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blast_seq_pair
#summary BLAST pairs of sequences in the stream against each other.
[blast_seq_pair] uses NCBI's bl2seq to BLAST the pairs of sequences found in the stream
against each other. The sequence type of the sequences is guessed automagically, but can
be specified using the -p switch (only necessary for tblastx).
Note that for blastx the first sequence should be nucleotide, and for tblastn the second sequence nucleotide.
[blast_seq_pair] emit records like the below example:
REC_TYPE: BLAST
Q_ID: test1
S_ID: test2
IDENT: 100.0
ALIGN_LEN: 20
MISMATCHES: 0
GAPS: 0
Q_BEG: 7
Q_END: 26
S_BEG: 7
S_END: 26
E_VAL: 5.0e-10
BIT_SCORE: 40.1
STRAND: +
---
Read more here:
... | blast_seq_pair [options]
[-? | --help] # Print full usage description.
[-p <string> | --program=<string> # blastn|blastp|tblastn|blastx|tblastx - Default=guessed!
[-e <float> | --e_val=<float>] # Expectation value - Default=10
[-f <string> | --filter=<string>] # Filter low complexity sequence (yes|no) - Default=no
[-w <uint> | --word_size=<uint>] # BLAST word size.
[-m | --megablast] # Enable megablast.
[-G | --no_gaps] # Disable gapped BLAST.
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-v | --verbose] # Verbose output.
Consider the following FASTA entries in the file test.fna:
>test1
CAGCACTAGCATCGACGACAGCACGCATAC
>test2
CAGCgggAGCATCGACGACAGCACGCA
In order to BLAST these against each other use [blast_seq_pair]:
read_fasta -i test.fna | blast_seq_pair
SEQ_NAME: test1
SEQ: CAGCACTAGCATCGACGACAGCACGCATAC
SEQ_LEN: 30
---
SEQ_NAME: test2
SEQ: CAGCgggAGCATCGACGACAGCACGCA
SEQ_LEN: 27
---
REC_TYPE: BLAST
Q_ID: test1
S_ID: test2
IDENT: 100.0
ALIGN_LEN: 20
MISMATCHES: 0
GAPS: 0
Q_BEG: 7
Q_END: 26
S_BEG: 7
S_END: 26
E_VAL: 5.0e-10
BIT_SCORE: 40.1
STRAND: +
---
[read_fasta]
[create_blast_index]
[blast_seq]
[write_blast]
[read_blast_tab]
Martin Asser Hansen - Copyright (C) - All rights reserved.
June 2011
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
[blast_seq_pair] is part of the Biopieces framework.