json_command

python/quantmsio/quantms_io/commands/convert_tsv_to_json_command.py

@@ -0,0 +1,25 @@
+from quantms_io.core.tools import convert_to_json
+import click
+import os
+CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
+
+
+@click.group(context_settings=CONTEXT_SETTINGS)
+def cli():
+    """
+    This is the main tool that gives access to all commands.
+    """
+
+
+@click.command("convert_tsv_to_json", short_help="Register the file to project.json.",)
+@click.option("--file", help="AE or DE file", required=True)
+@click.pass_context
+def convert_tsv_to_json(ctx,file):
+    if not os.path.exists(file):
+        raise click.UsageError("The file does not exist.")
+
+    convert_to_json(file)
+
+cli.add_command(convert_tsv_to_json)
+if __name__ == '__main__':
+    cli()

python/quantmsio/quantms_io/core/ae.py

@@ -29,7 +29,7 @@ class AbsoluteExpressionHander:
 #INFO=<ID=ibaq, Number=1, Type=Float, Description="Intensity based absolute quantification">
 #INFO=<ID=ribaq, Number=1, Type=Float, Description="relative iBAQ">\n"""
 
-    ABSOLUTE_EXPRESSION_EXTENSION = ".ae.absolute.tsv"
+    ABSOLUTE_EXPRESSION_EXTENSION = ".absolute.tsv"
 
     def __init__(self):
         self.ibaq_df = None

python/quantmsio/quantms_io/core/de.py

@@ -53,7 +53,7 @@ class DifferentialExpressionHandler:
 #INFO=<ID=adj.pvalue, Number=1, Type=Double, Description="P-values adjusted among all the proteins in the specific comparison using the approach by Benjamini and Hochberg">
 #INFO=<ID=issue, Number=1, Type=String, Description="Issue column shows if there is any issue for inference in corresponding protein and comparison">\n"""
 
-    DIFFERENTIAL_EXPRESSION_EXTENSION = ".de.differential.tsv"
+    DIFFERENTIAL_EXPRESSION_EXTENSION = ".differential.tsv"
 
     def __init__(self):
         """

python/quantmsio/quantms_io/core/tools.py

@@ -11,6 +11,7 @@
 """
 import os
 import re
+import json
 
 import pandas as pd
 import matplotlib.pyplot as plt
@@ -374,11 +375,15 @@ def convert_to_json(file_path):
     table,content = load_de_or_ae(file_path)
     output = {}
     pattern = r'[\\|\|//|/]'
-    output['id'] = re.split(pattern,file_path)[-1]
+    file_name = re.split(pattern,file_path)[-1]
+    output['id'] = file_name
     output['metadata'] = content
     records = {}
     for col in table.columns:
         records[col] = table.loc[:,col].to_list()
     output['records'] = records
-
-    return output
+    b = json.dumps(output)
+    output_path = ".".join(file_name.split('.')[:-1]) + '.json'
+    f = open(output_path, 'w')
+    f.write(b)
+    f.close()