Comments (7)
(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
from genomics-workspace.
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
from genomics-workspace.
Nice!! I will make one file named add2DB.cwl
from genomics-workspace.
I think you need not only add2DB.cwl but also devide to add2Organism.cwl, add2Blast.cwl and add2Hmmer.cwl
from genomics-workspace.
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
from genomics-workspace.
Complete the addhmmer.py scirpt for CWL pipeline .
from genomics-workspace.
@deming7h777 What's the difference between this and #259 ?
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Related Issues (20)
- Re-written [BLAST query page] by React JS library HOT 5
- [BLAST query page] Organism display order HOT 1
- Final step to Integrate the adding organism functionality to CWL and fix CI issue HOT 3
- All feature under manage.py command HOT 3
- Do we need the sequences table? HOT 1
- Adding delete feature to script HOT 2
- Test if linkouts appear when ENABLE_JBROWSE_INTEGRATION = False HOT 1
- add CLI function to set is_shown HOT 3
- The blast_sequence table is big and only getting bigger HOT 10
- Moving docker version to the new repo
- vulnerabilities of django 1.11.20 and update blastdbcmd argument HOT 3
- Update readthedocs with command line interface documentation
- Consider truncating BLAST results when they are too large
- manage.py addOrganism capitalizes the short_name entry
- Using dbtitle in blast-results.js is awkward
- disable travis CI HOT 1
- Problems with multiple space characters in organism name
- google analytics code is missing
- change draggableBlastFeature to draggableNeatBlastFeature HOT 1
- Add Apollo link-outs to transcript and protein features HOT 1
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