BP_SEARCH2ALNBLOCKS(1p) User Contributed Perl Documentation BP_SEARCH2ALNBLOCKS(1p)NAME
search2alnblocks - Turn SearchIO parseable reports(s) into a set of aligned blocks
SYNOPSIS
search2alnblocks --minid PERCENTID --minlen LEN --minevalue EVALUE file1.
blast file2.blast ...> out.fas
DESCRIPTION
This script will parse and filter BLAST (or other formats Bio::SearchIO can parse) output and format the alignment as blocks of alignments
based on the HSPs. Note this can only work if the input file parsed contains the necessary.
Typically this can be used to turn BLAST output into a FASTA alignment format for input into the QRNA comparative gene finder for RNA genes
(E.Rivas).
OPTIONS --maxevalue Maximum E-value for an HSP
--minevalue Minimum E-value for an HSP
--minlen Minimum length of an HSP [default 0]
--maxid Maximum Percent Id [default 100]
(to help remove sequences which are really close)
--minid Minimum Percent Identity for an HSP [default 0]
-i/--input An optional input filename (expects input on STDIN by default)
-o/--output An optional output filename (exports to STDOUT by default)
-f/--format Specify a different Search Alignment format-
{fasta, axt, waba, blast, blastxml} are all permitted
although the format must have actual alignment
sequence for this script to work
See L<Bio::SearchIO> for more information.
-of/--outformat Output format for the alignment blocks, anything
L<Bio::AlignIO> supports.
-v/--verbose Turn on debugging
AUTHOR - Jason Stajich
Jason Stajich, jason-at-bioperl-dot-org.
perl v5.14.2 2012-03-02 BP_SEARCH2ALNBLOCKS(1p)
Check Out this Related Man Page
BP_SEARCH2TRIBE(1p) User Contributed Perl Documentation BP_SEARCH2TRIBE(1p)NAME
search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrix
SYNOPSIS
Usage:
search2tribe [-o outputfile] [-f reportformat] [-w/--weight] file1 file2 ..
DESCRIPTION
This script is probably too slow for most people's uses. It is better to use something like scripts/searchio/fastam9_to_table, -m 9 output
from BLAST, or the blast2table from the BLAST O'Reilly book to get a tabular output from these programs and then feed the table into MCL
with the mcxdeblast script and the --m9 option.
This script will turn a protein Search report (BLASTP, FASTP, SSEARCH) into a Markov Matrix for TribeMCL clustering.
The options are:
-o filename - the output filename [default STDOUT]
-f format - search result format (blast, fasta)
(ssearch is fasta format). default is blast.
-w or --weight VALUE - Change the default weight for E(0.0) hits
to VALUE (default=200 (i.e. 1e-200) )
-h - this help menu
Additionally specify the filenames you want to process on the command-line. If no files are specified then STDIN input is assumed. You
specify this by doing: search2tribe < file1 file2 file3
AUTHOR
Jason Stajich, jason-at-bioperl-dot-org
perl v5.14.2 2012-03-02 BP_SEARCH2TRIBE(1p)
I have been thinking how to go around this problem but I just do not find a way to do it. So, I finally decided to ask. I have a real bunch of different sequences of different lenghts aligned in the following format:
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I am processing RNA-seq data files that have been aligned using RUM. One of the output files is a *.sam that includes:
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Non-unique alignments
original read files
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The below perl script parses a variety of formats. If I use the numeric text file as input the script works correctly. However using the alpha text file as input there is a black output file. The portion in bold splits the field to parse f or NC_000023.10:g.153297761C>A into a variable $common but... (3 Replies)