Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes
comparison get_chrom_sizes/calculating_chrom.sizes.py @ 15:c7e2879bf357 draft
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author | jackcurragh |
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date | Tue, 17 May 2022 13:49:26 +0000 |
parents | 84664985411c |
children | ab7b5928faea |
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14:afd11143fb67 | 15:c7e2879bf357 |
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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. | 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/ | 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 genome = str(argv[2]) | 6 prefix = str(argv[2]) |
7 builtin = str(argv[3]) | 7 output = str(argv[3]) |
8 prefix = str(argv[4]) | 8 genome = str(argv[4]) |
9 output = str(argv[5]) | 9 builtin = str(argv[5]) |
10 | |
10 # genome = 'test-data/test.fasta' | 11 # genome = 'test-data/test.fasta' |
11 # output = "test-data/test_chrom.sizes" | 12 # output = "test-data/test_chrom.sizes" |
12 print(fasta_source, genome, builtin, prefix, output) | 13 print(fasta_source, genome, builtin, prefix, output) |
13 if fasta_source == 'builtin': | 14 if fasta_source == 'builtin': |
14 genome = builtin | 15 genome = builtin |