update June 17, 2014
blast2gi.py - Given output from NCBI
Blast+ using the -remote option , create a file containing GI
numbers of hits listed in the output.
reads infile, which is Blast output from a
search done at NCBI using the -remote option in Blast+ programs.
When a Blast search is done at NCBI, the results are assigned a
unique RID number, shown in the output file on a line similar to:
The results can be accessed by EDirect programs using
the RID number for 36 hours after the search is complete. blast2gi
extracts the RID number from infile, and calls
blast_formatter to retrieve the GI numbers of Blast hits to outfile.
Each line in outfile contains either a comment, indicated
by a hash mark (#) or a GI number. An abbreviated example of the
output retrieved to outfile is shown below:
# BLASTN 2.2.26+
# RID: U0ST8SER013
# Database: nr
# Fields: subject gi
# 21 hits found
BLAST Command Line Applications User Manual at http://www.ncbi.nlm.nih.gov/books/NBK1763/
NCBI Entrez Help Manual at http://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Entrez_Searching_Options.
NCBI EDirect Utilities - http://www.ncbi.nlm.nih.gov/books/NBK179288
Dr. Brian Fristensky
Department of Plant Science
University of Manitoba
Winnipeg, MB Canada R3T 2N2