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A python library to parse Mass Spectrometry results and annotate with TAIR accessions
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README.md

README.md

MassSpec_parser

A python library to parse Mass Spectrometry results and annotate with TAIR accessions

Overview

Input

  • "MS infiles": At least one csv file with Mass Spectrometry results (with the GI accession number in the 3rd column). MANDATORY
  • "Blast db": One fasta file to blast against for "blast db". MANDATORY
  • "MS background": Csv files of background signal. OPTIONAL

Workflow

  1. The program will extract the GI accession numbers (currently, the GIs HAVE TO BE the 3rd column of your csv files)

  2. Sequences corresponding to the GIs will be extracted from Entrez and blasted against the reference given as "blast db".

  3. The best hits (highest scores) will be then reported together with the original Mass Spectrometry data in the _out.csv file. Blast results can be found in the .tab file.

  4. If you specify more than one file as "ms infiles", then the _out.csv file will display columns showing the presence (1) or absence (0) of a particular protein in the datasets given as infiles.

Usage with Docker

  • Install Docker

https://docs.docker.com/

  • In Docker:

docker run -p 8000:8000 -v OUTFOLDER_ON_YOUR_COMPUTER:/usr/src/user_data -d khourhin/bioinfo

For windows, a path like "C:\Users\folder" should be specified as "/c/Users/folder"

On Windows

To get the IP of your localhost by typing in the command line:

docker-machine ip

Open your internet browser, and type as URL:

PREVIOUS_STEP_IP:8000

On Linux (and Mac I guess)

Open your internet browser with URL:

localhost:8000

Classical Installation

Requirements

  • Python3
  • Numpy
  • Biopython
  • blast+

For the web platform version:

  • django 1.9.4
  • django-forms-bootstrap

Web interface Usage

python3 manage.py runserver

Then go to your web browser and go the URL:

http://localhost:8000/

Command line Usage

python3 ms_summary.py [-h] -i INPUTS -d DBBLAST [-b BACKGROUND] [-c CPUS] [-o OUTFOLDER] [-p PATHBLAST]

Arguments:

  • -h, --help

show this help message and exit

  • -i INPUT, --inputs INPUT

CSV file of MS results (more than one can be given). One csv at least is required.

  • -d DBBLAST, --dbBlast DBBLAST

A database in fasta format to blast against and then create the mapping. One fasta is required.

  • -b BACKGROUND, --background BACKGROUND

CSV file for the background (more than one can be given).

  • -c CPUS, --cpus CPUS

Number of cpus to use for blast.

  • -o OUTFOLDER, --outfolder OUTFOLDER

Folder where the output will be regenerated. Will be created if doesn't exist.

  • -p PATHBLAST, --pathBlast PATHBLAST

Folder where the blast+ executables are located, if not specified, will look in the environment PATH.

Contributing

  1. Fork it!
  2. Create your feature branch: git checkout -b my-new-feature
  3. Commit your changes: git commit -am 'Add some feature'
  4. Push to the branch: git push origin my-new-feature
  5. Submit a pull request :D

History

TODO

Credits

TODO

License

TODO

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