Difference between revisions of "Parsing Blast Results from Your Favorite Database"
From GcatWiki
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#:*-db = database to search | #:*-db = database to search | ||
#:*-outfmt = output format '''<span style="color:#FF0000">DO NOT CHANGE THIS UNLESS YOU KNOW HOW TO EDIT blastParse.py</span>''' | #:*-outfmt = output format '''<span style="color:#FF0000">DO NOT CHANGE THIS UNLESS YOU KNOW HOW TO EDIT blastParse.py</span>''' | ||
| + | #:*-out = output file for blast results | ||
#Download blastParse.py | #Download blastParse.py | ||
#Place blastParse.py into the same folder as your blast results file | #Place blastParse.py into the same folder as your blast results file | ||
Revision as of 19:39, 23 February 2011
This tutorial assumes the user has blast version __________ installed and has already made their local blast database (on their computer). It is also written for Macintosh users; however, all scripts and tools are Windows compatible or have similar programs for Windows.
- Run your search using the command
/usr/local/ncbi/blast/bin/blastn -query querySequence.fasta -db dataBase.fasta -outfmt "7 qacc sacc evalue qstart qend sstart send" -out blast_output.txt
- What does this command do? "-" indicates a command. The text that follows is the actual command parameters.
- -query = query file
- -db = database to search
- -outfmt = output format DO NOT CHANGE THIS UNLESS YOU KNOW HOW TO EDIT blastParse.py
- -out = output file for blast results
- What does this command do? "-" indicates a command. The text that follows is the actual command parameters.
- Download blastParse.py
- Place blastParse.py into the same folder as your blast results file
- Open terminal and navigate into the folder containing blastParse.py using following Unix commands
cd OR ls
- Run blastParse.py using the command
python blastParse.py
- Follow prompts of the BLASTPARSE program
- Results will be saved as tab delimited data in text files. If you would like to visualize the data, open files in excel to make graphs (right click > open with > excel).
