1BP_SEARCH2GFF(1) User Contributed Perl Documentation BP_SEARCH2GFF(1)
2
6 search2gff - Turn SearchIO parseable reports(s) into a GFF report
7
9 Usage:
10 search2gff [-o outputfile] [-f reportformat] [-i inputfilename] OR
11 file1 file2 ..
12
14 This script will turn a protein Search report (BLASTP, FASTP, SSEARCH,
15 AXT, WABA) into a GFF File.
16 The options are:
18 -i infilename - (optional) inputfilename, will read
20 either ARGV files or from STDIN
21 -o filename - the output filename [default STDOUT]
22 -f format - search result format (blast, fasta,waba,axt)
23 (ssearch is fasta format). default is blast.
24 -t/--type seqtype - if you want to see query or hit information
25 in the GFF report
26 -s/--source - specify the source (will be algorithm name
27 otherwise like BLASTN)
28 --method - the method tag (primary_tag) of the features
29 (default is similarity)
30 --scorefunc - a string or a file that when parsed evaluates
31 to a closure which will be passed a feature
32 object and that returns the score to be printed
33 --locfunc - a string or a file that when parsed evaluates
34 to a closure which will be passed two
35 features, query and hit, and returns the
36 location (Bio::LocationI compliant) for the
37 GFF3 feature created for each HSP; the closure
38 may use the clone_loc() and create_loc()
39 functions for convenience, see their PODs
40 --onehsp - only print the first HSP feature for each hit
41 -p/--parent - the parent to which HSP features should refer
42 if not the name of the hit or query (depending
43 on --type)
44 --target/--notarget - whether to always add the Target tag or not
45 -h - this help menu
46 --version - GFF version to use (put a 3 here to use gff 3)
47 --component - generate GFF component fields (chromosome)
48 -m/--match - generate a 'match' line which is a container
49 of all the similarity HSPs
50 --addid - add ID tag in the absence of --match
51 -c/--cutoff - specify an evalue cutoff
52 Additionally specify the filenames you want to process on the command-
54 line. If no files are specified then STDIN input is assumed. You
55 specify this by doing: search2gff < file1 file2 file3
56
58 Jason Stajich, jason-at-bioperl-dot-org
59
61 Hilmar Lapp, hlapp-at-gmx-dot-net
62 clone_loc
64 Title : clone_loc
65 Usage : my $l = clone_loc($feature->location);
66 Function: Helper function to simplify the task of cloning locations
67 for --locfunc closures.
68 Presently simply implemented using Storable::dclone().
70 Example :
71 Returns : A L<Bio::LocationI> object of the same type and with the
72 same properties as the argument, but physically different.
73 All structured properties will be cloned as well.
74 Args : A L<Bio::LocationI> compliant object
75 create_loc
77 Title : create_loc
78 Usage : my $l = create_loc("10..12");
79 Function: Helper function to simplify the task of creating locations
80 for --locfunc closures. Creates a location from a feature-
81 table formatted string.
82 Example :
84 Returns : A L<Bio::LocationI> object representing the location given
85 as formatted string.
86 Args : A GenBank feature-table formatted string.
87perl v5.12.0 2010-04-29 BP_SEARCH2GFF(1)