aargh :o) i was hoping there was a simple answer to this. the object im
investigating do apparantly inherets stuff :/
im not into OO perl at all, and i guess this is the reason why.
ok, so the problem is rather complex, but thats just another perl problem then.
and this one must have been solved by others. i have been looking at the
Class::Inspector module on CPAN, which can track the inheritance i think.
ill add my code snippet here to elaborate on the specific problem. and attach a
test file for the parser.
the problem is that the objects $hit and $hsp gives access to a lot of usefull
functions, but what are they???
################################################################
#!/usr/bin/perl -w
use strict;
use Data::Dumper;
use Bio::SearchIO;
my ( $script, $usage, @files, $file );
my ( $searchio, $result, $blast_report, $algorithm_type, $hit, $hit_name, $hsp,
$bit_score,
$query_beg, $query_end, $query_name, $subject_beg, $subject_end, $strand, $eval,
$frame );
$script = ( split "/", $0 )[ -1 ];
$usage = qq(
$script by Martin A. Hansen, July 2003.
$script parses blast repport files and writes GFF to STDOUT
Usage: $script <blast> <blast> <blast>
<blast> - blast report files
);
print $usage and exit if not @ARGV;
@files = @ARGV;
foreach $file ( @files )
{
$searchio = new Bio::SearchIO ( -format => 'blast', -file => $file );
$result = $searchio->next_result;
$query_name = $result->query_name;
$result->database_name;
$algorithm_type = $result->algorithm;
while ( $hit = $result->next_hit )
{
$hit_name = $hit->name;
$hsp = $hit->next_hsp;
$eval = $hsp->evalue;
$bit_score = $hsp->bits;
$strand = $hsp->strand( "subject" );
$frame = $hsp->frame;
$query_beg = $hsp->query->start;
$query_end = $hsp->query->end;
$subject_beg = $hsp->subject->start;
$subject_end = $hsp->subject->end;
if ( $strand eq "1" ) {
$strand = "+";
} elsif ( $strand eq "-1" ) {
$strand = "-";
} else {
$strand = ".";
}
print join( "\t",
$hit_name,
$algorithm_type,
"similarity",
$subject_beg,
$subject_end,
$bit_score,
$strand,
$frame,
"Target \"$query_name\" $query_beg $query_end ; E_value $eval"
);
print "\n";
}
}
################################################################
On Tue, Aug 05, 2003 at 05:48:04AM -0700, Ovid wrote:
> --- "Martin A. Hansen" <[EMAIL PROTECTED]> wrote:
> > hi
> >
> > i wonder how i can list all the methods availible from a given object?
> >
> > martin
>
> Hi Martin,
>
> The simple answer: You can't. Welcome to Perl.
>
> The long answer: there are a variety of strategies you can use to try and figure
> this out, but
> all of them fall short. For example, here's a snippet that prints out defined
> subroutines (or
> methods) in a given package:
>
> {
> no strict 'refs';
> my $namespace = sprintf "%s::", $CLASS;
> foreach (keys %{$namespace}) {
> my $test_sub = sprintf "%s%s", $namespace, $_;
> print "$test_sub\n" unless defined &$test_sub;
> }
> }
>
> The problem here is that it will not print inherited or AUTOLOADed methods. It
> might be
> sufficient for your needs now, but it's fragile. You can also test whether or not a
> particular
> method *is* implemented:
>
> if ($object->can('method_name_to_test')) {
> # this works if $object can have methods called on it. It will find
> # inherited methods. It can also find AUTOLOADed methods if they've
> # already been called and installed in the symbol table
> }
>
> A slightly more robust version of that syntax:
>
> if (UNIVERSAL::can($object, $method_name) {
> # almost the same thing, but doesn't die a horrible death if, for example,
> # $object is undef
> }
>
> If you explain the problem you're trying to solve, we might be able to come up with
> a better
> solution.
>
> Cheers,
> Ovid
>
> =====
> Silence is Evil
> http://users.easystreet.com/ovid/philosophy/indexdecency.htm
> Ovid http://www.perlmonks.org/index.pl?node_id=17000
> Web Programming with Perl http://users.easystreet.com/ovid/cgi_course/
>
> __________________________________
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BLASTN 2.2.5 [Nov-16-2002]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= mt0001-av25gc10k167_AV25_01
(110 letters)
Database: gbgene
2,966,325 sequences; 8,818,290,589 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
emb|AL772308|AL772308 Mouse DNA sequence from clone RP23-451I21 ... 218 1e-54
emb|AF303827|AF303827 Mus musculus structural maintenance of chr... 218 1e-54
emb|AX552873|AX552873 Sequence 165 from Patent WO02074953. 212 8e-53
emb|AX524135|AX524135 Sequence 165 from Patent EP1236798. 212 8e-53
emb|AC068278|AC068278 Homo sapiens BAC clone RP11-131G20 from 2,... 44 0.042
gb|U00040|U00040 Caenorhabditis elegans cosmid C18H2, complete s... 42 0.16
emb|AL033510|CEY40H7A Caenorhabditis elegans YAC Y40H7A, complet... 42 0.16
emb|AL139175|AL139175 Human DNA sequence from clone RP4-615P17 o... 42 0.16
emb|AJ313035|STO313035 Sorbus torminalis microsatelitte DNA, clo... 40 0.65
emb|AC007894|F21H2 Arabidopsis thaliana chromosome 1 BAC F21H2 s... 40 0.65
emb|AE003465|AE003465 Drosophila melanogaster chromosome 2R, sec... 40 0.65
emb|AC007884|AC007884 Drosophila melanogaster, chromosome 2R, re... 40 0.65
emb|AC007582|AC007582 Drosophila melanogaster, chromosome 2R, re... 40 0.65
emb|AE010893|AE010893 Methanosarcina acetivorans str. C2A, secti... 40 0.65
emb|AC083806|AC083806 Homo sapiens 12q BAC RP11-240G22 (Roswell ... 40 0.65
emb|AC055764|AC055764 Homo sapiens 3 BAC RP11-803P9 (Roswell Par... 40 0.65
emb|AC023456|AC023456 Homo sapiens chromosome 15, clone RP11-162... 40 0.65
emb|AC021851|AC021851 Homo sapiens BAC clone RP11-438L19 from 2,... 40 0.65
emb|AC015798|AC015798 Homo sapiens chromosome 15, clone RP11-341... 40 0.65
emb|AL161713|CNS01RHE Human chromosome 14 DNA sequence BAC R-22K... 40 0.65
>emb|AL772308|AL772308 Mouse DNA sequence from clone RP23-451I21 on chromosome 15,
>complete
sequence.
Length = 148496
Score = 218 bits (110), Expect = 1e-54
Identities = 110/110 (100%)
Strand = Plus / Plus
Query: 1 cagaattcaaaattttataaccaatttgtttcaaaacaaaagcccttaaaagcaaaagaa 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 63001 cagaattcaaaattttataaccaatttgtttcaaaacaaaagcccttaaaagcaaaagaa 63060
Query: 61 aaccatatacctcattcattgatgccataggaacctccattggaatgaca 110
||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 63061 aaccatatacctcattcattgatgccataggaacctccattggaatgaca 63110
>emb|AF303827|AF303827 Mus musculus structural maintenance of chromosomes 1beta mRNA,
complete cds.
Length = 4056
Score = 218 bits (110), Expect = 1e-54
Identities = 110/110 (100%)
Strand = Plus / Minus
Query: 1 cagaattcaaaattttataaccaatttgtttcaaaacaaaagcccttaaaagcaaaagaa 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 4037 cagaattcaaaattttataaccaatttgtttcaaaacaaaagcccttaaaagcaaaagaa 3978
Query: 61 aaccatatacctcattcattgatgccataggaacctccattggaatgaca 110
||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 3977 aaccatatacctcattcattgatgccataggaacctccattggaatgaca 3928
>emb|AX552873|AX552873 Sequence 165 from Patent WO02074953.
Length = 343
Score = 212 bits (107), Expect = 8e-53
Identities = 107/107 (100%)
Strand = Plus / Plus
Query: 1 cagaattcaaaattttataaccaatttgtttcaaaacaaaagcccttaaaagcaaaagaa 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6 cagaattcaaaattttataaccaatttgtttcaaaacaaaagcccttaaaagcaaaagaa 65
Query: 61 aaccatatacctcattcattgatgccataggaacctccattggaatg 107
|||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 66 aaccatatacctcattcattgatgccataggaacctccattggaatg 112
>emb|AX524135|AX524135 Sequence 165 from Patent EP1236798.
Length = 343
Score = 212 bits (107), Expect = 8e-53
Identities = 107/107 (100%)
Strand = Plus / Plus
Query: 1 cagaattcaaaattttataaccaatttgtttcaaaacaaaagcccttaaaagcaaaagaa 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6 cagaattcaaaattttataaccaatttgtttcaaaacaaaagcccttaaaagcaaaagaa 65
Query: 61 aaccatatacctcattcattgatgccataggaacctccattggaatg 107
|||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 66 aaccatatacctcattcattgatgccataggaacctccattggaatg 112
>emb|AC068278|AC068278 Homo sapiens BAC clone RP11-131G20 from 2, complete sequence.
Length = 156916
Score = 44.1 bits (22), Expect = 0.042
Identities = 25/26 (96%)
Strand = Plus / Plus
Query: 45 cttaaaagcaaaagaaaaccatatac 70
|||||||| |||||||||||||||||
Sbjct: 67792 cttaaaagaaaaagaaaaccatatac 67817
>gb|U00040|U00040 Caenorhabditis elegans cosmid C18H2, complete sequence.
Length = 41762
Score = 42.1 bits (21), Expect = 0.16
Identities = 21/21 (100%)
Strand = Plus / Plus
Query: 21 ccaatttgtttcaaaacaaaa 41
|||||||||||||||||||||
Sbjct: 13313 ccaatttgtttcaaaacaaaa 13333
>emb|AL033510|CEY40H7A Caenorhabditis elegans YAC Y40H7A, complete sequence.
Length = 86086
Score = 42.1 bits (21), Expect = 0.16
Identities = 21/21 (100%)
Strand = Plus / Plus
Query: 21 ccaatttgtttcaaaacaaaa 41
|||||||||||||||||||||
Sbjct: 58619 ccaatttgtttcaaaacaaaa 58639
>emb|AL139175|AL139175 Human DNA sequence from clone RP4-615P17 on chromosome
>1p13-14.3,
complete sequence.
Length = 103718
Score = 42.1 bits (21), Expect = 0.16
Identities = 21/21 (100%)
Strand = Plus / Minus
Query: 72 tcattcattgatgccatagga 92
|||||||||||||||||||||
Sbjct: 50163 tcattcattgatgccatagga 50143
>emb|AJ313035|STO313035 Sorbus torminalis microsatelitte DNA, clone 3.
Length = 587
Score = 40.1 bits (20), Expect = 0.65
Identities = 20/20 (100%)
Strand = Plus / Minus
Query: 6 ttcaaaattttataaccaat 25
||||||||||||||||||||
Sbjct: 430 ttcaaaattttataaccaat 411
>emb|AC007894|F21H2 Arabidopsis thaliana chromosome 1 BAC F21H2 sequence, complete
sequence.
Length = 88512
Score = 40.1 bits (20), Expect = 0.65
Identities = 20/20 (100%)
Strand = Plus / Plus
Query: 11 aattttataaccaatttgtt 30
||||||||||||||||||||
Sbjct: 55582 aattttataaccaatttgtt 55601
>emb|AE003465|AE003465 Drosophila melanogaster chromosome 2R, section 73 of 74 of the
>complete
sequence.
Length = 343835
Score = 40.1 bits (20), Expect = 0.65
Identities = 20/20 (100%)
Strand = Plus / Minus
Query: 46 ttaaaagcaaaagaaaacca 65
||||||||||||||||||||
Sbjct: 342713 ttaaaagcaaaagaaaacca 342694
>emb|AC007884|AC007884 Drosophila melanogaster, chromosome 2R, region 60F-60F, BAC
>clone
BACR08I14, complete sequence.
Length = 190616
Score = 40.1 bits (20), Expect = 0.65
Identities = 20/20 (100%)
Strand = Plus / Minus
Query: 46 ttaaaagcaaaagaaaacca 65
||||||||||||||||||||
Sbjct: 190407 ttaaaagcaaaagaaaacca 190388
>emb|AC007582|AC007582 Drosophila melanogaster, chromosome 2R, region 60F-60F, BAC
>clone
BACR17E16, complete sequence.
Length = 180162
Score = 40.1 bits (20), Expect = 0.65
Identities = 20/20 (100%)
Strand = Plus / Plus
Query: 46 ttaaaagcaaaagaaaacca 65
||||||||||||||||||||
Sbjct: 162536 ttaaaagcaaaagaaaacca 162555
>emb|AE010893|AE010893 Methanosarcina acetivorans str. C2A, section 238 of 534 of the
complete genome.
Length = 10486
Score = 40.1 bits (20), Expect = 0.65
Identities = 23/24 (95%)
Strand = Plus / Plus
Query: 29 tttcaaaacaaaagcccttaaaag 52
||||||||||||||||||| ||||
Sbjct: 9833 tttcaaaacaaaagcccttcaaag 9856
>emb|AC083806|AC083806 Homo sapiens 12q BAC RP11-240G22 (Roswell Park Cancer Institute
>Human BAC
Library) complete sequence.
Length = 164461
Score = 40.1 bits (20), Expect = 0.65
Identities = 26/28 (92%)
Strand = Plus / Plus
Query: 34 aaacaaaagcccttaaaagcaaaagaaa 61
|||||| | |||||||||||||||||||
Sbjct: 142022 aaacaatatcccttaaaagcaaaagaaa 142049
>emb|AC055764|AC055764 Homo sapiens 3 BAC RP11-803P9 (Roswell Park Cancer Institute
>Human
BAC Library) complete sequence.
Length = 74486
Score = 40.1 bits (20), Expect = 0.65
Identities = 20/20 (100%)
Strand = Plus / Plus
Query: 41 agcccttaaaagcaaaagaa 60
||||||||||||||||||||
Sbjct: 2018 agcccttaaaagcaaaagaa 2037
>emb|AC023456|AC023456 Homo sapiens chromosome 15, clone RP11-162P24, complete
>sequence.
Length = 163502
Score = 40.1 bits (20), Expect = 0.65
Identities = 20/20 (100%)
Strand = Plus / Plus
Query: 43 cccttaaaagcaaaagaaaa 62
||||||||||||||||||||
Sbjct: 142105 cccttaaaagcaaaagaaaa 142124
>emb|AC021851|AC021851 Homo sapiens BAC clone RP11-438L19 from 2, complete sequence.
Length = 202078
Score = 40.1 bits (20), Expect = 0.65
Identities = 20/20 (100%)
Strand = Plus / Plus
Query: 41 agcccttaaaagcaaaagaa 60
||||||||||||||||||||
Sbjct: 114308 agcccttaaaagcaaaagaa 114327
>emb|AC015798|AC015798 Homo sapiens chromosome 15, clone RP11-341E5, complete sequence.
Length = 182107
Score = 40.1 bits (20), Expect = 0.65
Identities = 20/20 (100%)
Strand = Plus / Plus
Query: 43 cccttaaaagcaaaagaaaa 62
||||||||||||||||||||
Sbjct: 84710 cccttaaaagcaaaagaaaa 84729
>emb|AL161713|CNS01RHE Human chromosome 14 DNA sequence BAC R-22K10 of library RPCI-11
>from
chromosome 14 of Homo sapiens (Human), complete sequence.
Length = 157383
Score = 40.1 bits (20), Expect = 0.65
Identities = 20/20 (100%)
Strand = Plus / Plus
Query: 41 agcccttaaaagcaaaagaa 60
||||||||||||||||||||
Sbjct: 45265 agcccttaaaagcaaaagaa 45284
Database: gbgene
Posted date: Jun 30, 2003 9:45 PM
Number of letters in database: 4,294,902,594
Number of sequences in database: 310,819
Database: /usr/cbs/databases/blastdb/gbgene.01
Posted date: Jun 30, 2003 10:11 PM
Number of letters in database: 4,294,967,166
Number of sequences in database: 2,583,428
Database: /usr/cbs/databases/blastdb/gbgene.02
Posted date: Jun 30, 2003 10:16 PM
Number of letters in database: 228,420,829
Number of sequences in database: 72,078
Lambda K H
1.37 0.711 1.31
Gapped
Lambda K H
1.37 0.711 1.31
Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 1,132,852
Number of Sequences: 2966325
Number of extensions: 1132852
Number of successful extensions: 100759
Number of sequences better than 1.0: 20
Number of HSP's better than 1.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 100714
Number of HSP's gapped (non-prelim): 45
length of query: 110
length of database: 8,818,290,589
effective HSP length: 20
effective length of query: 90
effective length of database: 8,758,964,089
effective search space: 788306768010
effective search space used: 788306768010
T: 0
A: 0
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 20 (40.1 bits)
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