blast2gi.py - retrieve GI numbers for Blast hits

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