A python library to parse Mass Spectrometry results and annotate with TAIR accessions
- "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
The program will extract the GI accession numbers (currently, the GIs HAVE TO BE the 3rd column of your csv files)
Sequences corresponding to the GIs will be extracted from Entrez and blasted against the reference given as "blast db".
The best hits (highest scores) will be then reported together with the original Mass Spectrometry data in the
_out.csvfile. Blast results can be found in the
If you specify more than one file as "ms infiles", then the
_out.csvfile 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
- 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"
To get the IP of your localhost by typing in the command line:
Open your internet browser, and type as URL:
On Linux (and Mac I guess)
Open your internet browser with URL:
For the web platform version:
- django 1.9.4
Web interface Usage
python3 manage.py runserver
Then go to your web browser and go the URL:
Command line Usage
python3 ms_summary.py [-h] -i INPUTS -d DBBLAST [-b BACKGROUND] [-c CPUS] [-o OUTFOLDER] [-p PATHBLAST]
- -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.
- Fork it!
- Create your feature branch:
git checkout -b my-new-feature
- Commit your changes:
git commit -am 'Add some feature'
- Push to the branch:
git push origin my-new-feature
- Submit a pull request :D