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@wwood
Created September 25, 2011 03:40
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Evidence that you cannot know from a blast archive whether the db queried was run with -parse_seqids if you output in CSV (outfmt 6)
sequenceserver/tests/database/nucleotide$ blast_formatter -version
blast_formatter: 2.2.25+
Package: blast 2.2.25, build Mar 21 2011 12:13:17
sequenceserver/tests/database/nucleotide$ ln -s Sinvicta2-2-3.cdna.subset.fasta parse.fa
sequenceserver/tests/database/nucleotide$ ln -s Sinvicta2-2-3.cdna.subset.fasta no_parse.fa
sequenceserver/tests/database/nucleotide$ makeblastdb -in parse.fa -parse_seqids -dbtype nucl
Building a new DB, current time: 09/25/2011 10:05:33
New DB name: parse.fa
New DB title: parse.fa
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1073741824B
Adding sequences from FASTA; added 473 sequences in 0.109626 seconds.
sequenceserver/tests/database/nucleotide$ makeblastdb -in no_parse.fa -dbtype nucl
Building a new DB, current time: 09/25/2011 10:05:42
New DB name: no_parse.fa
New DB title: no_parse.fa
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1073741824B
Adding sequences from FASTA; added 473 sequences in 0.084784 seconds.
sequenceserver/tests/database/nucleotide$ head Sinvicta2-2-3.cdna.subset.fasta >head.fa
sequenceserver/tests/database/nucleotide$ blastn -query head.fa -db parse.fa -outfmt 11 -out headVparse.archive
sequenceserver/tests/database/nucleotide$ blastn -query head.fa -db no_parse.fa -outfmt 11 -out headVno_parse.archive
sequenceserver/tests/database/nucleotide$ blast_formatter -archive headVparse.archive -outfmt '6 qseqid qgi qacc qaccver qlen sseqid sallseqid sgi sallgi sacc saccver sallacc slen qstart qend sstart send qseq sseq evalue bitscore score length pident nident mismatch positive gapopen gaps ppos frames qframe sframe btop' >headVparse.archive.csv
sequenceserver/tests/database/nucleotide$ blast_formatter -archive headVno_parse.archive -outfmt '6 qseqid qgi qacc qaccver qlen sseqid sallseqid sgi sallgi sacc saccver sallacc slen qstart qend sstart send qseq sseq evalue bitscore score length pident nident mismatch positive gapopen gaps ppos frames qframe sframe btop' >headVno_parse.archive.csv
sequenceserver/tests/database/nucleotide$ diff headVparse.archive.csv headVno_parse.archive.csv
sequenceserver/tests/database/nucleotide$
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