Commit 8e68c018 authored by Schoorlemmer, Joran's avatar Schoorlemmer, Joran
Browse files

Replace extractcounts.py

parent efef5d64
......@@ -50,7 +50,9 @@ def group_replicates(sample_names):
with open(sample_names) as f_names:
for f in f_names:
f = f.strip("\n")
rep_dict_key = f[:-5]
# strip redundant info out of string
fn = f[:-4].split('-')
rep_dict_key = fn[0] + fn[1][0:3]+ fn[1][4:]
if not rep_dict_key in rep_dict:
rep_dict[rep_dict_key] = {}
rep_dict[rep_dict_key][f] = parse_gtf('samples/'+ str(f))
......@@ -107,4 +109,5 @@ def main(ref_name, sample_names):
# Run script
if __name__ == "__main__":
main(argv[1], argv[2])
\ No newline at end of file
#main(argv[1], argv[2])
print(group_replicates(argv[1]))
\ No newline at end of file
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