Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes
diff get_chrom_sizes/calculating_chrom.sizes.py @ 1:27f3669eda60 draft
Uploaded
author | jackcurragh |
---|---|
date | Mon, 04 Apr 2022 09:56:18 +0000 |
parents | |
children | cfdf764b9226 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_chrom_sizes/calculating_chrom.sizes.py Mon Apr 04 09:56:18 2022 +0000 @@ -0,0 +1,28 @@ +# 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]) +output = str(argv[2]) +# genome = 'test-data/test.fasta' +# output = "test-data/test_chrom.sizes" + +chromSizesoutput = open(output,"w") + +records = [] +record = False +for line in open(genome, 'r').readlines(): + if line[0] == '>': + if record: + records.append(record) + record = [line.strip("\n").split(' ')[0][1:], 0] + + else: + sequence = line.strip('\n') + record[1] += len(sequence) + +for seq_record in records: + output_line = '%s\t%i\n' % (seq_record[0], seq_record[1]) + chromSizesoutput.write(output_line) + +chromSizesoutput.close()