MrY -- 📚 Management of references for yourself

Why this mini-manager?

When human, mouse, zebrafish, roundworm (C. elegans), yeast (S. cerevisiae), and bacteria (salmonella and M. tuberculosis) show up together in one zoo, a manager is suggested.

What does it do for you?

• Download genome sequence (.fasta). It downloads the primary_assembly version, if not available, toplevel version is downloaded.
• Download annotation (both .gff3 and .gtf).
• Build aligner index.
• Maintain references in a folder structure which is making sense.

How to install MrY?

git clone git@github.com:Puriney/MrY.git
cd MrY
pip install ./

How to use MrY?

There are 3 common operations:

1. install
2. list
3. delete

Install references

yun install  --root-dir /path/to/your/zoo \
--species zebrafish \
--assembly GRCz10 \
--org Ensembl \
--release 90 \
--target all

MrY will generate a folder named zebrafish under /path/to/your/zoo to create references for zebrafish of which the assembly name is GRCz10 in release 90 of Ensembl.

zebrafish/
├── aligner_index
│   ├── bowtie2
│   │   └── Ensembl
│   │       └── GRCz10
│   │           └── release_90
│   │               ├── GRCz10.dna.1.bt2
│   │               ├── GRCz10.dna.2.bt2
│   │               ├── GRCz10.dna.3.bt2
│   │               ├── GRCz10.dna.4.bt2
│   │               ├── GRCz10.dna.rev.1.bt2
│   │               └── GRCz10.dna.rev.2.bt2
│   └── star
│       └── Ensembl
│           └── GRCz10
│               └── release_90
│                   ├── chrLength.txt
│                   ├── chrNameLength.txt
│                   ├── chrName.txt
│                   ├── chrStart.txt
│                   ├── exonGeTrInfo.tab
│                   ├── exonInfo.tab
│                   ├── geneInfo.tab
│                   ├── Genome
│                   ├── genomeParameters.txt
│                   ├── Log.out
│                   ├── SA
│                   ├── SAindex
│                   ├── sjdbInfo.txt
│                   ├── sjdbList.fromGTF.out.tab
│                   ├── sjdbList.out.tab
│                   └── transcriptInfo.tab
├── annotation
│   └── Ensembl
│       └── GRCz10
│           └── release_90
│               ├── ensembl.GRCz10.90.gff3
│               ├── ensembl.GRCz10.90.gff3.gz
│               ├── ensembl.GRCz10.90.gtf
│               └── ensembl.GRCz10.90.gtf.gz
└── genome
    └── Ensembl
        └── GRCz10
            └── release_90
                ├── Danio_rerio.GRCz10.dna.toplevel.fa.gz
                ├── GRCz10.dna.fa
                └── GRCz10.dna.fa.gz -> /path/to/your/zoo/zebrafish/genome/Ensembl/GRCz10/release_90/Danio_rerio.GRCz10.dna.toplevel.fa.gz

Alternatively, more than one species can be installed in the same time:

yun install --root-dir /ifs/data/yanailab/ref \
--species zebrafish roundworm brewer_yeast \
--assembly GRCz10 WBcel235 R64-1-1 \
--release  90 90 90 \
--org Ensembl \
--target all

List available references

List available references for specific zibrafish:

yun list  --root-dir /path/to/your/zoo \
--species zebrafish \
--assembly GRCz10 \
--org Ensembl \
--release 90

==========
zebrafish-GRCz10-Ensembl-90 was queried:
            Genome (.fa): Installed
       Annotation (.gtf): Installed
      Annotation (.gff3): Installed
                 Bowtie2: Installed
                    STAR: Installed

Alternatively, list all available references and a markdown table will be generated.

yun list  --root-dir /path/to/your/zoo

Species	Assembly	Org	Release	Genome (.fa)	Annotation (.gtf)	Annotation (.gff3)	Bowtie2	STAR
zebrafish	GRCz10	Ensembl	90	True	True	True	True	True
roundworm	WBcel235	Ensembl	90	True	True	True	False	False
mouse	GRCm38	GENCODE	M15	True	True	True	True	True
mouse	GRCm38	Ensembl	90	True	True	True	True	True
human	GRCh38	GENCODE	27	True	True	True	True	True
human	GRCh38	GENCODE	23	False	True	True	False	False
human	GRCh38	Ensembl	90	True	True	True	True	True
brewer_yeast	R64-1-1	Ensembl	90	True	True	True	True	True

Delete references

Check which GTF and GFF3 files are to be deleted before actually removing them.

yun delete  --root-dir /path/to/your/zoo \
--species zebrafish \
--assembly GRCz10 \
--org Ensembl \
--release 90 \
--target task_annotation \
-n

Run above command without -n and actually remove them. Change task_annotation to all to delete all references of specific zebrafish.

More Examples

here

FAQ

here