From 403ff4786e1a376dc061e2b32083ba22e87ee973 Mon Sep 17 00:00:00 2001 From: Blaise Li <blaise.li__git@nsup.org> Date: Mon, 30 Apr 2018 13:59:43 +0200 Subject: [PATCH] Consider mCherry a protein_coding. This is so that the small RNA annotation script does not miss mCherry. --- make_mCherry_transgene.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/make_mCherry_transgene.py b/make_mCherry_transgene.py index 7cca330..165c3e9 100755 --- a/make_mCherry_transgene.py +++ b/make_mCherry_transgene.py @@ -50,7 +50,7 @@ def main(): with fs.open("mCherry_transcript.fa", "w") as transcript_file: transcript_file.write(f">mCherry\n{mCherry_seq}\n") with fs.open("mCherry.gtf", "w") as transcript_gtf_file: - annotations = "gene_id \"mCherry\"; transcript_id \"mCherry\"; gene_biotype \"mCherry\";" + annotations = "gene_id \"mCherry\"; transcript_id \"mCherry\"; gene_biotype \"protein_coding\";" transcript_gtf_file.write("\t".join([ "mCherry", "local", "transcript", "1", str(len(mCherry_seq)), "0", "+", ".", annotations])) @@ -77,7 +77,7 @@ def main(): "mCherry_transgene", "local", "exon", str(start_in_transgene), str(end_in_transgene), "0", "+", ".", annotations])) transgene_gtf_file.write("\n") - annotations = f"exon_id \"mCherry.e{exon_number}\"; exon_number \"{exon_number}\"; gene_id \"mCherry\"; transcript_id \"mCherry\"; gene_biotype \"mCherry\";" + annotations = f"exon_id \"mCherry.e{exon_number}\"; exon_number \"{exon_number}\"; gene_id \"mCherry\"; transcript_id \"mCherry\"; gene_biotype \"protein_coding\";" transcript_gtf_file.write("\t".join([ "mCherry", "local", "exon", str(start_in_transcript), str(end_in_transcript), "0", "+", ".", annotations])) -- GitLab