Commit e4de5bd4 authored by Jerome Mariette's avatar Jerome Mariette
Browse files

use ng6.SeqIO instead of Bio.SeqIO

parent d59c5a29
......@@ -71,8 +71,8 @@ def reads_to_sff (sff_file, seqs, output_file):
# First creates the to_write file
tmp_file = os.path.join(os.path.dirname(output_file), "reads_to_sff.txt")
to_write_file = open(tmp_file, 'wr')
for read in seqs:
to_write_file.write(read.id + "\n")
for id, desc, seq, qual in seqs:
to_write_file.write(id + "\n")
to_write_file.close()
# Use the sfffile tools
cmd = "sfffile -i " + tmp_file + " -o " + output_file + " " + sff_file
......
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