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adapter-parser
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Document the functions

This commit is contained in:
coolneng 2021-12-27 17:33:05 +01:00
parent 7ed975c7ce
commit 93a403182b
Signed by: coolneng
GPG Key ID: 9893DA236405AF57
1 changed files with 18 additions and 0 deletions
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18
parser.py
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@ -7,11 +7,17 @@ from pandas import DataFrame, read_html, Series
def remove_parenthesis(identifier): def remove_parenthesis(identifier):
"""
Remove parenthesis from the sequence identifier
"""
sequence_str = "".join(map(str, identifier)) sequence_str = "".join(map(str, identifier))
return sub(r"[()]", "", sequence_str) return sub(r"[()]", "", sequence_str)
def extract_adapters(files) -> Tuple[Series, List]: def extract_adapters(files) -> Tuple[Series, List]:
"""
Extract the adapters sequences and statistics from the files
"""
all_adapters = DataFrame() all_adapters = DataFrame()
for entry in files: for entry in files:
tables = read_html(entry) tables = read_html(entry)
@ -27,6 +33,9 @@ def extract_adapters(files) -> Tuple[Series, List]:
def preprocess_dataframe(adapters) -> Series: def preprocess_dataframe(adapters) -> Series:
"""
Remove empty sequences and duplicates
"""
na_free_adapters = adapters.dropna(axis=1) na_free_adapters = adapters.dropna(axis=1)
stacked_adapters = na_free_adapters.stack() stacked_adapters = na_free_adapters.stack()
duplicate_free_adapters = stacked_adapters.drop_duplicates() duplicate_free_adapters = stacked_adapters.drop_duplicates()
@ -34,6 +43,9 @@ def preprocess_dataframe(adapters) -> Series:
def save_to_file(filename, adapters) -> None: def save_to_file(filename, adapters) -> None:
"""
Save the adapter sequences as a FASTA file
"""
with open(filename, "w") as f: with open(filename, "w") as f:
for index, value in adapters.iteritems(): for index, value in adapters.iteritems():
sequence_id = remove_parenthesis(index) sequence_id = remove_parenthesis(index)
@ -42,6 +54,9 @@ def save_to_file(filename, adapters) -> None:
def parse_arguments(): def parse_arguments():
"""
Parse the command-line arguments
"""
parser = ArgumentParser() parser = ArgumentParser()
parser.add_argument("input", help="directory containing the fastqc reports") parser.add_argument("input", help="directory containing the fastqc reports")
parser.add_argument("output", help="file where to export the sequences") parser.add_argument("output", help="file where to export the sequences")
@ -49,6 +64,9 @@ def parse_arguments():
def main(): def main():
"""
Extract the adapters from FASTQC reports to a FASTA file and show sequence length statistics
"""
args = parse_arguments() args = parse_arguments()
file_list = glob(args.input + "/*fastqc.html") file_list = glob(args.input + "/*fastqc.html")
adapters, stats = extract_adapters(file_list) adapters, stats = extract_adapters(file_list)