyAppName "directlfq"
-#define MyAppVersion "0.2.16"
+#define MyAppVersion "0.2.17"
 #define MyAppPublisher "Max Planck Institute of Biochemistry and the University of Copenhagen, Mann Labs"
 #define MyAppURL "https://github.com/MannLabs/directlfq"
 #define MyAppExeName "directlfq_gui.exe"

settings.ini

@@ -13,7 +13,7 @@ author = Constantin Ammar
 author_email = constantin.ammar@gmail.com
 copyright = fast.ai
 branch = master
-version = 0.2.16
+version = 0.2.17
 min_python = 3.6
 audience = Developers
 language = English