Blast - How to get the no hits result on table output?
Hi,
I use BLASTN with python.
I prefer -outfmt 6 parameter (table output) because its easy to read on python but the problem is, this output format doesn't gives result if there is no match.
for example:
blastn -query genes.fasta -db genome.fasta -outfmt 6
this command gives me 3 result with matches
gene1 NC_000913.3 100.000 2030 0 0 1 2030 1
gene2 NC_000913.3 99.444 1260 7 0 1 1260 2101
gene3 NC_000913.3 100.000 1190 0 0 1 1190 3431
blastn -query genes.fasta -db genome.fasta -outfmt 7
this command gives me 4 result with 3 match and 1 zero match.
# BLASTN 2.11.0+
# Query: nogene
# Database: genome1.fasta
# 0 hits found
# BLASTN 2.11.0+
# Query: gene1
# Database: genome1.fasta
# Fields: query acc.ver, subject acc.ver, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 1 hits found
gene1 NC_000913.3 100.000 2030 0 0 1 2030 1 2030 0.0 3749
# BLASTN 2.11.0+
# Query: gene2
# Database: genome1.fasta
# Fields: query acc.ver, subject acc.ver, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 1 hits found
gene2 NC_000913.3 99.444 1260 7 0 1 1260 2101 3360 0.0 2289
# BLASTN 2.11.0+
# Query: gene3
# Database: genome1.fasta
# Fields: query acc.ver, subject acc.ver, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 1 hits found
gene3 NC_000913.3 100.000 1190 0 0 1 1190 3431 4620 0.0 2198
# BLAST processed 4 queries
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As you discovered you have to use
-outfmt 7if you want to get queries with no hits listed in output.If there isn't any easiest way to do it, I will try to parse -outfmt 7.
Either you parse the
-outfmt 7output or then you parse the headers (up until first space I think) from your query file andcomm -3with the first column of your-outfmt 6output. IMO the latter is "easier"