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1 #!/usr/bin/env python3
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2
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3 from Bio import SeqIO
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4 import hashlib
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5 import sys
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6 import os
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7 import pandas as pd
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8
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9 def fasta_info(sample_name,file_path):
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10
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11 if not os.path.exists(file_path):
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12 sys.exit(f"File {file_path} does not exist.")
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13 elif not file_path.lower().endswith(('.fa', '.fasta', '.fna')):
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14 sys.exit(f"File {file_path} is not a .fa, .fasta, or .fna file.")
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15
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16 records = list(SeqIO.parse(file_path, 'fasta'))
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17 contig_count = int(len(records))
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18 lengths = sorted([len(record) for record in records], reverse=True)
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19 assembly_bases = sum(lengths)
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20
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21 with open(file_path, 'rb') as file:
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22 sha256 = hashlib.sha256(file.read()).hexdigest()
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23
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24 cumulative_length = 0
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25 n50 = None
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26 n90 = None
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27 l50 = None
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28 l90 = None
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29
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30 for i, length in enumerate(lengths, start=1):
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31 cumulative_length += length
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32 if cumulative_length >= assembly_bases * 0.5 and n50 is None:
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33 n50 = length
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34 l50 = i
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35 if cumulative_length >= assembly_bases * 0.9 and n90 is None:
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36 n90 = length
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37 l90 = i
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38 if n50 is not None and n90 is not None:
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39 break
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40
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41 print(f"{sample_name},{file_path},{contig_count},{assembly_bases},{n50},{n90},{l50},{l90},{sha256}")
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42
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43 fasta_tsv = pd.read_csv(sys.argv[1], sep='\t', header=None, names=['Sample_ID','Fasta_Path'])
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44 [fasta_info(sample_name, file_path) for sample_name, file_path in fasta_tsv.values] |
