command

docs/command/AE_or_DE_command.md

@@ -0,0 +1,59 @@
+# Generate AE or DE file
+
+## DE
+### use case
+- PRIDE projet(make sure you have run the `project_command.py`)
+
+```
+python differential_expression_command.py
+--msstats_file PXD014414.sdrf_openms_design_msstats_in_comparisons.csv
+--project_file result/PXD014414.json
+--sdrf_file PXD014414.sdrf.tsv
+--output_folder result
+```
+
+- Non-PRIDE project(Don't not need to run the `project_command.py`)
+
+```
+python differential_expression_command.py
+--msstats_file PXD014414.sdrf_openms_design_msstats_in_comparisons.csv
+--generate_project False
+--sdrf_file PXD014414.sdrf.tsv
+--output_folder result
+```
+
+### Optional parameter
+- --fdr_threshold FDR threshold to use to filter the results
+- --output_prefix_file Prefix of the df expression file
+- --delete_existing Delete existing files in the output folder
+
+## AE
+### use case
+- PRIDE projet(make sure you have run the `project_command.py`)
+
+```
+python absolute_expression_command.py
+--ibaq_file PXD004452-ibaq.csv
+--project_file result/PXD004452.json
+--output_folder result
+```
+
+- Non-PRIDE project(Don't not need to run the `project_command.py`)
+
+```
+python absolute_expression_command.py
+--ibaq_file PXD004452-ibaq.csv
+--generate_project False
+--output_folder result
+```
+
+### Optional parameter
+- --output_prefix_file Prefix of the df expression file
+- --delete_existing Delete existing files in the output folder
+
+
+
+
+
+
+

docs/command/Feature_command.md

@@ -0,0 +1,28 @@
+# Generate feature.parquet
+
+## Use cases
+- pride projet(make sure you have run the `project_command.py`)
+
+```python
+python feature_command.py
+--sdrf_file PXD014414.sdrf.tsv
+--msstats_file PXD014414.sdrf_openms_design_msstats_in.csv
+--mztab_file PXD014414.sdrf_openms_design_openms.mzTab
+--output_folder result
+```
+
+- Non-PRIDE project(Don't not need to run the `project_command.py`)
+
+```python
+python feature_command.py
+--sdrf_file PXD014414.sdrf.tsv
+--msstats_file PXD014414.sdrf_openms_design_msstats_in.csv
+--mztab_file PXD014414.sdrf_openms_design_openms.mzTab
+--generate_project False
+--output_folder result
+```
+
+### Optional parameter
+- --use_cache  Whether to use disk instead of memory.
+- --output_prefix_file The prefix of the result file.
+- --consensusxml_file The consensusXML file used to retrieve the mz/rt

docs/command/Other_command.md

@@ -0,0 +1,46 @@
+## generate_spectra_message
+### Use case
+generate_spectra_message support psm and parquet.
+Since the result file is too large, you can specify --partition to split the result file.
+
+```
+python generate_spectra_message_command.py 
+--parquet_path PXD014414-f4fb88f6-0a45-451d-a8a6-b6d58fb83670.psm.parquet
+--mzml_directory mzmls
+--output_path psm/PXD014414.parquet
+--label psm
+--partition charge
+```
+
+## get_unanimous_name
+### use case
+get_unanimous_name support parquet and tsv.
+For parquet, map_parameter have two option (map_protein_name or map_protein_accession), and the label controls whether it is PSM or Feature.
+
+- parquet
+```
+python get_unanimous_command.py map-unanimous-for-parquet
+--parquet_path PXD014414-f4fb88f6-0a45-451d-a8a6-b6d58fb83670.psm.parquet
+--fasta Reference fasta database
+--output_path psm/PXD014414.psm.parquet
+--map_parameter map_protein_name
+--label psm
+```
+
+- tsv
+```
+python get_unanimous_command.py get-unanimous-for-tsv
+--path PXD014414-c2a52d63-ea64-4a64-b241-f819a3157b77.differential.tsv
+--fasta Reference fasta database
+--output_path psm/PXD014414.de.tsv
+--map_parameter map_protein_name
+```
+
+## compare parquet_of_pqrquet
+### use case
+```
+python parquet_command.py
+--parquet_path_one res_lfq2_discache.parquet
+--parquet_path_two res_lfq2_no_cache.parquet
+--report_path report.txt
+```

docs/command/Project_command.md

@@ -0,0 +1,10 @@
+# Generate project.json
+
+## use case
+```
+python project_command.py
+--project_accession PXD014414
+--sdrf PXD014414.sdrf.tsv
+--quantms_version 1.12
+--output_folder result 
+```

docs/command/Psm_command.md

@@ -0,0 +1,32 @@
+# Generate Psm.parquet or compare psm.parquet
+
+## Generate Psm.parquet
+### Use cases
+- PRIDE projet(make sure you have run the `project_command.py`)
+
+```
+python psm_command.py convert-psm-file
+--mztab_file PXD014414.sdrf_openms_design_openms.mzTab
+--output_folder result
+```
+
+- Non-PRIDE project(Don't not need to run the `project_command.py`)
+
+```
+python feature_command.py convert-psm-file
+--mztab_file PXD014414.sdrf_openms_design_openms.mzTab
+--generate_project False
+--output_folder result
+```
+
+### Optional parameter
+- --output_prefix_file The prefix of the result file.
+- --verbose Output debug information.
+
+## Compare psm.parquet
+### Use case
+```
+python feature_command.py compare-set-of-psms
+--parquets PXD014414-comet.parquet PXD014414-sage.parquet PXD014414-msgf.parquet
+--tags comet sage msgf
+```

python/quantmsio/quantms_io/commands/absolute_expression_command.py

@@ -12,7 +12,7 @@
 @click.option(
     "--output_folder", help="Folder to generate the df expression file.", required=True
 )
-@click.option("--output_file", help="Prefix of the df expression file", required=False)
+@click.option("--output_prefix_file", help="Prefix of the df expression file", required=False)
 @click.option(
     "--generate_project",
     help="Generate project.json for pride project, Otherwise, False",
@@ -26,7 +26,7 @@
 def convert_ibaq_absolute(
     ibaq_file:str,
     output_folder: str,
-    output_file: str,
+    output_prefix_file: str,
     generate_project: bool = True,
     delete_existing: bool = True,
     project_file:str = None,
@@ -37,7 +37,7 @@ def convert_ibaq_absolute(
     :param ibaq_file: IBAQ file
     :param project_file: quantms.io project file
     :param output_folder: Folder to generate the df expression file.
-    :param output_file: Prefix of the df expression file
+    :param output_prefix_file: Prefix of the df expression file
     :param generate_project: "Generate project.json for pride project, Otherwise, False"
     :param delete_existing: Delete existing files in the output folder
     :return: none
@@ -48,7 +48,7 @@ def convert_ibaq_absolute(
     de_handler.load_ibaq_file(ibaq_file)
     de_handler.convert_ibaq_to_quantms(
         output_folder=output_folder,
-        output_file_prefix=output_file,
+        output_prefix_file_prefix=output_prefix_file,
         delete_existing=delete_existing,
     )
     if generate_project:

python/quantmsio/quantms_io/commands/differential_expression_command.py

@@ -23,7 +23,7 @@
 @click.option(
     "--output_folder", help="Folder to generate the df expression file.", required=True
 )
-@click.option("--output_file", help="Prefix of the df expression file", required=False)
+@click.option("--output_prefix_file", help="Prefix of the df expression file", required=False)
 @click.option(
     "--generate_project",
     help="Generate project.json for pride project, Otherwise, False",
@@ -38,7 +38,7 @@ def convert_msstats_differential(
     sdrf_file: str,
     fdr_threshold: float,
     output_folder: str,
-    output_file: str,
+    output_prefix_file: str,
     generate_project: bool= True,
     delete_existing: bool=True,
     project_file: str = None,
@@ -50,7 +50,7 @@ def convert_msstats_differential(
     :param project_file: quantms.io project file
     :param sdrf_file: the SDRF file needed to extract some of the metadata
     :param output_folder: Folder to generate the df expression file.
-    :param output_file: Prefix of the df expression file
+    :param output_prefix_file: Prefix of the df expression file
     :param delete_existing: Delete existing files in the output folder
     :param fdr_threshold: FDR threshold to use to filter the results
     :param generate_project: "Generate project.json for pride project, Otherwise, False"
@@ -68,7 +68,7 @@ def convert_msstats_differential(
     de_handler.set_fdr_threshold(fdr_threshold=fdr_threshold)
     de_handler.convert_msstats_to_quantms(
         output_folder=output_folder,
-        output_file_prefix=output_file,
+        output_file_prefix=output_prefix_file,
         delete_existing=delete_existing,
     )
     if generate_project:

python/quantmsio/quantms_io/commands/get_unanimous_command.py

@@ -3,7 +3,7 @@
 
 #parquet
 @click.command(
-    "map_protein_name_for_parquet", short_help="According fasta database to map the proteins accessions to uniprot names."
+    "map-unanimous-for-parquet", short_help="According fasta database to map the proteins accessions to uniprot names."
 )
 @click.option('--parquet_path',  help='Psm or feature parquet path')
 @click.option('--fasta', help='Reference fasta database')
@@ -27,7 +27,7 @@ def get_unanimous_for_parquet(parquet_path,fasta,output_path,map_parameter,label
 
 # tsv
 @click.command(
-    "map_protein_name_for_de_or_ae", short_help="According fasta database to map the proteins accessions to uniprot names."
+    "get-unanimous-for-tsv", short_help="According fasta database to map the proteins accessions to uniprot names."
 )
 @click.option('--path',  help='ae or de path')
 @click.option('--fasta', help='Reference fasta database')

python/quantmsio/quantms_io/commands/psm_command.py

@@ -65,7 +65,7 @@ def convert_psm_file(mztab_file: str, output_folder: str,generate_project:bool =
 
 
 @click.command(
-    "compare-psm-parquet", short_help="plot venn for a set of Psms parquet"
+    "compare-set-of-psms", short_help="plot venn for a set of Psms parquet"
 )
 @click.option('--parquets', type=str, help='List of psm parquet path', multiple=True)
 @click.option('--tags', type=str, help='List of parquet label', multiple=True)