1BP_SEARCH2GFF(1) User Contributed Perl Documentation BP_SEARCH2GFF(1)
2
6 Usage:
7 search2gff [-o outputfile] [-f reportformat] [-i inputfilename] OR
8 file1 file2 ..
9
11 This script will turn a protein Search report (BLASTP, FASTP, SSEARCH,
12 AXT, WABA) into a GFF File.
13 The options are:
15 -i infilename - (optional) inputfilename, will read
17 either ARGV files or from STDIN
18 -o filename - the output filename [default STDOUT]
19 -f format - search result format (blast, fasta,waba,axt)
20 (ssearch is fasta format). default is blast.
21 -t/--type seqtype - if you want to see query or hit information
22 in the GFF report
23 -s/--source - specify the source (will be algorithm name
24 otherwise like BLASTN)
25 --method - the method tag (primary_tag) of the features
26 (default is similarity)
27 --scorefunc - a string or a file that when parsed evaluates
28 to a closure which will be passed a feature
29 object and that returns the score to be printed
30 --locfunc - a string or a file that when parsed evaluates
31 to a closure which will be passed two
32 features, query and hit, and returns the
33 location (Bio::LocationI compliant) for the
34 GFF3 feature created for each HSP; the closure
35 may use the clone_loc() and create_loc()
36 functions for convenience, see their PODs
37 --onehsp - only print the first HSP feature for each hit
38 -p/--parent - the parent to which HSP features should refer
39 if not the name of the hit or query (depending
40 on --type)
41 --target/--notarget - whether to always add the Target tag or not
42 -h - this help menu
43 --version - GFF version to use (put a 3 here to use gff 3)
44 --component - generate GFF component fields (chromosome)
45 -m/--match - generate a 'match' line which is a container
46 of all the similarity HSPs
47 --addid - add ID tag in the absence of --match
48 -c/--cutoff - specify an evalue cutoff
49 Additionally specify the filenames you want to process on the com‐
51 mand-line. If no files are specified then STDIN input is assumed. You
52 specify this by doing: search2gff < file1 file2 file3
53
55 Jason Stajich, jason-at-bioperl-dot-org
56
58 Hilmar Lapp, hlapp-at-gmx-dot-net
59 clone_loc
61 Title : clone_loc
63 Usage : my $l = clone_loc($feature->location);
64 Function: Helper function to simplify the task of cloning locations
65 for --locfunc closures.
66 Presently simply implemented using Storable::dclone().
68 Example :
69 Returns : A L<Bio::LocationI> object of the same type and with the
70 same properties as the argument, but physically different.
71 All structured properties will be cloned as well.
72 Args : A L<Bio::LocationI> compliant object
73 create_loc
75 Title : create_loc
77 Usage : my $l = create_loc("10..12");
78 Function: Helper function to simplify the task of creating locations
79 for --locfunc closures. Creates a location from a feature-
80 table formatted string.
81 Example :
83 Returns : A L<Bio::LocationI> object representing the location given
84 as formatted string.
85 Args : A GenBank feature-table formatted string.
86perl v5.8.8 2007-05-07 BP_SEARCH2GFF(1)