hdrs处理脚本

# -*- coding: utf-8 -*-
"""
version: python 3.0
usage: python get_ASprofile_ref_hdrs.py path/species.genome.fa species
"""

import sys
import re
import fileinput
import pandas as pd
import os.path

if len(sys.argv) < 3:
    sys.exit("python error")

FA = sys.argv[1]
species = sys.argv[2]

dic_chr = {}
temp_chr = ''

for line in fileinput.input(FA):
    line = line.strip()

    pat = re.compile(r'^>')

    match = pat.match(line)
    if match:
        a = line.split(" ")[0]
        temp_chr = a

        dic_chr.setdefault(temp_chr, [0, 0])
    else:
        dic_chr[temp_chr][0] += len(line)
        dic_chr[temp_chr][1] += (line.count("N") + line.count("n"))

fileinput.close()

# Create DataFrame with explicit column names
df = pd.DataFrame.from_dict(dic_chr, orient='index', columns=['length', 'nonNlen'])
df = df.reset_index()
df.columns = ['index', 'length', 'nonNlen']

# Convert columns to appropriate types before assignment
df['length'] = df['length'].astype(str)
df['nonNlen'] = df['nonNlen'].astype(str)

for i in range(0, len(df)):
    df.iloc[i, 1] = "/len=" + df.iloc[i, 1]
    df.iloc[i, 2] = "/nonNlen=" + df.iloc[i, 2]

df["species"] = "/org=" + species

# Save to text file
df.to_csv(species + '.fa.hdrs.txt', sep=' ', header=False, index=False, quoting=3)