Document the functions

parser.py

@@ -7,11 +7,17 @@ from pandas import DataFrame, read_html, Series
 
 
 def remove_parenthesis(identifier):
+    """
+    Remove parenthesis from the sequence identifier
+    """
     sequence_str = "".join(map(str, identifier))
     return sub(r"[()]", "", sequence_str)
 
 
 def extract_adapters(files) -> Tuple[Series, List]:
+    """
+    Extract the adapters sequences and statistics from the files
+    """
     all_adapters = DataFrame()
     for entry in files:
         tables = read_html(entry)
@@ -27,6 +33,9 @@ def extract_adapters(files) -> Tuple[Series, List]:
 
 
 def preprocess_dataframe(adapters) -> Series:
+    """
+    Remove empty sequences and duplicates
+    """
     na_free_adapters = adapters.dropna(axis=1)
     stacked_adapters = na_free_adapters.stack()
     duplicate_free_adapters = stacked_adapters.drop_duplicates()
@@ -34,6 +43,9 @@ def preprocess_dataframe(adapters) -> Series:
 
 
 def save_to_file(filename, adapters) -> None:
+    """
+    Save the adapter sequences as a FASTA file
+    """
     with open(filename, "w") as f:
         for index, value in adapters.iteritems():
             sequence_id = remove_parenthesis(index)
@@ -42,6 +54,9 @@ def save_to_file(filename, adapters) -> None:
 
 
 def parse_arguments():
+    """
+    Parse the command-line arguments
+    """
     parser = ArgumentParser()
     parser.add_argument("input", help="directory containing the fastqc reports")
     parser.add_argument("output", help="file where to export the sequences")
@@ -49,6 +64,9 @@ def parse_arguments():
 
 
 def main():
+    """
+    Extract the adapters from FASTQC reports to a FASTA file and show sequence length statistics
+    """
     args = parse_arguments()
     file_list = glob(args.input + "/*fastqc.html")
     adapters, stats = extract_adapters(file_list)