Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes
comparison get_chrom_sizes/calculating_chrom.sizes.py @ 21:cc021a23613b draft
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author | jackcurragh |
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date | Wed, 18 May 2022 08:47:20 +0000 |
parents | 06c2eaff31e5 |
children | feeee18b0084 |
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20:147706e55621 | 21:cc021a23613b |
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2 # adapted from https://bioexpressblog.wordpress.com/2014/04/15/calculate-length-of-all-sequences-in-an-multi-fasta-file/ | 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 | 3 from sys import argv |
4 # python calculating_chrom.sizes.py genome_input.fa output.chrom.sizes | 4 # python calculating_chrom.sizes.py genome_input.fa output.chrom.sizes |
5 fasta_source = str(argv[1]) | 5 fasta_source = str(argv[1]) |
6 prefix = str(argv[2]) | 6 prefix = str(argv[2]) |
7 # output = str(argv[3]) | |
8 genome = str(argv[3]) | 7 genome = str(argv[3]) |
9 builtin = str(argv[4]) | 8 builtin = str(argv[4]) |
9 output = str(argv[5]) | |
10 | 10 |
11 # genome = 'test-data/test.fasta' | 11 # genome = 'test-data/test.fasta' |
12 # output = "test-data/test_chrom.sizes" | 12 # output = "test-data/test_chrom.sizes" |
13 if fasta_source == 'builtin': | 13 if fasta_source == 'builtin': |
14 genome = builtin | 14 genome = builtin |
28 record[1] += len(sequence) | 28 record[1] += len(sequence) |
29 | 29 |
30 if record not in records: | 30 if record not in records: |
31 records.append(record) | 31 records.append(record) |
32 | 32 |
33 | |
34 | |
33 for seq_record in records: | 35 for seq_record in records: |
34 if prefix != 'none': | 36 if prefix != 'none': |
35 output_line = f"{prefix}{seq_record[0]}\t{seq_record[1]}\n" | 37 output_line = f"{prefix}{seq_record[0]}\t{seq_record[1]}\n" |
36 else: | 38 else: |
37 output_line = f"{seq_record[0]}\t{seq_record[1]}\n" | 39 output_line = f"{seq_record[0]}\t{seq_record[1]}\n" |