---
title: "downloading clam transcriptomes"
author: "Olivia"
date: "2023-04-12"
output: html_document
---

# Mercenaria merceneria everything
```{bash}
cd ../data
curl -OJX GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCF_021730395.1/download?include_annotation_type=GENOME_FASTA,GENOME_GFF,RNA_FASTA,CDS_FASTA,PROT_FASTA,SEQUENCE_REPORT&filename=GCF_021730395.1.zip" -H "Accept: application/zip" 
```

```{bash}
cd ../data
unzip GCF_021730395.1
#rna.fna is the file to blast against geoduck transcriptome
#GCF...genomic.fna is the file to build mercenaria genome db
```



#Manila Clam 
- transcriptome
```{r}
Manilla_transcriptome<-read.table(file="https://gannet.fish.washington.edu/gigas/data/p.generosa/Manilla_Pgenenerosa_blastx.tab")
```

- genome v1
```{bash}
curl -OJX GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCA_026571515.1/download?include_annotation_type=GENOME_FASTA,GENOME_GFF,RNA_FASTA,CDS_FASTA,PROT_FASTA,SEQUENCE_REPORT&filename=GCA_026571515.1.zip" -H "Accept: application/zip"
```

```{bash}
cd /home/olivia/gitrepos/olivia-geoduck/data
unzip GCA_026571515.1.zip
```

- genome v2
```{bash}
curl -OJX GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCA_009026015.1/download?include_annotation_type=GENOME_FASTA,GENOME_GFF,RNA_FASTA,CDS_FASTA,PROT_FASTA,SEQUENCE_REPORT&filename=GCA_009026015.1.zip" -H "Accept: application/zip"
```

# Mercenaria
```{bash}
cd ../data
/home/shared/datasets \
download genome accession GCF_021730395.1 \
--include gff3,rna,cds,protein,genome,seq-report \
--filename GCF_021730395.1.zip
```


## Spisula solida genome
```{bash}
cd ../data
/home/shared/datasets \
download genome accession GCA_947247005.1 \ 
--include gff3,rna,cds,protein,genome,seq-report \ 
--filename GCA_947247005.1.zip
```

#Mactra quadrangularis, GCA_025267735.1
```{bash}
/home/shared/datasets \
datasets download genome accession GCA_025267735.1 --include gff3,rna,cds,protein,genome,seq-report --filename GCA_025267735.1.zip
```

```{bash}
cd ~/gitrepos/olivia-geoduck/data/Mactra
curl -OJX GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCA_025267735.1/download?include_annotation_type=GENOME_FASTA,GENOME_GFF,RNA_FASTA,CDS_FASTA,PROT_FASTA,SEQUENCE_REPORT&filename=GCA_025267735.1.zip" -H "Accept: application/zip"
```

```{bash}
cd ~/gitrepos/olivia-geoduck/data/Mactra
unzip GCA_025267735.1.zip
```

#Archivesica marissinica
```{bash}
cd ~/gitrepos/olivia-geoduck/data/
wget https://gannet.fish.washington.edu/gigas/data/GCA_014843695.1_ASM1484369v1_genomic.fna


```