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9.5 years ago
clear.choi
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I have one output files which is coming from NCBI Blast program.
blastn -db .DB/ABC_Exon23.fasta.db -query ./test.fasta -out ./test.out -num_descriptions 100 -num_alignments 0 -word_size 10
I want to get only score and top score allele lists.
So Blast Output as
BLASTN 2.2.29+
Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb
Miller (2000), "A greedy algorithm for aligning DNA sequences", J
Comput Biol 2000; 7(1-2):203-14.
Database: /shared/MiSeq/ABC_Exon23.fasta
7,546 sequences; 4,346,452 total letters
Query= BarcodeS14--S14_Cluster0_Phase0_NumReads236
Length=1006
Score E
Sequences producing significant alignments: (Bits) Value
C_08_94 510 7e-145
C_08_90 510 7e-145
C_08_75 510 7e-145
C_08_74 510 7e-145
C_08_73 510 7e-145
C_08_69 510 7e-145
C_08_68 510 7e-145
C_08_67 510 7e-145
C_08_55N 510 7e-145
C_08_53 510 7e-145
C_08_52N 510 7e-145
C_08_45 510 7e-145
C_08_37 510 7e-145
C_08_28 510 7e-145
C_08_25 510 7e-145
C_08_18 510 7e-145
C_08_17 510 7e-145
C_08_05 510 7e-145
C_08_02_08 510 7e-145
<allele lists>
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 4101954802
Database: /shared/MiSeq/ABC_Exon23.fasta
Posted date: Jul 22, 2014 5:00 PM
Number of letters in database: 4,346,452
Number of sequences in database: 7,546
I want to get below score information only.
BarcodeS14--S14_Cluster0_Phase0_NumReads236 C_08_94 510
BarcodeS14--S14_Cluster0_Phase0_NumReads236 C_08_90 510
BarcodeS14--S14_Cluster0_Phase0_NumReads236 C_08_75 510
..... <lists>
Almost all parser need to have alignment information for parsing data. But I need only score and reduce time.
Does anyone has good idea?
Thank you!