---
# System prepended metadata

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

---

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

# Govind wasp annotations 2022

[toc]

## 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
```bash
# 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

```bash
# 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
```
