pyblastbio 0.1.5

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pyblast

This is a wrapper for other applications to run blast searches

Installation

You can install BLAST to the pyblast directory using the following command:

pyblast install

This will install it to pyblast/blast_bin. If you want BLAST installed somewhere else, move the ncbi-blast-X.X.X+ folder to your desired location and add path/to/ncbi-blast-X.X.X+/bin to you $PATH. PyBlast will prefer to use the blast stored in your executable path. If it cannot find a blast executable there, it looks for it in that paths in the pyblast/blast_bin/_paths.txt. file. _paths.txt is automatically updated when you run install_blast.py so theres no need to manage the paths manually.

After installing and verifying the blastn command works from the cmd line,

pip install pyblastbio

Status

In alpha, but let me know if you are interested in this repo.

Usage

This package is a python wrapper for the BLAST command line, intended to be run along with a microservice (e.g. Flask). This package also includes a basic python-based installation script which is used in unit-testing.

Input options

To use blast...

from pyblast import JSONBlast

# load your DNA from where ever you keep it
query = json.load(...)
subjects = json.load(...)

# BLAST cmd object
myblast = JSONBlast(subjects, query)

# build the db, run the search, & parse the results
congig = {...}
myblast.quick_blastn(**config)

# get the results object
results = myblast.results  # get the results object

Input Format

Input sequences have the following format:

  {
    "name": "attB-mCh-Dnmt3b1-Poly(A",
    "sequence": "gatGCCAGCTCATTCCTCCCACTCATGATCTATAGATCCCCCGGGCTGCAGGAATTCTACCGGGTAGGGGAGGCGCTTTTCCCAAGGCAGTCTGGAGCATGCGCTTTAGCAGCCCCGCTGGGCACTTGGCGCTACACAAGTGGCCTCTGGCCTCGCACACATTCCACATCCACCGGTAGGCGCCAACCGGCTCCGTTCTTTGGTGGCCCCTTCGCGCCACCTTCTACTCCTCCCCTAGTCAGGAAGTTCCCCCCCGCCCCGCAGCTCGCGTCGTGCAGGACGTGACAAATGGAAGTAGCACGTCTCACTAGTCTCGTGCAGATGGACAGCACCGCTGAGCAATGGAAGCGGGTAGGCCTTTGGGGCAGCGGCCAATAGCAGCTTTGCTCCTTCGCTTTCTGGGCTCAGAGGCTGGGAAGGGGTGGGTCCGGGGGCGGGCTCAGGGGCGGGCTCAGGGGCGGGGCGGGCGCCCGAAGGTCCTCCGGAGGCCCGGCATTCTGCACGCTTCAAAAGCGCACGTCTGCCGCGCTGTTCTCCTCTTCCTCATCTCCGGGCCTTTCGACCGATCATCAAGCTTAATGATTGAACAAGATGGATTGCACGCAGGTTCTCCGGCCGCTTGGGTGGAGAGGCTATTCGGCTATGACTGGGCACAACAGACAATCGGCTGCTCTGATGCCGCCGTGTTCCGGCTGTCAGCGCAGGGGCGCCCGGTTCTTTTTGTCAAGACCGACCTGTCCGGTGCCCTGAATGAACTGCAAGACGAGGCAGCGCGGCTATCGTGGCTGGCCACGACGGGCGTTCCTTGCGCAGCTGTGCTCGACGTTGTCACTGAAGCGGGAAGGGACTGGCTGCTATTGGGCGAAGTGCCGGGGCAGGATCTCCTGTCATCTCACCTTGCTCCTGCCGAGAAAGTATCCATCATGGCTGATGCAATGCGGCGGCTGCATACGCTTGATCCGGCTACCTGCCCATTCGACCACCAAGCGAAACATCGCATCGAGCGAGCACGTACTCGGATGGAAGCCGGTCTTGTCGATCAGGATGATCTGGACGAAGAGCATCAGGGGCTCGCGCCAGCCGAACTGTTCGCCAGGCTCAAGGCGAGCATGCCCGACGGCGAGGATCTCGTCGTGACCCATGGCGATGCCTGCTTGCCGAATATCATGGTGGAAAATGGCCGCTTTTCTGGATTCATCGACTGTGGCCGGCTGGGTGTGGCGGACCGCTATCAGGACATAGCGTTGGCTACCCGTGATATTGCTGAAGAGCTTGGCGGCGAATGGGCTGACCGCTTCCTCGTGCTTTACGGTATCGCCGCTCCCGATTCGCAGCGCATCGCCTTCTATCGCCTTCTTGACGAGTTCTTCTGAGCGGGACTCTGGGGTTCGAAATGACCGACCAAGCGACGCCCAACCTGCCATCACGAGATTTCGATTCCACCGCCGCCTTCTATGAAAGGTTGGGCTTCGGAATCGTTTTCCGGGACGCCGGCTGGATGATCCTCCAGCGCGGGGATCTCATGCTGGAGTTCTTCGCCCACCCTAGGGGGAGGCTAACTGAAACACGGAAGGAGACAATACCGGAAGGAACCCGCGCTATGACGGCAATAAAAAGACAGAATAAAACGCACGGTGTTGGGTCGTTTGTTCATAAACGCGGGGTTCGGTCCCAGGGCTGGCACTCTGTCGATACCCCACCGAGACCCCATTGGGGCCAATACGCCCGCGTTTCTTCCTTTTCCCCACCCCACCCCCCAAGTTCGGGTGAAGGCCCAGGGCTCGCAGCCAACGTCGGGGCGGCAAGCTTACATCGAGatcCCGGCTTGTCGACGACGGCGgtCTCCGTCGTCAGGATCATCCGTGAGCAAGGGCGAGGAGGATAACATGGCCATCATCAAGGAGTTCATGCGCTTCAAGGTGCACATGGAGGGCTCCGTGAACGGCCACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTACGAGGGCACCCAGACCGCCAAGCTGAAGGTGACCAAGGGTGGCCCCCTGCCCTTCGCCTGGGACATCCTGTCCCCTCAGTTCATGTACGGCTCCAAGGCCTACGTGAAGCACCCCGCCGACATCCCCGACTACTTGAAGCTGTCCTTCCCCGAGGGCTTCAAGTGGGAGCGCGTGATGAACTTCGAGGACGGCGGCGTGGTGACCGTGACCCAGGACTCCTCCCTGCAGGACGGCGAGTTCATCTACAAGGTGAAGCTGCGCGGCACCAACTTCCCCTCCGACGGCCCCGTAATGCAGAAGAAGACCATGGGCTGGGAGGCCTCCTCCGAGCGGATGTACCCCGAGGACGGCGCCCTGAAGGGCGAGATCAAGCAGAGGCTGAAGCTGAAGGACGGCGGCCACTACGACGCTGAGGTCAAGACCACCTACAAGGCCAAGAAGCCCGTGCAGCTGCCCGGCGCCTACAACGTCAACATCAAGTTGGACATCACCTCCCACAACGAGGACTACACCATCGTGGAACAGTACGAACGCGCCGAGGGCCGCCACTCCACCGGCGGCATGGACGAGCTGTACAAGAGCGGCCTGAGGAGCAGAGCCCAGGCGAGCAACAGCGCCGTGGACGCCACCATGGGCGatCGCATGAAGGGAGACAGCAGACATCTGAATGAAGAAGAGGGTGCCAGCGGGTATGAGGAGTGCATTATCGTTAATGGGAACTTCAGTGACCAGTCCTCAGACACGAAGGATGCTCCCTCACCCCCAGTCTTGGAGGCAATCTGCACAGAGCCAGTCTGCACACCAGAGACCAGAGGCCGCAGGTCAAGCTCCCGGCTGTCTAAGAGGGAGGTCTCCAGCCTTCTGAATTACACGCAGGACATGACAGGAGATGGAGACAGAGATGATGAAGTAGATGATGGGAATGGCTCTGATATTCTAATGCCAAAGCTCACCCGTGAGACCAAGGACACCAGGACGCGCTCTGAAAGCCCGGCTGTCCGAACCCGACATAGCAATGGGACCTCCAGCTTGGAGAGGCAAAGAGCCTCCCCCAGAATCACCCGAGGTCGGCAGGGCCGCCACCATGTGCAGGAGTACCCTGTGGAGTTTCCGGCTACCAGGTCTCGGAGACGTCGAGCATCGTCTTCAGCAAGCACGCCATGGTCATCCCCTGCCAGCGTCGACTTCATGGAAGAAGTGACACCTAAGAGCGTCAGTACCCCATCAGTTGACTTGAGCCAGGATGGAGATCAGGAGGGTATGGATACCACACAGGTGGATGCAGAGAGCAGAGATGGAGACAGCACAGAGTATCAGGATGATAAAGAGTTTGGAATAGGTGACCTCGTGTGGGGAAAGATCAAGGGCTTCTCCTGGTGGCCTGCCATGGTGGTGTCCTGGAAAGCCACCTCCAAGCGACAGGCCATGCCCGGAATGCGCTGGGTACAGTGGTTTGGTGATGGCAAGTTTTCTGAGATCTCTGCTGACAAACTGGTGGCTCTGGGGCTGTTCAGCCAGCACTTTAATCTGGCTACCTTCAATAAGCTGGTTTCTTATAGGAAGGCCATGTACCACACTCTGGAGAAAGCCAGGGTTCGAGCTGGCAAGACCTTCTCCAGCAGTCCTGGAGAGTCACTGGAGGACCAGCTGAAGCCCATGCTGGAGTGGGCCCACGGTGGCTTCAAGCCTACTGGGATCGAGGGCCTCAAACCCAACAAGAAGCAACCAGTGGTTAATAAGTCGAAGGTGCGTCGTTCAGACAGTAGGAACTTAGAACCCAGGAGACGCGAGAACAAAAGTCGAAGACGCACAACCAATGACTCTGCTGCTTCTGAGTCCCCCCCACCCAAGCGCCTCAAGACAAATAGCTATGGCGGGAAGGACCGAGGGGAGGATGAGGAGAGCCGAGAACGGATGGCTTCTGAAGTCACCAACAACAAGGGCAATCTGGAAGACCGCTGTTTGTCCTGTGGAAAGAAGAACCCTGTGTCCTTCCACCCCCTCTTTGAGGGTGGGCTCTGTCAGAGTTGCCGGGATCGCTTCCTAGAGCTCTTCTACATGTATGATGAGGACGGCTATCAGTCCTACTGCACCGTGTGCTGTGAGGGCCGTGAACTGCTGCTGTGCAGTAACACAAGCTGCTGCAGATGCTTCTGTGTGGAGTGTCTGGAGGTGCTGGTGGGCGCAGGCACAGCTGAGGATGCCAAGCTGCAGGAACCCTGGAGCTGCTATATGTGCCTCCCTCAGCGCTGCCATGGGGTCCTCCGACGCAGGAAAGATTGGAACATGCGCCTGCAAGACTTCTTCACTACTGATCCTGACCTGGAAGAATTTGAGCCACCCAAGTTGTACCCAGCAATTCCTGCAGCCAAAAGGAGGCCCATTAGAGTCCTGTCTCTGTTTGATGGAATTGCAACGGGGTACTTGGTGCTCAAGGAGTTGGGTATTAAAGTGGAAAAGTACATTGCCTCCGAAGTCTGTGCAGAGTCCATCGCTGTGGGAACTGTTAAGCATGAAGGCCAGATCAAATATGTCAATGACGTCCGGAAAATCACCAAGAAAAATATTGAAGAGTGGGGCCCGTTCGACTTGGTGATTGGTGGAAGCCCATGCAATGATCTCTCTAACGTCAATCCTGCCCGCAAAGGTTTATATGAGGGCACAGGAAGGCTCTTCTTCGAGTTTTACCACTTGCTGAATTATACCCGCCCCAAGGAGGGCGACAACCGTCCATTCTTCTGGATGTTCGAGAATGTTGTGGCCATGAAAGTGAATGACAAGAAAGACATCTCAAGATTCCTGGCATGTAACCCAGTGATGATCGATGCCATCAAGGTGTCTGCTGCTCACAGGGCCCGGTACTTCTGGGGTAACCTACCCGGAATGAACAGGCCCGTGATGGCTTCAAAGAATGATAAGCTCGAGCTGCAGGACTGCCTGGAGTTCAGTAGGACAGCAAAGTTAAAGAAAGTGCAGACAATAACCACCAAGTCGAACTCCATCAGACAGGGCAAAAACCAGCTTTTCCCTGTAGTCATGAATGGCAAGGACGACGTTTTGTGGTGCACTGAGCTCGAAAGGATCTTCGGCTTCCCTGCTCACTACACGGACGTGTCCAACATGGGCCGCGGCGCCCGTCAGAAGCTGCTGGGCAGGTCCTGGAGTGTACCGGTCATCAGACACCTGTTTGCCCCCTTGAAGGACTACTTTGCCTGTGAATAGGCggccGCAGTTAACGAATTCtctagaggatccagacatgataagatacattgatgagtttggacaaaccacaactagaatgcagtgaaaaaaatgctttatttgtgaaatttgtgatgctattgctttatttgtaaccattataagctgcaataaacaagttaacaacaacaattgcattcattttatgtttcaggttcagggggaggtgtgggaggttttttaaagcaagtaaaacctctacaaatgtggtatggctgattatgatcctgcaagcctcgtcgccgcggtttATTCTGTTGACAATTAATCATCGGCATAGTATATCGGCATAGTATAATACGACAAGGTGAGGAACTAAACCATGGGATCGGCCATTGAACAAGATGGATTGCACGCAGGTTCTCCGGCCGCTTGGGTGGAGAGGCTATTCGGCTATGACTGGGCACAACAGACGATCGGCTGCTCTGATGCCGCCGTGTTCCGGCTGTCAGCGCAGGGGCGCCCGGTTCTTTTTGTCAAGACCGACCTGTCCGGTGCCCTGAATGAACTGCAGGACGAGGCAGCGCGGCTATCGTGGCTGGCCACGACGGGCGTTCCTTGCGCAGCTGTGCTCGACGTTGTCACTGAAGCGGGAAGGGACTGGCTGCTATTGGGCGAAGTGCCGGGGCAGGATCTCCTGTCATCTCACCTTGCTCCTGCCGAGAAAGTATCCATCATGGCTGATGCAATGCGGCGGCTGCATACGCTTGATCCGGCTACCTGCCCATTCGACCACCAAGCGAAACATCGCATCGAGCGAGCACGTACTCGGATGGAAGCCGGTCTTGTCGATCAGGATGATCTGGACGAAGAGCATCAGGGGCTCGCGCCAGCCGAACTGTTCGCCAGGCTCAAGGCGCGCATGCCCGACGGCGAGGATCTCGTCGTGACCCATGGCGATGCCTGCTTGCCGAATATCATGGTGGAAAATGGCCGCTTTTCTGGATTCATCGACTGTGGCCGGCTGGGTGTGGCGGACCGCTATCAGGACATAGCGTTGGCTACCCGTGATATTGCTGAAGAGCTTGGCGGCGAATGGGCTGACCGCTTCCTCGTGCTTTACGGTATCGCCGCCCCCGATTCGCAGCGCATCGCCTTCTATCGCCTTCTTGACGAGTTCTTCTGAGCGGGACTCTGGGGTTCGAATAAAGACCGACCAAGCGACGTCTGAGAGCTCCCTGGCGAATTCGGTACCAATAAAAGAGCTTTATTTTCATGATCTGTGTGTTGGTTTTTGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGAACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTAGTGTGCG",
    "circular": true,
    "description": null,
    "features": [
      {
        "name": "END",
        "type": "misc_feature",
        "id": null,
        "start": 5194,
        "end": 5209,
        "strand": 1
      },
      ...
    }

Output Format

BLAST results returns an AlignmentResults object, which contains a list of alignments at .alignments

Alignments have the following format:

[
  {
    "meta": {
      "gaps_open": 0,
      "bit_score": 7792,
      "gaps": 0,
      "identical": 4219,
      "score": 4219.0,
      "evalue": 0.0,
      "alignment_length": 4219
    },
    "query": {
      "length": 18816,
      "acc": "pMODKan-HO-pACT1-Z4-",
      "sequence": "GGAGCAG...",
      "start": 1,
      "circular": null,
      "end": 4219,
      "name": null
    },
    "subject": {
      "length": 7883,
      "acc": "pMODKan-HO-pACT1-ZEV4",
      "sequence": "TCAGT...",
      "start": 1,
      "circular": null,
      "strand": "plus",
      "end": 4219,
      "name": null
    }
]]