Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes
comparison get_chrom_sizes/calculating_chrom.sizes.py @ 1:27f3669eda60 draft
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author | jackcurragh |
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date | Mon, 04 Apr 2022 09:56:18 +0000 |
parents | |
children | cfdf764b9226 |
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0:6d5d1b56c286 | 1:27f3669eda60 |
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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 genome = str(argv[1]) | |
6 output = str(argv[2]) | |
7 # genome = 'test-data/test.fasta' | |
8 # output = "test-data/test_chrom.sizes" | |
9 | |
10 chromSizesoutput = open(output,"w") | |
11 | |
12 records = [] | |
13 record = False | |
14 for line in open(genome, 'r').readlines(): | |
15 if line[0] == '>': | |
16 if record: | |
17 records.append(record) | |
18 record = [line.strip("\n").split(' ')[0][1:], 0] | |
19 | |
20 else: | |
21 sequence = line.strip('\n') | |
22 record[1] += len(sequence) | |
23 | |
24 for seq_record in records: | |
25 output_line = '%s\t%i\n' % (seq_record[0], seq_record[1]) | |
26 chromSizesoutput.write(output_line) | |
27 | |
28 chromSizesoutput.close() |