---
tags: GeneLab
title: Govind-wasp-annotations-2022
---

# Govind wasp annotations 2022

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## Looking for GAJC IDs in NCBI files for *Leptopilina heterotoma*

Getting RefSeq files from here: https://www.ncbi.nlm.nih.gov/genome/17698?genome_assembly_id=1491693

### Getting gff file

# getting and unzipping gff file
curl -LO https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/476/425/GCF_015476425.1_ASM1547642v1/GCF_015476425.1_ASM1547642v1_genomic.gff.gz

gunzip GCF_015476425.1_ASM1547642v1_genomic.gff.gz

### Investigating lines with a GAJC ID

# how many lines total in file
wc -l GCF_015476425.1_ASM1547642v1_genomic.gff
    # 444152 GCF_015476425.1_ASM1547642v1_genomic.gff
  
# how many lines with a GAJC
grep -c "GAJC" GCF_015476425.1_ASM1547642v1_genomic.gff
    # 17
    
# how many unique GAJC IDs
grep "GAJC" GCF_015476425.1_ASM1547642v1_genomic.gff | sed 's/GAJC/\|GAJC/g' | cut -f 2 -d "|" | cut -f 1 -d ";" | sort -u
    # GAJC01001300.1
    # GAJC01028679.1
    # GAJC01029969.1