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format_gc_tsv.py
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format_gc_tsv.py
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"""
python format_gc_tsv.py pfamtxt.size.txt md5_checksums
"""
import os.path
import argparse
import base64
import pandas as pd
def main():
parser = argparse.ArgumentParser()
parser.add_argument('sizes')
parser.add_argument('md5')
parser.add_argument('--loc',
default="http://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/database_files/")
args = parser.parse_args()
df_sizes = pd.read_table(args.sizes, sep='\s+', header=None,
usecols=[4, 8],
index_col=1, names=['size', 'name'])
df_check = pd.read_csv(args.md5, sep='\s+', header=None,
index_col=1, names=['check'])
df_join = pd.merge(df_sizes, df_check, how='left',
left_index=True, right_index=True)
print('TsvHttpData-1.0')
for ind, row in df_join.iterrows():
location = os.path.join(args.loc, ind)
size = row['size']
check_b64 = base64.b64encode(bytes.fromhex(row['check']))
print(location, size, check_b64.decode(), sep='\t')
return
if __name__ == '__main__':
main()