comparison get_chrom_sizes/calculating_chrom.sizes.py @ 6:c96b29e00427 draft

Uploaded

5:ec8651ac3d61

# 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.
# adapted from https://bioexpressblog.wordpress.com/2014/04/15/calculate-length-of-all-sequences-in-an-multi-fasta-file/
from sys import argv
# python calculating_chrom.sizes.py genome_input.fa output.chrom.sizes
genome = str(argv[1])
prefix = str(argv[2])
output = str(argv[3])
# genome = 'test-data/test.fasta'
# output = "test-data/test_chrom.sizes"

chromSizesoutput = open(output,"w")

6:c96b29e00427

# 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.
# adapted from https://bioexpressblog.wordpress.com/2014/04/15/calculate-length-of-all-sequences-in-an-multi-fasta-file/
from sys import argv
# python calculating_chrom.sizes.py genome_input.fa output.chrom.sizes
fasta_source = str(argv[1])
genome = str(argv[2])
builtin = str(argv[3])
prefix = str(argv[4])
output = str(argv[5])
# genome = 'test-data/test.fasta'
# output = "test-data/test_chrom.sizes"

chromSizesoutput = open(output,"w")