Commit 3380e3aa authored by Tizian Schulz's avatar Tizian Schulz
Browse files

Revised rule to download reads

parent 1e99f93c
......@@ -152,7 +152,7 @@ rule downloadReadSets:
output:
["arabidopsis/reads/" + basename(f) for l in open("arabidopsis/reads/filereport_read_run_PRJEB2457_tsv.txt", 'r') for f in l.split('\t')[6].split(';')]
shell:
"wget {input}; mv *.fastq.gz arabidopsis/reads"
"wget $(python3 scripts/getReadLocations.py {input}); mv *.fastq.gz arabidopsis/reads"
rule createAssemblyList:
input:
......
#!/usr/bin/env python3
import sys
isFirst = True
addresses = []
for l in open(sys.argv[1]):
if isFirst:
isFirst = False
continue
for a in l.split('\t')[6].split(';'):
addresses.append(a)
print(' '.join(addresses))
\ No newline at end of file
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment