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A small module to join gene data tables from GenBank
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# Version: 2022/12/07 - 10:51 | |
import pandas as pd | |
import os | |
import sys | |
# Return all files in the given directory as a list | |
dir = "./tables" | |
files: list[str] = [] | |
for file in os.listdir(dir): | |
# List files that end with specific extension (.tab) | |
if file.endswith(".tab"): | |
files.append(os.path.join(dir, file)) | |
# Exit if files list is empty | |
if not files: | |
sys.exit(f"No table files in {dir}.") | |
# Iterate throw files and concatenate tables with Taxa and Lineages only | |
# no Accession Numbers for now. | |
table_list: list[pd.DataFrame] = [] | |
for file in files: | |
table = pd.read_table(file, header=None)[[0, 1]] | |
table.columns = ["Taxa", "Lineage"] # type: ignore | |
table_list.append(table) | |
Taxa = pd.concat(table_list) | |
# Create a dictionary of all Lineages and Taxa attributed to them | |
names = Taxa.groupby('Lineage').Taxa.apply( # type: ignore | |
list).to_dict() | |
# Identify Taxa with more than one name and mark it with an * | |
for k, v in names.items(): | |
if len(set(v)) == 1: | |
names[k] = v[0] | |
else: | |
names[k] = f"*{v[0]}" | |
# Turn names dict into a pandas dataframe | |
names = pd.DataFrame(list(names.items()), columns=["Lineage", "Taxa"]) | |
# Merge dataframes and recover the Accession Numbers and other variables | |
# that may exist | |
for file in files: | |
table = pd.read_table(file, header=None)[[1, 2]] | |
table.columns = ["Lineage", | |
f"{os.path.basename(file.split('final', 1)[0])}"] # type: ignore | |
names = names.merge(table, how="outer", on="Lineage") | |
# Save final table with merged results as tab separated csv | |
names.to_csv('./JointTable.tab', sep="\t", index=False) |
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