update: black

quantmsio/commands/absolute_expression_command.py

@@ -22,15 +22,9 @@
     help="quantms.io project file",
     required=False,
 )
-@click.option(
-    "--output_folder", help="Folder to generate the df expression file.", required=True
-)
-@click.option(
-    "--output_prefix_file", help="Prefix of the df expression file", required=False
-)
-@click.option(
-    "--delete_existing", help="Delete existing files in the output folder", is_flag=True
-)
+@click.option("--output_folder", help="Folder to generate the df expression file.", required=True)
+@click.option("--output_prefix_file", help="Prefix of the df expression file", required=False)
+@click.option("--delete_existing", help="Delete existing files in the output folder", is_flag=True)
 def convert_ibaq_absolute(
     ibaq_file: str,
     sdrf_file: str,

quantmsio/commands/attach_file_command.py

@@ -8,9 +8,7 @@
     short_help="Register the file to project.json.",
 )
 @click.option("--project_file", help="the project.json file", required=True)
-@click.option(
-    "--attach_file", help="The path of the file that will be registered", required=True
-)
+@click.option("--attach_file", help="The path of the file that will be registered", required=True)
 @click.option(
     "--category",
     type=click.Choice(

quantmsio/commands/diann_convert_command.py

@@ -20,9 +20,7 @@
     help="the design file path",
     required=True,
 )
-@click.option(
-    "--qvalue_threshold", help="qvalue_threshold", required=True, default=0.05
-)
+@click.option("--qvalue_threshold", help="qvalue_threshold", required=True, default=0.05)
 @click.option(
     "--mzml_info_folder",
     help="the foldef of mzml_info tsv file",
@@ -47,9 +45,7 @@
     "--duckdb_max_memory",
     help="The maximum amount of memory allocated by the DuckDB engine (e.g 4GB)",
 )
-@click.option(
-    "--duckdb_threads", help="The number of threads for the DuckDB engine (e.g 4)"
-)
+@click.option("--duckdb_threads", help="The number of threads for the DuckDB engine (e.g 4)")
 @click.option(
     "--file_num",
     help="The number of files being processed at the same time",
@@ -85,14 +81,8 @@ def diann_convert_to_parquet(
     if not output_prefix_file:
         output_prefix_file = ""
 
-    feature_output_path = (
-        output_folder
-        + "/"
-        + create_uuid_filename(output_prefix_file, ".feature.parquet")
-    )
-    psm_output_path = (
-        output_folder + "/" + create_uuid_filename(output_prefix_file, ".psm.parquet")
-    )
+    feature_output_path = output_folder + "/" + create_uuid_filename(output_prefix_file, ".feature.parquet")
+    psm_output_path = output_folder + "/" + create_uuid_filename(output_prefix_file, ".psm.parquet")
 
     dia_nn = DiaNNConvert()
 

quantmsio/commands/differential_expression_command.py

@@ -24,15 +24,9 @@
     required=False,
     default="0.05",
 )
-@click.option(
-    "--output_folder", help="Folder to generate the df expression file.", required=True
-)
-@click.option(
-    "--output_prefix_file", help="Prefix of the df expression file", required=False
-)
-@click.option(
-    "--delete_existing", help="Delete existing files in the output folder", is_flag=True
-)
+@click.option("--output_folder", help="Folder to generate the df expression file.", required=True)
+@click.option("--output_prefix_file", help="Prefix of the df expression file", required=False)
+@click.option("--delete_existing", help="Delete existing files in the output folder", is_flag=True)
 def convert_msstats_differential(
     msstats_file: str,
     sdrf_file: str,

quantmsio/commands/feature_command.py

@@ -62,24 +62,15 @@ def convert_feature_file(
     :return: none
     """
 
-    if (
-        sdrf_file is None
-        or msstats_file is None
-        or mztab_file is None
-        or output_folder is None
-    ):
+    if sdrf_file is None or msstats_file is None or mztab_file is None or output_folder is None:
         raise click.UsageError("Please provide all the required parameters")
     if use_cache is None:
         use_cache = False
 
     feature_manager = FeatureHandler()
     if not output_prefix_file:
         output_prefix_file = ""
-    feature_manager.parquet_path = (
-        output_folder
-        + "/"
-        + create_uuid_filename(output_prefix_file, ".feature.parquet")
-    )
+    feature_manager.parquet_path = output_folder + "/" + create_uuid_filename(output_prefix_file, ".feature.parquet")
     if consensusxml_file is not None:
         feature_manager.convert_mztab_msstats_to_feature(
             mztab_file=mztab_file,

quantmsio/commands/generate_gene_msg_command.py

@@ -14,9 +14,7 @@
 )
 @click.option(
     "--map_parameter",
-    type=click.Choice(
-        ["map_protein_name", "map_protein_accession"], case_sensitive=False
-    ),
+    type=click.Choice(["map_protein_name", "map_protein_accession"], case_sensitive=False),
     help="map type",
 )
 @click.option("--species", help="species", default="human")
@@ -40,6 +38,4 @@ def map_gene_msg_to_parquet(
     if not output_path.endswith("parquet"):
         raise click.UsageError("Please provide file extension(.parquet)")
 
-    map_gene_msgs_to_parquet(
-        parquet_path, fasta_path, map_parameter, output_path, label, species
-    )
+    map_gene_msgs_to_parquet(parquet_path, fasta_path, map_parameter, output_path, label, species)

quantmsio/commands/generate_project_report_command.py

@@ -7,9 +7,7 @@
     "generate-project-report",
     short_help="generate report of project " "format",
 )
-@click.option(
-    "--project_folder", help="Folder to generate the df expression file.", required=True
-)
+@click.option("--project_folder", help="Folder to generate the df expression file.", required=True)
 def generate_report_about_project(project_folder):
     """
     project_folder: The folder path for the full project.

quantmsio/commands/generate_spectra_message_command.py

@@ -46,6 +46,4 @@ def map_spectrum_message_to_parquet(
     """
     if not output_path.endswith("parquet"):
         raise click.UsageError("Please provide file extension(.parquet)")
-    generate_features_of_spectrum(
-        parquet_path, mzml_directory, output_path, label, file_num, partition
-    )
+    generate_features_of_spectrum(parquet_path, mzml_directory, output_path, label, file_num, partition)

quantmsio/commands/generate_start_and_end_command.py

@@ -15,9 +15,7 @@
     help="parquet type",
 )
 @click.option("--output_path", help="save path", required=True)
-def inject_start_and_end_from_fasta(
-    parquet_path: str, fasta_path: str, label: str, output_path: str
-):
+def inject_start_and_end_from_fasta(parquet_path: str, fasta_path: str, label: str, output_path: str):
     """
     Register the file with project.json
     :param parquet_path: psm or feature parquet file path

quantmsio/commands/get_unanimous_command.py

@@ -22,9 +22,7 @@ def labels():
 @click.option("--output_path", help="output file path")
 @click.option(
     "--map_parameter",
-    type=click.Choice(
-        ["map_protein_name", "map_protein_accession"], case_sensitive=False
-    ),
+    type=click.Choice(["map_protein_name", "map_protein_accession"], case_sensitive=False),
     help="map type",
 )
 @click.option(
@@ -55,9 +53,7 @@ def get_unanimous_for_parquet(parquet_path, fasta, output_path, map_parameter, l
 @click.option("--output_path", help="output file path")
 @click.option(
     "--map_parameter",
-    type=click.Choice(
-        ["map_protein_name", "map_protein_accession"], case_sensitive=False
-    ),
+    type=click.Choice(["map_protein_name", "map_protein_accession"], case_sensitive=False),
     help="map type",
 )
 def get_unanimous_for_tsv(path, fasta, output_path, map_parameter):

quantmsio/commands/load_best_scan_number_command.py

@@ -8,13 +8,9 @@
     short_help="inject bset_psm_scan_number to feature",
 )
 @click.option("--diann_psm_path", help="diann psm parquet file path", required=True)
-@click.option(
-    "--diann_feature_path", help="diann feature parquet file path", required=True
-)
+@click.option("--diann_feature_path", help="diann feature parquet file path", required=True)
 @click.option("--output_path", help="save path", required=True)
-def inject_bset_psm_scan_number(
-    diann_psm_path: str, diann_feature_path: str, output_path: str
-):
+def inject_bset_psm_scan_number(diann_psm_path: str, diann_feature_path: str, output_path: str):
     """
     Register the file with project.json
     :param diann_psm_path: diann psm parquet file path

quantmsio/commands/plot.py

@@ -32,21 +32,15 @@ def plot_peptides(ctx, psm_parquet_path: str, sdrf_path: str, save_path: str):
     :param save_path: img save path [xxx.png]
     :return: none
     """
-    plot_peptides_of_lfq_condition(
-        psm_parquet_path=psm_parquet_path, sdrf_path=sdrf_path, save_path=save_path
-    )
+    plot_peptides_of_lfq_condition(psm_parquet_path=psm_parquet_path, sdrf_path=sdrf_path, save_path=save_path)
 
 
-@plot.command(
-    "plot-ibaq-distribution", short_help="plot ibaq distribution of expression"
-)
+@plot.command("plot-ibaq-distribution", short_help="plot ibaq distribution of expression")
 @click.option("--ibaq_path", help="ibaq file path", required=True)
 @click.option("--save_path", help="img save path [xxx.svg]", required=True)
 @click.option("--select_column", help="Selected column in Ibaq File", required=False)
 @click.pass_context
-def plot_ibaq_distribution(
-    ctx, ibaq_path: str, save_path: str, select_column: str
-) -> None:
+def plot_ibaq_distribution(ctx, ibaq_path: str, save_path: str, select_column: str) -> None:
     """
     plot ibaq distribution of expression
     :param ibaq_path: ibaq file path
@@ -65,9 +59,7 @@ def plot_ibaq_distribution(
 @click.option("--save_path", help="img save path [xxx.svg]", required=True)
 @click.option("--num_samples", help="The number of samples plotted", default=10)
 @click.pass_context
-def plot_kde_intensity_distribution(
-    feature_path: str, save_path: str, num_samples: int
-):
+def plot_kde_intensity_distribution(feature_path: str, save_path: str, num_samples: int):
     """
     plot ibaq distribution of expression
     :param feature_path: feature file path
@@ -107,9 +99,7 @@ def plot_bar_peptide_distribution(feature_path: str, save_path: str, num_samples
 @click.option("--save_path", help="img save path [xxx.svg]", required=True)
 @click.option("--num_samples", help="The number of samples plotted", default=10)
 @click.pass_context
-def plot_box_intensity_distribution(
-    feature_path: str, save_path: str, num_samples: int
-):
+def plot_box_intensity_distribution(feature_path: str, save_path: str, num_samples: int):
     """
     plot ibaq distribution of expression
     :param feature_path: feature file path

quantmsio/commands/psm_command.py

@@ -31,9 +31,7 @@
     help="Prefix of the parquet file needed to generate the file name",
     required=False,
 )
-@click.option(
-    "--verbose", help="Output debug information.", default=False, is_flag=True
-)
+@click.option("--verbose", help="Output debug information.", default=False, is_flag=True)
 def convert_psm_file(
     mztab_file: str,
     output_folder: str,
@@ -57,9 +55,7 @@ def convert_psm_file(
         output_prefix_file = ""
 
     psm_manager = PSMHandler()
-    psm_manager.parquet_path = (
-        output_folder + "/" + create_uuid_filename(output_prefix_file, ".psm.parquet")
-    )
+    psm_manager.parquet_path = output_folder + "/" + create_uuid_filename(output_prefix_file, ".psm.parquet")
     psm_manager.convert_mztab_to_psm(
         mztab_path=mztab_file,
         parquet_path=psm_manager.parquet_path,
@@ -69,9 +65,7 @@ def convert_psm_file(
 
 
 @click.command("compare-set-psms", short_help="plot venn for a set of Psms parquet")
-@click.option(
-    "-p", "--parquets", type=str, help="List of psm parquet path", multiple=True
-)
+@click.option("-p", "--parquets", type=str, help="List of psm parquet path", multiple=True)
 @click.option("-t", "--tags", type=str, help="List of parquet label", multiple=True)
 def compare_set_of_psms(parquets, tags):
     """
@@ -80,9 +74,7 @@ def compare_set_of_psms(parquets, tags):
     :param tags: a set of psm label
     """
     if len(parquets) != len(tags):
-        raise click.UsageError(
-            "Please provide same length of parquet_list and label_list"
-        )
+        raise click.UsageError("Please provide same length of parquet_list and label_list")
 
     plot_peptidoform_charge_venn(parquets, tags)
     plot_sequence_venn(parquets, tags)

quantmsio/commands/statistics.py

@@ -23,8 +23,7 @@ def statistics():
 @click.option("--parquet_path", help="psm parquet path in lfq", required=True)
 @click.option(
     "--save_path",
-    help="file with the statistics (e.g. statistics.csv), if not provided,"
-    " will print to stdout",
+    help="file with the statistics (e.g. statistics.csv), if not provided," " will print to stdout",
 )
 @click.pass_context
 def feature_file_statistics(ctx, absolute_path: str, parquet_path: str, save_path: str):
@@ -41,15 +40,11 @@ def write_stats(file, stats: ParquetStatistics):
         file.write("Number of proteins: {}\n".format(stats.get_number_of_proteins()))
         file.write("Number of peptides: {}\n".format(stats.get_number_of_peptides()))
         file.write("Number of samples: {}\n".format(stats.get_number_of_samples()))
-        file.write(
-            "Number of peptidoforms: {}\n".format(stats.get_number_of_peptidoforms())
-        )
+        file.write("Number of peptidoforms: {}\n".format(stats.get_number_of_peptidoforms()))
         file.write("Number of msruns: {}\n".format(stats.get_number_msruns()))
 
     def write_absolute_stats(file, stats: IbaqStatistics):
-        file.write(
-            "Ibaq Number of proteins: {}\n".format(stats.get_number_of_proteins())
-        )
+        file.write("Ibaq Number of proteins: {}\n".format(stats.get_number_of_proteins()))
         file.write("Ibaq Number of samples: {}\n".format(stats.get_number_of_samples()))
 
     if save_path:
@@ -70,8 +65,7 @@ def write_absolute_stats(file, stats: IbaqStatistics):
 @click.option("--parquet_path", help="psm parquet path in lfq", required=True)
 @click.option(
     "--save_path",
-    help="file with the statistics (e.g. statistics.csv), if not provided,"
-    " will print to stdout",
+    help="file with the statistics (e.g. statistics.csv), if not provided," " will print to stdout",
 )
 @click.pass_context
 def parquet_psm_statistics(ctx, parquet_path: str, save_path: str):
@@ -85,9 +79,7 @@ def parquet_psm_statistics(ctx, parquet_path: str, save_path: str):
     def write_stats(file, stats: ParquetStatistics):
         file.write("Number of proteins: {}\n".format(stats.get_number_of_proteins()))
         file.write("Number of peptides: {}\n".format(stats.get_number_of_peptides()))
-        file.write(
-            "Number of peptidoforms: {}\n".format(stats.get_number_of_peptidoforms())
-        )
+        file.write("Number of peptidoforms: {}\n".format(stats.get_number_of_peptidoforms()))
         file.write("Number of psms: {}\n".format(stats.get_number_of_psms()))
         file.write("Number of msruns: {}\n".format(stats.get_number_msruns()))
 

quantmsio/core/ae.py

@@ -85,25 +85,13 @@ def convert_ibaq_to_quantms(
         output_lines = ""
         if self.project_manager:
             output_lines += (
-                "#project_accession: "
-                + self.project_manager.project.project_info["project_accession"]
-                + "\n"
+                "#project_accession: " + self.project_manager.project.project_info["project_accession"] + "\n"
             )
+            output_lines += "#project_title: " + self.project_manager.project.project_info["project_title"] + "\n"
             output_lines += (
-                "#project_title: "
-                + self.project_manager.project.project_info["project_title"]
-                + "\n"
-            )
-            output_lines += (
-                "#project_description: "
-                + self.project_manager.project.project_info["project_description"]
-                + "\n"
-            )
-            output_lines += (
-                "#quantms_version: "
-                + self.project_manager.project.project_info["quantms_version"]
-                + "\n"
+                "#project_description: " + self.project_manager.project.project_info["project_description"] + "\n"
             )
+            output_lines += "#quantms_version: " + self.project_manager.project.project_info["quantms_version"] + "\n"
         factor_value = self.get_factor_value()
         if factor_value is not None:
             output_lines += "#factor_value: " + factor_value + "\n"
@@ -139,12 +127,8 @@ def convert_ibaq_to_quantms(
             f.write(output_lines)
 
         if self.project_manager:
-            self.project_manager.add_quantms_file(
-                file_category="absolute_file", file_name=output_filename
-            )
-        logger.info(
-            f"Absolute expression file copied to {output_filename} and added to the project information"
-        )
+            self.project_manager.add_quantms_file(file_category="absolute_file", file_name=output_filename)
+        logger.info(f"Absolute expression file copied to {output_filename} and added to the project information")
 
     def get_factor_value(self):
         """

quantmsio/core/core.py

@@ -18,9 +18,7 @@ def __init__(self, name_prefix: str):
         # Create a cache name using a hash and uuid
         if name_prefix is None:
             name_prefix = "generic"
-        self._cache_name = str(
-            "_cache_name_{}_{}".format(name_prefix, uuid.uuid4().hex)
-        )
+        self._cache_name = str("_cache_name_{}_{}".format(name_prefix, uuid.uuid4().hex))
         self.cache = diskcache.Cache(self._cache_name, statistics=True)
         self.cache.create_tag_index()