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)
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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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