Update add_ncbi_annotation.sh

#
perl -lne 'print "@m" if @m=(/((?:transcript_id|gene_id)\s+\S+)/g);' novel-genes-coding.gtf > novel_annotated.tab
awk '{print $(NF)}' novel_annotated.tab > novel-coding-transcripts.matches
sed -i 's/;//g' novel-coding-transcripts.matches
sed -i 's/"//g' novel-coding-transcripts.matches
awk '!a[$0]++' novel-coding-transcripts.matches > novel-coding-transcripts.tab && rm novel-coding-transcripts.matches
mv novel-coding-transcripts.tab novel-coding-transcripts.matches
#

bash_scripts/add_ncbi_annotation.sh

@@ -467,14 +467,12 @@ cp ./transcriptome_metrics/novel-transcripts-lncRNA.fa ./
 cp ./transcriptome_metrics/known-transcripts-lncRNA.fa ./
 #
 perl -lne 'print "@m" if @m=(/((?:transcript_id|gene_id)\s+\S+)/g);' novel-genes-coding.gtf > novel_annotated.tab
-sed -i 's/transcript_id //g' novel_annotated.tab
-sed -i 's/;/\t/g' novel_annotated.tab
-sed -i 's/gene_id//g' novel_annotated.tab
-sed -i 's/"//g' novel_annotated.tab
-awk '!a[$0]++' novel_annotated.tab > novel-transcripts_and_genes.tab && rm novel_annotated.tab
-awk '{print $2"\t"$1}' novel-transcripts_and_genes.tab > novel-coding-genes-and-transcripts.tab && rm novel-transcripts_and_genes.tab
-awk '{print $1}' novel-coding-genes-and-transcripts.tab > novel-coding-transcripts.matches
-rm novel-coding-genes-and-transcripts.tab
+awk '{print $(NF)}' novel_annotated.tab > novel-coding-transcripts.matches
+sed -i 's/;//g' novel-coding-transcripts.matches
+sed -i 's/"//g' novel-coding-transcripts.matches
+awk '!a[$0]++' novel-coding-transcripts.matches > novel-coding-transcripts.tab && rm novel-coding-transcripts.matches
+mv novel-coding-transcripts.tab novel-coding-transcripts.matches
+#
 seqkit fx2tab cds.fa > cds.tab
 seqkit fx2tab prot.fa > prot.tab
 grep -w -F -f novel-coding-transcripts.matches cds.tab > novel-coding-cds.tab