1BP_SEARCH2ALNBLOCKS(1)User Contributed Perl DocumentationBP_SEARCH2ALNBLOCKS(1)
2
6 search2alnblocks - Turn SearchIO parseable reports(s) into a set of
7 aligned blocks
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10 search2alnblocks --minid PERCENTID --minlen LEN --minevalue EVALUE file1.
11 blast file2.blast ...> out.fas
12
14 This script will parse and filter BLAST (or other formats Bio::SearchIO
15 can parse) output and format the alignment as blocks of alignments
16 based on the HSPs. Note this can only work if the input file parsed
17 contains the necessary.
18 Typically this can be used to turn BLAST output into a FASTA alignment
20 format for input into the QRNA comparative gene finder for RNA genes
21 (E.Rivas).
22
24 --maxevalue Maximum E-value for an HSP
25 --minevalue Minimum E-value for an HSP
26 --minlen Minimum length of an HSP [default 0]
27 --maxid Maximum Percent Id [default 100]
28 (to help remove sequences which are really close)
29 --minid Minimum Percent Identity for an HSP [default 0]
30 -i/--input An optional input filename (expects input on STDIN by default)
31 -o/--output An optional output filename (exports to STDOUT by default)
32 -f/--format Specify a different Search Alignment format-
33 {fasta, axt, waba, blast, blastxml} are all permitted
34 although the format must have actual alignment
35 sequence for this script to work
36 See L<Bio::SearchIO> for more information.
37 -of/--outformat Output format for the alignment blocks, anything
38 L<Bio::AlignIO> supports.
39 -v/--verbose Turn on debugging
40
42 Jason Stajich, jason-at-bioperl-dot-org.
43perl v5.8.8 2007-05-07 BP_SEARCH2ALNBLOCKS(1)