diff get_chrom_sizes/calculating_chrom.sizes.py @ 1:27f3669eda60 draft

Uploaded

--- /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()