[Bioperl-l] Can't parse blast report written by Bio::SearchIO::Writer::TextResultWriter
Chris Fields
cjfields at uiuc.edu
Fri May 9 00:03:11 UTC 2008
You can always post it as an enhancement request in bugzilla. I don't
think it would be too hard to implement.
chris
On May 8, 2008, at 5:35 PM, Prachi Shah wrote:
>> I suspect somehow you are not reconstituting the Hit or Result
>> objects properly,
>> but I didn't try and debug this myself.
>
> Its possible, but I haven't been to point out what is going wrong. But
> then, the writer object is able to write the report without incident.
> I am at a loss.
>
>> 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.
>
> That would be ideal! But, until that is available, I will have to
> make-do with such a solution.
>
> Thanks,
> Prachi
>
>
>> 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.
>>>
>>>
>>> Smallest
>>> 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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>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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