Commit ce840017 authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Update parsing.

parent a4875986
......@@ -6,10 +6,10 @@ awk '{if($20=="\"snoRNA\";"){print $0}}' gencode.v19.annotation.gtf > gencode.v1
# Make a index to map gene_id to gene_names
cut -f9 gencode.v19.annotation_protein_coding.gtf | cut -f1,2,5 -d ";" | cut -f2,4,6 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' > gencode.v19.annotation_protein_coding_mapping.txt
cut -f9 gencode.v19.annotation_lncRNA.gtf | cut -f1,2,5 -d ";" | cut -f2,4,6 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' > gencode.v19.annotation_lncRNA_mapping.txt
cut -f9 gencode.v19.annotation_snRNA.gtf | cut -f1,2,5 -d ";" | cut -f2,4,6 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' > gencode.v19.annotation_snRNA_mapping.txt
cut -f9 gencode.v19.annotation_snoRNA.gtf | cut -f1,2,5 -d ";" | cut -f2,4,6 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' > gencode.v19.annotation_snoRNA_mapping.txt
grep transcript gencode.v19.annotation_protein_coding.gtf | cut -f9 | cut -f1,2,5,8 -d ";" | cut -f2,4,6,8 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' > gencode.v19.annotation_protein_coding_mapping.txt
grep transcript gencode.v19.annotation_lncRNA.gtf | cut -f9 | cut -f1,2,5,8 -d ";" | cut -f2,4,6,8 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' > gencode.v19.annotation_lncRNA_mapping.txt
grep transcript gencode.v19.annotation_snRNA.gtf | cut -f9 | cut -f1,2,5,8 -d ";" | cut -f2,4,6,8 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' > gencode.v19.annotation_snRNA_mapping.txt
grep transcript gencode.v19.annotation_snoRNA.gtf | cut -f9 | cut -f1,2,5,8 -d ";" | cut -f2,4,6,8 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' > gencode.v19.annotation_snoRNA_mapping.txt
cut -f9 gencode.v19.annotation.gtf | cut -f1,2,5 -d ";" | cut -f2,4,6 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' > mapping.txt
grep transcript gencode.v19.annotation.gtf | cut -f9 | cut -f1,2,5,8 -d ";" | cut -f2,4,6,8 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' > mapping.txt
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