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.csv
file. Blast results can be found in the.tab
file. -
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.
- 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:
docker-machine ip
Open your internet browser, and type as URL:
PREVIOUS_STEP_IP:8000
Open your internet browser with URL:
localhost:8000
- Python3
- Numpy
- Biopython
- blast+
For the web platform version:
- django 1.9.4
- django-forms-bootstrap
python3 manage.py runserver
Then go to your web browser and go the URL:
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.
- 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
TODO
TODO
TODO