update June 17, 2014
NAME
blast2gi.py - Given output from NCBI
Blast+ using the -remote option , create a file containing GI
numbers of hits listed in the output.
SYNOPSIS
blast2gi.py
infile outfile
DESCRIPTION
blast2gi
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:
RID: TBYDU60X015
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+
# Query:
# RID: U0ST8SER013
# Database: nr
# Fields: subject gi
# 21 hits found
332656411
145340181
21386936
19698840
7268028
4678371
51870270
297804977
567222507
567222505
REFERENCES
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
SEE ALSO
blast_formatter
AUTHOR
Dr. Brian Fristensky
Department of Plant Science
University of Manitoba
Winnipeg, MB Canada R3T 2N2
frist@cc.umanitoba.ca
http://home.cc.umanitoba.ca/~frist