Adding blast & hmmer database by script

[deming7h777]

Also make the script for blast and hmmer that can add the database by one command and can be easier to integrate with CWL.

ideal command : python manage.py addblast [Genus] [species] -t [sequence_type] -f [fasta_filename]

[deming7h777]

(py2.7) [vagrant@localhost genomics-workspace]$ python manage.py addblast Anoplophora glabripennis -t prot protein -f Agla_Btl03082013.genome.fa
{'settings': None, 'pythonpath': None, 'verbosity': 1, 'traceback': False, 'Genus_Species': ['Anoplophora', 'glabripennis'], 'filename': ['Agla_Btl03082013.genome.fa'], 'no_color': False, 'type': ['prot', 'protein']}
Anoplophora glabripennis
<class 'app.models.Organism'>
prot
protein
Peptide - protein
Agla_Btl03082013.genome.fa
/home/vagrant/genomics-workspace/media/blast/db/Agla_Btl03082013.genome.fa
next step is going to add in the database

it success to add to the blastdb however there are some problem about the input argument

[deming7h777]

Case 1.
No matter the input of argument is peptide or nucleotide we can transfer it to the prot and nucl automatically and is not sensitive for the capitalization, see the example above for type

(py2.7) [vagrant@localhost genomics-workspace]$ python manage.py addblast Anoplophora glabripennis -t nucleotide Genome assembly -f Agla_Btl03082013.genome.fa
Anoplophora glabripennis
nucl
Genome Assembly
<QuerySet [<SequenceType: Nucleotide - Genome Assembly>]>
Genome Assembly
Nucleotide - Genome Assembly
Agla_Btl03082013.genome.fa
/home/vagrant/genomics-workspace/media/blast/db/Agla_Btl03082013.genome.fa
next step is going to add in the database

Case 2.
It can check if the fasta file exist in media/blast/db .

(py2.7) [vagrant@localhost genomics-workspace]$ python manage.py addblast Anoplophora glabripennis -t nucleotide Genome assembly -f Agla_Btl03082013.genome.fa
Anoplophora glabripennis
nucl
Genome Assembly
<QuerySet [<SequenceType: Nucleotide - Genome Assembly>]>
Genome Assembly
Nucleotide - Genome Assembly
Agla_Btl03082013.genome.fa
No fasta file in media/blast/db

Case 3.
It can check if the molecule_type or dataset_type is correct or not.

(py2.7) [vagrant@localhost genomics-workspace]$ python manage.py addblast Anoplophora glabripennis -t nucleoide Genome assembly -f Agla_Btl03082013.genome.fa
Anoplophora glabripennis
please enter the correct molecule_type, must be nucleotide or peptide

(py2.7) [vagrant@localhost genomics-workspace]$ python manage.py addblast Anoplophora glabripennis -t nucleotide Genome asembly -f Agla_Btl03082013.genome.fa
Anoplophora glabripennis
nucl
check your dataset_type, must be Protein or Transcript or Genome Assembly

Case 4.
It can check the combination of molecule_type and dataset_type

(py2.7) [vagrant@localhost genomics-workspace]$ python manage.py addblast Anoplophora glabripennis -t peptiDe Genome assembly -f Agla_Btl03082013.genome.fa
Anoplophora glabripennis
prot
Genome Assembly
<QuerySet [<SequenceType: Nucleotide - Genome Assembly>]>
Genome Assembly
there are no Peptide - Genome Assembly combination in the database

[r06942072]

Nice!! I will make one file named add2DB.cwl

[deming7h777]

I think you need not only add2DB.cwl but also devide to add2Organism.cwl, add2Blast.cwl and add2Hmmer.cwl

[r06942072]

Good idea. I deleted add2DB.cwl and I made one cwl file for each app.

Link:
https://github.com/NAL-i5K/CWL_Common-Workflow-Language/tree/dev_0328

[deming7h777]

Complete the addhmmer.py scirpt for CWL pipeline .

[hsiaoyi0504]

@deming7h777 What's the difference between this and #259 ?