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Commit 403ff478 authored by Blaise Li's avatar Blaise Li
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Consider mCherry a protein_coding.

This is so that the small RNA annotation script does not miss mCherry.
parent a7edc1f0
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...@@ -50,7 +50,7 @@ def main(): ...@@ -50,7 +50,7 @@ def main():
with fs.open("mCherry_transcript.fa", "w") as transcript_file: with fs.open("mCherry_transcript.fa", "w") as transcript_file:
transcript_file.write(f">mCherry\n{mCherry_seq}\n") transcript_file.write(f">mCherry\n{mCherry_seq}\n")
with fs.open("mCherry.gtf", "w") as transcript_gtf_file: 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([ transcript_gtf_file.write("\t".join([
"mCherry", "local", "transcript", "1", str(len(mCherry_seq)), "mCherry", "local", "transcript", "1", str(len(mCherry_seq)),
"0", "+", ".", annotations])) "0", "+", ".", annotations]))
...@@ -77,7 +77,7 @@ def main(): ...@@ -77,7 +77,7 @@ def main():
"mCherry_transgene", "local", "exon", str(start_in_transgene), str(end_in_transgene), "mCherry_transgene", "local", "exon", str(start_in_transgene), str(end_in_transgene),
"0", "+", ".", annotations])) "0", "+", ".", annotations]))
transgene_gtf_file.write("\n") 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([ transcript_gtf_file.write("\t".join([
"mCherry", "local", "exon", str(start_in_transcript), str(end_in_transcript), "mCherry", "local", "exon", str(start_in_transcript), str(end_in_transcript),
"0", "+", ".", annotations])) "0", "+", ".", annotations]))
......
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