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1
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1 # input a genome file and return a file genome.chrom.sizes to be associated with the custom build (or just have it as an output to be used later in the history.
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2 # adapted from https://bioexpressblog.wordpress.com/2014/04/15/calculate-length-of-all-sequences-in-an-multi-fasta-file/
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3 from sys import argv
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4 # python calculating_chrom.sizes.py genome_input.fa output.chrom.sizes
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6
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5 fasta_source = str(argv[1])
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15
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6 prefix = str(argv[2])
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7 output = str(argv[3])
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8 genome = str(argv[4])
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9 builtin = str(argv[5])
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10
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1
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11 # genome = 'test-data/test.fasta'
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12 # output = "test-data/test_chrom.sizes"
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8
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13 print(fasta_source, genome, builtin, prefix, output)
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14 if fasta_source == 'builtin':
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15 genome = builtin
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1
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16
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17 chromSizesoutput = open(output,"w")
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18
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19 records = []
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20 record = False
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21 for line in open(genome, 'r').readlines():
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22 if line[0] == '>':
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23 if record:
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24 records.append(record)
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25 record = [line.strip("\n").split(' ')[0][1:], 0]
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26
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27 else:
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28 sequence = line.strip('\n')
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29 record[1] += len(sequence)
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3
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30
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31 if record not in records:
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32 records.append(record)
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33
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1
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34 for seq_record in records:
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4
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35 if prefix != 'none':
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36 output_line = f"{prefix}{seq_record[0]}\t{seq_record[1]}\n"
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37 else:
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38 output_line = f"{seq_record[0]}\t{seq_record[1]}\n"
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39
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1
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40 chromSizesoutput.write(output_line)
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41
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42 chromSizesoutput.close()
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