Mercurial > repos > triasteran > ribogalaxy_get_chrom_sizes_upd
comparison get_chrom_sizes/calculating_chrom.sizes.py @ 0:b93d6b2e561b draft
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author | triasteran |
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date | Mon, 13 Feb 2023 15:49:26 +0000 |
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-1:000000000000 | 0:b93d6b2e561b |
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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. | |
2 # adapted from https://bioexpressblog.wordpress.com/2014/04/15/calculate-length-of-all-sequences-in-an-multi-fasta-file/ | |
3 from sys import argv | |
4 # python calculating_chrom.sizes.py genome_input.fa output.chrom.sizes | |
5 fasta_source = str(argv[1]) | |
6 prefix = str(argv[2]) | |
7 genome = str(argv[3]) | |
8 builtin = str(argv[4]) | |
9 output = str(argv[5]) | |
10 | |
11 # genome = 'test-data/test.fasta' | |
12 # output = "test-data/test_chrom.sizes" | |
13 if fasta_source == 'builtin': | |
14 genome = builtin | |
15 | |
16 chromSizesoutput = open(output,"w") | |
17 | |
18 records = [] | |
19 record = False | |
20 for line in open(genome, 'r').readlines(): | |
21 if line[0] == '>': | |
22 if record: | |
23 records.append(record) | |
24 record = [line.strip("\n").split(' ')[0].split(" ")[0][1:], 0] | |
25 | |
26 else: | |
27 sequence = line.strip('\n') | |
28 record[1] += len(sequence) | |
29 | |
30 if record not in records: | |
31 records.append(record) | |
32 | |
33 | |
34 | |
35 for seq_record in records: | |
36 if prefix != 'none': | |
37 output_line = f"{prefix}{seq_record[0]}\t{seq_record[1]}\n" | |
38 else: | |
39 output_line = f"{seq_record[0]}\t{seq_record[1]}\n" | |
40 | |
41 chromSizesoutput.write(output_line) | |
42 | |
43 chromSizesoutput.close() |