[Bioperl-l] Can't parse blast report written by Bio::SearchIO::Writer::TextResultWriter
Jason Stajich
jason at bioperl.org
Thu May 8 22:29:40 UTC 2008
I suspect somehow you are not reconstituting the Hit or Result
objects properly, but I didn't try and debug this myself.
You can specify a sort order function to the Result object now to
specify the Hit order, maybe we should add sort function to Hit
object for retrieving the underlying HSPs in a
programmable order. Seems like that would be a cleaner fix.
-jason
On May 8, 2008, at 1:54 PM, Prachi Shah wrote:
> Hi all,
>
> I am trying to order of HSPs within each BLAST Hit in the order of
> ascending P-values. So, I parse my WU-BLAST report using Bio::SearchIO
> and create new Result, Hit and HSP objects in the order and then write
> out another BLAST report with the
> Bio::SearchIO::Writer::TextResultWriter module. All this works fine.
> But, when I try to parse this new blast report with
> Bio::SearchIO::blast, I get the following error:
>
> ------------- EXCEPTION -------------
> MSG: no data for midline Query: 0 1
> STACK Bio::SearchIO::blast::next_result
> /tools/perl/5.6.1/lib/site_perl/5.6.1/Bio/SearchIO/blast.pm:1151
> STACK toplevel bin/testBlastParse.pl:12
> --------------------------------------
>
> I have copied below sample sections of both blast reports and the
> code. Any hints/ pointers/ suggestions are greatly appreciated.
>
> Thanks,
> Prachi
>
>
>
> The old vs new blast reports look slightly different, esp. note the
> HSP start and stop coordinates for the QUERY sequence.
>
> **Snippet of OLD blast report (generated by WU-BLAST):
> ----------------------------------------------------------------------
> ------------------------------
> Query= orf19.4890
> (4931 letters)
>
> Database: Ca21_Chromosomes
> 9 sequences; 14,324,492 total letters.
> Searching....
> 10....20....30....40....50....60....70....80....90....100% done
>
> WARNING: hspmax=1000 was exceeded by 8 of the database sequences,
> causing the
> associated cutoff score, S2, to be transiently set as
> high as 113.
>
> S
> mallest
>
> Sum
> High
> Probability
> Sequences producing High-scoring Segment Pairs: Score
> P(N) N
>
> Ca21chr1 Assembly 21, Ca21chr1 (3188577 nucleotides) 24655
> 0. 1
> Ca21chr5 Assembly 21, Ca21chr5 (1190941 nucleotides) 1682
> 3.4e-68 3
> Ca21chr6 Assembly 21, Ca21chr6 (1033553 nucleotides) 908
> 3.0e-34 3
> Ca21chr2 Assembly 21, Ca21chr2 (2232049 nucleotides) 859
> 4.7e-30 1
> Ca21chr7 Assembly 21, Ca21chr7 (949626 nucleotides) 492
> 7.3e-24 3
> Ca21chr4 Assembly 21, Ca21chr4 (1603475 nucleotides) 528
> 9.8e-21 2
> Ca21chrR Assembly 21, Ca21chrR (2286425 nucleotides) 520
> 1.4e-19 5
> Ca21chr3 Assembly 21, Ca21chr3 (1799426 nucleotides) 502
> 1.7e-14 2
> Ca19-mtDNA Assembly 19, Ca19-mtDNA (40420 nucleotides) 313
> 2.9e-06 2
>
>
>> Ca21chr1 Assembly 21, Ca21chr1 (3188577 nucleotides)
> Length = 3,188,577
>
> Plus Strand HSPs:
>
> Score = 506 (82.0 bits), Expect = 4.9e-14, P = 4.9e-14
> Identities = 850/1549 (54%), Positives = 850/1549 (54%), Strand =
> Plus / Plus
>
> Query: 3450 ATGCATATGGTAATGTTAA-AATCACTGATTTTGGA-
> TTTTGTGCTAAATTAAC-T-GAT 3505
> | | ||| | | || |||| ||| ||||| ||| | ||||| || | ||
> | | | |
> Sbjct: 155924 AGGGATACGATTAT-TTAAGAATT-CTGATATTGAAATTTTG-GC-
> ATTTTCATATAGTT
> 155979
>
> Query: 3506 CAAAGA--AATAAACGTGCC-ACAATGGTGGGGACACCATATTGG-
> ATGGCACCTGAAGT 3561
> |||| | |||||| | | |||| || | ||| | | |||
> | | | |
> Sbjct: 155980 CAAACATTAATAAATATATTGAAAATGTTGATTTAATCAT-TAGTCATG---
> CTGGTACT
> 156035
>
> Query: 3562
> GGTTAAACAAAAGGAATATGATGAAAAAGTTGATGTTTGGTCATTGGGGATTATGACTAT 3621
> || | || | | || || | | | |||| | ||||
> |||| ||
> Sbjct: 156036 GGATCAATCATTG--AT-TGTTTACAT--TTGAA--
> TAAACCATTAATTGTTATTGTTAA
> 156088
>
> Query: 3622 TGAAATGATTGAAGGAGAACCACCTTATTTGAA-T-
> GAAGAACCATTAAAAGCATTATAT 3679
> ----------------------------------------------------------------------
> ------------------------------
>
> **Snippet of NEW blast report (generated using
> Bio::SearchIO::Writer::TextResultWriter)
> ----------------------------------------------------------------------
> ------------------------------
> uery= orf19.4890
> (4,931 letters)
>
> Database: Ca21_Chromosomes
> 9 sequences; 14,324,492 total letters
>
>
> Score E
> Sequences producing significant alignments:
> (bits) value
> Ca21chr1 Assembly 21, Ca21chr1 (3188577 nucleotides)
> 24655 0.
> Ca21chr5 Assembly 21, Ca21chr5 (1190941 nucleotides)
> 1682 3.4e-68
> Ca21chr6 Assembly 21, Ca21chr6 (1033553 nucleotides)
> 908 3.0e-34
> Ca21chr2 Assembly 21, Ca21chr2 (2232049 nucleotides)
> 859 4.7e-30
> Ca21chr7 Assembly 21, Ca21chr7 (949626 nucleotides)
> 492 7.3e-24
> Ca21chr4 Assembly 21, Ca21chr4 (1603475 nucleotides)
> 528 9.8e-21
> Ca21chrR Assembly 21, Ca21chrR (2286425 nucleotides)
> 520 1.4e-19
> Ca21chr3 Assembly 21, Ca21chr3 (1799426 nucleotides)
> 502 1.7e-14
> Ca19-mtDNA Assembly 19, Ca19-mtDNA (40420 nucleotides)
> 313 2.9e-06
>
>
>> Ca21chr1 Assembly 21, Ca21chr1 (3188577 nucleotides)
> Length = 3188577
>
> Score = 3705.3 bits (24655), Expect = 0., P = 0.
> Identities = 4931/4931 (100%)
> Frame = -1 / +1
>
> Query: 1
> ATAAAGGATGCCAAATAGTAGTAGTAAAATAGTAAATAGAATTGCAAAACAAAAATGATT -58
>
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 2248574
> ATAAAGGATGCCAAATAGTAGTAGTAAAATAGTAAATAGAATTGCAAAACAAAAATGATT
> 2248633
>
> Query: -59
> AAATAGCCCTTTATCAATAAATTTTTAAAGTTAGTTTCTTCTGGAACCCTACCCTCTTGG -118
>
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 2248634
> AAATAGCCCTTTATCAATAAATTTTTAAAGTTAGTTTCTTCTGGAACCCTACCCTCTTGG
> 2248693
>
> Query: -119
> TGTTAATCTTTTAAGTTAATATTTATAGTTAATAAAGTAGAAGTGTCTATTTATTGATTG -178
>
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 2248694
> TGTTAATCTTTTAAGTTAATATTTATAGTTAATAAAGTAGAAGTGTCTATTTATTGATTG
> 2248753
>
> Query: -179
> TTGTTGTTGTTGATTAAGAATATAAAGAAAAACAGAAAAGAAAAAAAGAAGGTTTAAAAA -238
>
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 2248754
> TTGTTGTTGTTGATTAAGAATATAAAGAAAAACAGAAAAGAAAAAAAGAAGGTTTAAAAA
> 2248813
>
> Query: -239
> AGTTAATTGTGAAGTAAAAGGGTTGAAAAATTTTTTTTTTTTCTGTTTCTCTCTTTGAGA -298
>
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 2248814
> AGTTAATTGTGAAGTAAAAGGGTTGAAAAATTTTTTTTTTTTCTGTTTCTCTCTTTGAGA
> 2248873
>
> Query: -299
> TTCTTTGACATATTTATTATTATAACACTATGCTATACTAAAAACAGTACTACCAATTGA -358
>
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 2248874
> TTCTTTGACATATTTATTATTATAACACTATGCTATACTAAAAACAGTACTACCAATTGA
> 2248933
>
> Query: -359
> ATTAAATTAAATTAAATTAAATTAAATTATTAGACCAATTTCAATAAAGATAAGCAATTT -418
>
> ----------------------------------------------------------------------
> ------------------------------
>
> **Here is the snippet of code that reads the old report, generates new
> objects and writes new report:
> ----------------------------------------------------------------------
> ------------------------------
> my $blast_report = Bio::SearchIO->new(-format => 'blast',
> -file => $blastOutputTmp);
>
> my $writer =
> Bio::SearchIO::Writer::TextResultWriter->new(-no_wublastlinks => 0);
> my $out_blast_report = Bio::SearchIO->new(-writer => $writer,
> -file => ">$blastOutputFile");
>
> my $sorted_blast_report;
>
> while( my $result = $blast_report->next_result ) {
>
> my (%parameters, %statistics);
>
> foreach my $param ($result->available_parameters) {
>
> $parameters{$param} = $result->get_parameter($param);
> }
>
> foreach my $stat ($result->available_statistics) {
>
> $statistics{$stat} = $result->get_statistic($stat);
> }
>
> my $generic_result =
> Bio::Search::Result::BlastResult->new(-query_name =>
> $result->query_name,
> -query_length =>
> $result->query_length,
> -database_name =>
> $result->database_name,
> -database_entries =>
> $result->database_entries,
> -parameters => \%
> parameters,
> -statistics => \%
> statistics,
> -algorithm => $result-
> >algorithm,
> -query_description =>
> $result->query_description,
> -algorithm_reference =>
> $result->algorithm_reference,
> -algorithm_version =>
> $result->algorithm_version,
> -database_letters =>
> $result->database_letters);
>
> while( my $hit = $result->next_hit ) {
>
> my $generic_hit = Bio::Search::Hit::BlastHit->new(-name
> => $hit->name,
> -algorithm => $hit->algorithm,
> -description => $hit->description,
> -length => $hit->length,
> -score => $hit->score,
> -bits => $hit->bits,
> -significance => $hit-
> >significance);
>
> my (@hsp_sorted, @hsps);
> while( my $hsp = $hit->next_hsp ) {
>
> push(@hsps, $hsp);
> }
>
> @hsp_sorted = sort {$a->pvalue <=> $b->pvalue} @hsps;
>
> for(my $i=0; $i<=$#hsp_sorted; $i++) {
>
> $generic_hit->add_hsp($hsp_sorted[$i]);
>
> }
>
> $generic_result->add_hit($generic_hit);
>
> }
>
> $out_blast_report->write_result($generic_result);
>
> }
> ----------------------------------------------------------------------
> ------------------------------
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