Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes

changeset 18:06c2eaff31e5 draft

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Uploaded
author jackcurragh
date Tue, 17 May 2022 14:00:40 +0000
parents f87a4b64e6ef
children 4a020e3ddc1b
files get_chrom_sizes/calculating_chrom.sizes.py
diffstat 1 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/get_chrom_sizes/calculating_chrom.sizes.py	Tue May 17 13:57:39 2022 +0000
+++ b/get_chrom_sizes/calculating_chrom.sizes.py	Tue May 17 14:00:40 2022 +0000
@@ -4,16 +4,16 @@
 # python calculating_chrom.sizes.py genome_input.fa output.chrom.sizes
 fasta_source = str(argv[1])
 prefix = str(argv[2])
-output = str(argv[3])
-genome = str(argv[4])
-builtin = str(argv[5])
+# output = str(argv[3])
+genome = str(argv[3])
+builtin = str(argv[4])
 
 # genome = 'test-data/test.fasta'
 # output = "test-data/test_chrom.sizes"
 if fasta_source == 'builtin':
 	genome = builtin
 
-chromSizesoutput = open(output,"w")
+chromSizesoutput = open('output',"w")
 
 records = []
 record = False