From 048b9f36f41caf3134ac7606057a1d2b5f720878 Mon Sep 17 00:00:00 2001
From: juguang <juguang@sanger.ac.uk>
Date: Thu, 13 Mar 2003 02:48:44 +0000
Subject: [PATCH] converter from GenericHSP to BaseAlignFeature's submodules,
for blast report
GenericHPS::algorithm tells what program of blastall is used, and in response of this, the code try to find the specific alignment feature in EnsEMBL.
---
.../EnsEMBL/Utils/Converter/bio_ens_hit.pm | 138 ++++++
modules/t/converter.blast | 434 ++++++++++++++++++
modules/t/converter.t | 47 +-
3 files changed, 615 insertions(+), 4 deletions(-)
create mode 100644 modules/Bio/EnsEMBL/Utils/Converter/bio_ens_hit.pm
create mode 100644 modules/t/converter.blast
diff --git a/modules/Bio/EnsEMBL/Utils/Converter/bio_ens_hit.pm b/modules/Bio/EnsEMBL/Utils/Converter/bio_ens_hit.pm
new file mode 100644
index 0000000000..b99fc62746
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Utils/Converter/bio_ens_hit.pm
@@ -0,0 +1,138 @@
+
+=head1
+
+Sequence alignment hits were previously stored within the core database as
+ungapped alignments. This imposed 2 major constraints on alignments:
+
+a) alignments for a single hit record would require multiple rows in the
+database, and
+b) it was not possible to accurately retrieve the exact original alignment.
+
+Therefore, in the new branch sequence alignments are now stored as ungapped
+alignments in the cigar line format (where CIGAR stands for Concise
+Idiosyncratic Gapped Alignment Report).
+
+In the cigar line format alignments are sotred as follows:
+
+M: Match
+D: Deletino
+I: Insertion
+
+An example of an alignment for a hypthetical protein match is shown below:
+
+
+Query: 42 PGPAGLP----GSVGLQGPRGLRGPLP-GPLGPPL...
+ PG P G GP R PLGP
+Sbjct: 1672 PGTP*TPLVPLGPWVPLGPSSPR--LPSGPLGPTD...
+
+protein_align_feature table as the following cigar line:
+
+7M4D12M2I2MD7M
+
+
+=cut
+
+package Bio::EnsEMBL::Utils::Converter::bio_ens_hit;
+
+use strict;
+use vars qw(@ISA);
+use Bio::EnsEMBL::Utils::Converter::bio_ens;
+use Bio::EnsEMBL::DnaDnaAlignFeature;
+use Bio::EnsEMBL::DnaPepAlignFeature;
+use Bio::EnsEMBL::PepDnaAlignFeature;
+
+@ISA = qw(Bio::EnsEMBL::Utils::Converter::bio_ens);
+
+sub _initialize {
+ my ($self, @args) = @_;
+ $self->SUPER::_initialize(@args);
+
+ # After super initialized, analysis and contig are ready.
+ my $bio_ens_seqFeature_converter = new Bio::EnsEMBL::Utils::Converter(
+ -in => 'Bio::SeqFeature::Generic',
+ -out => 'Bio::EnsEMBL::SeqFeature',
+ -analysis => $self->analysis,
+ -contig => $self->contig
+ );
+ $self->_bio_ens_seqFeature_converter($bio_ens_seqFeature_converter);
+
+}
+
+sub _convert_single {
+ my ($self, $input) = @_;
+
+ my $in = $self->in;
+ my $out = $self->out;
+
+ if($in =~ /Bio::Search::Hit::GenericHit/){
+ return $self->_convert_single_hit($input);
+ }elsif($in =~ /Bio::Search::HSP::GenericHSP/){
+ return $self->_convert_single_hsp($input);
+ }else{
+ $self->throw("[$in]->[$out], not implemented");
+ }
+}
+
+sub _convert_single_hit {
+
+
+}
+
+sub _convert_single_hsp {
+ my ($self, $hsp) = @_;
+
+ unless(ref($hsp) && $hsp->isa('Bio::Search::HSP::GenericHSP')){
+ $self->throw("a GenericHSP object needed");
+ }
+
+ my $bio_ens_seqFeature_converter = $self->_bio_ens_seqFeature_converter;
+ my $ens_feature1 = $bio_ens_seqFeature_converter->_convert_single(
+ $hsp->feature1);
+ my $ens_feature2 = $bio_ens_seqFeature_converter->_convert_single(
+ $hsp->feature2);
+
+ $ens_feature1->p_value($hsp->evalue);
+ $ens_feature1->score($hsp->score);
+ $ens_feature1->percent_id($hsp->percent_identity);
+ $ens_feature2->p_value($hsp->evalue);
+ $ens_feature2->score($hsp->score);
+ $ens_feature2->percent_id($hsp->percent_identity);
+
+ my $cigar_string = $hsp->cigar_string;
+ my @args = (
+ -feature1 => $ens_feature1,
+ -feature2 => $ens_feature2,
+ -cigar_string => $cigar_string
+ );
+
+ my $contig = $self->contig;
+ # choose the AlignFeature based on the blast program
+ my $program = $hsp->algorithm;
+
+ $self->throw("HSP does not have algorithm value") unless(defined($program));
+ my $align_feature;
+
+ if($program =~ /blastn/i){
+ $align_feature = new Bio::EnsEMBL::DnaDnaAlignFeature(@args);
+ $align_feature->attach_seq($contig);
+ }elsif($program =~ /blastx/i){
+ $align_feature = new Bio::EnsEMBL::DnaPepAlignFeature(@args);
+ $align_feature->attach_seq($contig);
+ }else{
+ $self->throw("$program is not supported yet");
+ }
+
+ return $align_feature;
+}
+
+# an internal getter/setter for a converter used for seq feature conversion.
+
+sub _bio_ens_seqFeature_converter {
+ my ($self, $arg) = @_;
+ if(defined $arg){
+ $self->{_bio_ens_seqFeature_converter} = $arg;
+ }
+ return $self->{_bio_ens_seqFeature_converter};
+}
+
+1;
diff --git a/modules/t/converter.blast b/modules/t/converter.blast
new file mode 100644
index 0000000000..1b70f8a5f1
--- /dev/null
+++ b/modules/t/converter.blast
@@ -0,0 +1,434 @@
+TBLASTN 2.0.4 [Feb-24-1998]
+
+Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A.
+Schäffer, 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=
+gi|1401126
+ (504 letters)
+
+Database: Non-redundant GenBank+EMBL+DDBJ+PDB sequences
+ 336,723 sequences; 677,679,054 total letters
+
+Searchingdone
+
+
+ Score E
+Sequences producing significant alignments: (bits) Value
+
+gb|U49928|HSU49928 Homo sapiens TAK1 binding protein (TAB1) mRNA... 1009 0.0
+emb|Z36985|PTPP2CMR P.tetraurelia mRNA for protein phosphatase t... 58 4e-07
+emb|X77116|ATMRABI1 A.thaliana mRNA for ABI1 protein 53 1e-05
+gb|U12856|ATU12856 Arabidopsis thaliana Col-0 abscisic acid inse... 53 1e-05
+dbj|D38109|ATHPP2CA Arabidopsis thaliana mRNA for protein phosph... 52 3e-05
+emb|Y08965|ATABI2RNA A.thaliana mRNA for ABI2 protein 47 8e-04
+emb|AL010222|PFSC04009 Plasmodium falciparum DNA *** SEQUENCING ... 45 0.004
+gb|AC002409|ATAC002409 Arabidopsis thaliana chromosome II BAC T2... 43 0.012
+emb|Z98762|SPAC4A8 S.pombe chromosome I cosmid c4A8 42 0.020
+gb|AF006827|AF006827 Magnaporthe grisea adenylate cyclase (MAC1)... 41 0.045
+emb|Y13936|HSY13936 Homo sapiens mRNA for protein phosphatase 2C... 41 0.059
+gb|U81159|BTU81159 Bos taurus magnesium-dependent calcium inhibi... 40 0.077
+emb|Y10438|SPFKBAD Streptomyces sp. MA6548 fkbA gene and partial... 40 0.077
+gb|AF012921|AF012921 Magnaporthe grisea adenylate cyclase (mac1)... 40 0.10
+gb|U42383|MMU42383 Mus musculus fibroblast growth factor inducib... 40 0.10
+gb|AF023665|AF023665 Plasmodium falciparum protein phosphatase 2... 39 0.13
+gb|M24942|YSPCYR1A Yeast (S.pombe) adenylate cyclase (CYR1) gene... 39 0.17
+gb|M26699|YSPADC Yeast (S.pombe) cyr1 gene encoding adenylyl cyc... 39 0.17
+gb|L43413|PANADCY Podospora anserina adenyl cyclase gene, exons 1-4 38 0.30
+gb|M89651|HUMMMDBC Human DNA from cosmid DNA MMDB (f10080) and M... 38 0.30
+emb|Z99161|SPAC11G7 S.pombe chromosome I cosmid c11G7 38 0.30
+emb|X56042|SKADECYC Saccharomyces kluyveri gene for adenylyl cyc... 37 0.88
+gb|M29235|CELPOLII C.elegans RNA polymerase II largest subunit (... 36 1.1
+dbj|D45132|HUMHOXY1 Human kidney mRNA for zinc-finger DNA-bindin... 36 1.1
+gb|U70654|MMU70654 Mus musculus musculus sex determining protein... 36 1.1
+gb|U53333|CELF36A4 Caenorhabditis elegans cosmid F36A4. 36 1.1
+gb|L29028|CREWP6A Chlamydomonas eugametos WP6 mRNA, complete cds 36 1.1
+gb|U70653|MMU70653 Mus musculus musculus sex determining protein... 36 1.1
+gb|U17838|HSU17838 Human zinc finger protein RIZ mRNA, complete cds 36 1.1
+emb|X56432|DMRUNTR D.melanogaster mRNA for runt segmentation gene 36 1.5
+emb|X67204|MMSRYLOC M.musculus DNA sequence of Sry locus 36 1.5
+gb|U00051|CELF42G9 Caenorhabditis elegans cosmid F42G9. 36 1.5
+gb|U70655|MMU70655 Mus musculus sex determining protein (Sry) ge... 36 1.5
+gb|AF019985|AF019985 Dictyostelium discoideum Spalten (spnA) mRN... 36 2.0
+emb|X78886|ATABI1G A.thaliana (Landsberg erecta) ABI1 gene 36 2.0
+gb|U70651|MMU70651 Mus musculus musculus sex determining protein... 36 2.0
+gb|U70652|MMU70652 Mus musculus musculus sex determining protein... 36 2.0
+emb|X58924|HVRPL11E H.volcanii genes for ribosomal proteins L11e... 36 2.0
+emb|X05806|CHAMPER Acetabularia plastid DNA homologous to Drosop... 36 2.0
+gb|U82833|OSU82833 Oryza sativa S-adenosyl-L-methionine syntheta... 35 2.6
+emb|Z27084|HLHOLLI H.lanatus mRNA for allergen Hol-lI 35 2.6
+dbj|D00676|SH1RSP40 Pseudorabies virus genome, RSp40 and pk genes 35 2.6
+emb|Y10421|CCATCOLE1 C.curvatus strain ATCC 20509 Ole1 gene 35 2.6
+gb|L14320|HSBBICP4A Bovine herpesvirus type 1 early-intermediate... 35 2.6
+emb|AJ004801|BHV1CGEN Bovine herpesvirus 1 complete genome 35 2.6
+dbj|AB010074|AB010074 Arabidopsis thaliana genomic DNA, chromoso... 35 3.4
+gb|AC004490|AC004490 Homo sapiens chromosome 19, cosmid R29381, ... 35 3.4
+dbj|AB011474|AB011474 Arabidopsis thaliana genomic DNA, chromoso... 35 3.4
+gb|U03645|MMU03645 Mus musculus domesticus Torino (Sry) gene, co... 35 3.4
+gb|U70641|MMU70641 Mus musculus domesticus sex determining prote... 35 3.4
+gb|U70650|MMU70650 Mus musculus domesticus sex determining prote... 35 3.4
+gb|U70642|MMU70642 Mus musculus domesticus sex determining prote... 35 3.4
+gb|U70647|MMU70647 Mus musculus domesticus sex determining prote... 35 3.4
+emb|Y11840|ATABI2 Arabidopsis thaliana ABI2 gene 35 3.4
+emb|Y08966|ATABI2DNA A.thaliana gene encoding ABI2 protein 35 3.4
+emb|X16144|SVGRA S. violaceoruber DNA for granaticin polyketide ... 35 3.4
+emb|X16300|SVPKS Streptomyces violaceoruber polyketide synthase ... 35 3.4
+gb|U70657|MMU70657 Mus musculus castaneus sex determining protei... 35 3.4
+gb|M57417|HUMMUCCF Human (cystic fibrosis patient) mucin mRNA, p... 35 3.4
+gb|L04286|DDIGP100 Dictyostelium discoideum glycoprotein gp100 (... 35 3.4
+emb|Z46938|BTTESDNA B.taurus DNA (protamine gene cluster) 35 3.4
+gb|L13054|DROZESTEL Drosophila melanogaster zeste (z) gene, part... 34 4.4
+gb|L13058|DROZESTEP Drosophila melanogaster zeste (z) gene, part... 34 4.4
+gb|M60590|YSCAAGLCS S.cerevisiae a-agglutinin core subunit (AGA1... 34 4.4
+gb|AF009521|AF009521 Mus spretus sex determining protein (Sry) g... 34 4.4
+emb|Z71659|SCYNR044W S.cerevisiae chromosome XIV reading frame O... 34 4.4
+gb|U19361|PMU19361 Petromyzon marinus neurofilament subunit NF-1... 34 4.4
+gb|U70646|MMU70646 Mus musculus domesticus sex determining prote... 34 4.4
+gb|U23477|DDU23477 Dictyostelium discoideum phosphatidylinositol... 34 4.4
+emb|X55695|LEEXTEN15 Tomato mRNA for a glycine-rich protein (clo... 34 4.4
+emb|Z95556|MTCY07A7 Mycobacterium tuberculosis cosmid SCY07A7 34 4.4
+dbj|AB007645|AB007645 Arabidopsis thaliana genomic DNA, chromoso... 34 5.8
+emb|X64346|HSGEND Herpesvirus saimiri complete genome DNA 34 5.8
+emb|Z95620|SPBC3D6 S.pombe chromosome II cosmid c3D6 34 5.8
+gb|U70644|MMU70644 Mus musculus domesticus sex determining prote... 34 5.8
+gb|U70649|MMU70649 Mus musculus domesticus sex determining prote... 34 5.8
+gb|U43491|SCU43491 Saccharomyces cerevisiae cosmid clone pEOA156... 34 5.8
+dbj|D00909|NEUNAC N.crassa nac gene coding for adenylate cyclase... 34 5.8
+gb|U70645|MMU70645 Mus musculus domesticus sex determining prote... 34 5.8
+gb|AF009519|AF009519 Mus musculus domesticus sex determining pro... 34 5.8
+gb|M77174|MUSPERPA Mouse perlecan mRNA, complete cds. 34 5.8
+emb|Z74917|SCYOR009W S.cerevisiae chromosome XV reading frame OR... 34 5.8
+gb|J04054|MUSPCGBM Mouse basement membrane proteoglycan mRNA, pa... 34 5.8
+emb|Z47072|CEF26C11 Caenorhabditis elegans cosmid F26C11, comple... 34 5.8
+gb|U70643|MMU70643 Mus musculus sex determining protein (Sry) ge... 34 5.8
+gb|AC003671|AC003671 Arabidopsis thaliana chromosome 1 BAC F17O7... 34 5.8
+emb|X16481|RN11ZNBP Rat mRNA for zinc(2+) binding protein 34 5.8
+gb|U46156|SSU46156 Synechococcus sp. CcmK (ccmK) gene, complete ... 34 5.8
+gb|AC000098|YUP8H12 Arabidopsis thaliana chromosome 1 YAC yUP8H1... 34 5.8
+emb|Z71781|SCCIVL37K S.cerevisiae chromosome IV left arm (EU) DN... 34 5.8
+emb|Y13332|SSTO1AMY Streptomyces sp. TO1 amy gene 34 5.8
+gb|M30473|NEULEURSC N.crassa cytoplasmic leucyl-tRNA synthetase ... 34 5.8
+emb|Z74085|SCYDL037C S.cerevisiae chromosome IV reading frame OR... 34 5.8
+gb|AF029858|AF029858 Sorghum bicolor cytochrome P450 CYP71E1 (CY... 34 5.8
+gb|S47414|S47414 glycine-rich protein {clone atGRP-5} [Arabidops... 34 7.6
+emb|X60294|SCSEC1A S.cereale Sec1 gene for omega secalin 34 7.6
+emb|Z37975|BTPLAKOPH B.taurus mRNA for plakophilin. 34 7.6
+emb|X60295|SCSEC1B S.cereale Sec1 gene for omega secalin 34 7.6
+dbj|D87895|D87895 Aspergillus nidulans DNA for chitinase, comple... 34 7.6
+gb|AF017789|AF017789 Homo sapiens putative transcription factor ... 34 7.6
+
+>gb|U49928|HSU49928 Homo sapiens TAK1 binding protein (TAB1) mRNA, complete cds.
+ Length = 3096
+
+ Score = 1009 bits (2580), Expect = 0.0
+ Identities = 504/504 (100%), Positives = 504/504 (100%)
+
+Query: 1 MAAQRRSLLQSEQQPSWTDDLPLCHLSGVGSASNRSYSADGKGTESHPPEDSWLKFRSEN 60
+ MAAQRRSLLQSEQQPSWTDDLPLCHLSGVGSASNRSYSADGKGTESHPPEDSWLKFRSEN
+Sbjct: 21 MAAQRRSLLQSEQQPSWTDDLPLCHLSGVGSASNRSYSADGKGTESHPPEDSWLKFRSEN 200
+
+Query: 61 NCFLYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVERSFLES 120
+ NCFLYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVERSFLES
+Sbjct: 201 NCFLYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVERSFLES 380
+
+Query: 121 IDDALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGAMAVVAVLLNNKLYV 180
+ IDDALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGAMAVVAVLLNNKLYV
+Sbjct: 381 IDDALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGAMAVVAVLLNNKLYV 560
+
+Query: 181 ANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKIKQVGIICGQEST 240
+ ANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKIKQVGIICGQEST
+Sbjct: 561 ANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKIKQVGIICGQEST 740
+
+Query: 241 RRIGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVTGFLVLMSEGLYKALEAAH 300
+ RRIGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVTGFLVLMSEGLYKALEAAH
+Sbjct: 741 RRIGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVTGFLVLMSEGLYKALEAAH 920
+
+Query: 301 GPGQANQEIAAMIDTEFAKQTSLDAVAQAVVDRVKRIHSDTFASGGERARFCPRHEDMTL 360
+ GPGQANQEIAAMIDTEFAKQTSLDAVAQAVVDRVKRIHSDTFASGGERARFCPRHEDMTL
+Sbjct: 921 GPGQANQEIAAMIDTEFAKQTSLDAVAQAVVDRVKRIHSDTFASGGERARFCPRHEDMTL 1100
+
+Query: 361 LVRNFGYPLGEMSQPTPSPAPAAGGRVYPVSVPYSSAQSTSKTSVTLSLVMPSQGQMVNG 420
+ LVRNFGYPLGEMSQPTPSPAPAAGGRVYPVSVPYSSAQSTSKTSVTLSLVMPSQGQMVNG
+Sbjct: 1101LVRNFGYPLGEMSQPTPSPAPAAGGRVYPVSVPYSSAQSTSKTSVTLSLVMPSQGQMVNG 1280
+
+Query: 421 AHSASTLDEATPTLTNQSPTLTLQSTNTHTQSSSSSSDGGLFRSRPAHSLPPGEDGRVEP 480
+ AHSASTLDEATPTLTNQSPTLTLQSTNTHTQSSSSSSDGGLFRSRPAHSLPPGEDGRVEP
+Sbjct: 1281AHSASTLDEATPTLTNQSPTLTLQSTNTHTQSSSSSSDGGLFRSRPAHSLPPGEDGRVEP 1460
+
+Query: 481 YVDFAEFYRLWSVDHGEQSVVTAP 504
+ YVDFAEFYRLWSVDHGEQSVVTAP
+Sbjct: 1461YVDFAEFYRLWSVDHGEQSVVTAP 1532
+
+
+>emb|Z36985|PTPP2CMR P.tetraurelia mRNA for protein phosphatase type 2C
+ Length = 969
+
+ Score = 57.8 bits (137), Expect = 4e-07
+ Identities = 64/261 (24%), Positives = 112/261 (42%), Gaps = 2/261 (0%)
+
+Query: 64 LYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVERSFLESIDD 123
+ ++GVF+G+ G V FV + ELL + + E+ F E++ +
+Sbjct: 182 VFGVFDGHGGREVA*FVEKHFVDELLKNK------------------NFKEQKFEEALKE 307
+
+Query: 124 ALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREIS-GGAMAVVAVLLNNKLYVAN 182
+ + L L P+ QK L K + + S G A VA++ N LYVAN
+Sbjct: 308 TFLKMDELL-----------LTPEGQKELN*YKATDTDESYAGCTANVALIYKNTLYVAN 454
+
+Query: 183 VGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKIKQVGIICGQESTRR 242
+ G +R++LC++ + ++VDH +N +E R+ + G G + + +R
+Sbjct: 455 AGDSRSVLCRNNTN----HDMSVDHKPDNPEEKSRIERAG---GFVSDGRVNGNLNLSRA 613
+
+Query: 243 IGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVTGFLVLMSEGLYKALEAAHGP 302
+ +GD + K D + IIA P++ + L F+++ +G+++ L
+Sbjct: 614 LGDLEYKR-----DNKLRSNE*LIIALPDVKKTE-LTP*DKFILMGCDGVFETLNH*ELL 775
+
+Query: 303 GQANQEIA-AMIDTEFAKQTSLD 324
+ Q N I A + E K+ + D
+Sbjct: 776 KQVNSTIG*AQVTEELLKKAAED 844
+
+
+>emb|X77116|ATMRABI1 A.thaliana mRNA for ABI1 protein
+ Length = 1981
+
+ Score = 52.7 bits (124), Expect = 1e-05
+ Identities = 59/242 (24%), Positives = 105/242 (43%), Gaps = 6/242 (2%)
+
+Query: 55 KFRSENNCFLYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVE 114
+ +F ++ +GV++G+ G++V N+ +R+ L AE A + +L +E
+Sbjct: 918 RFDPQSAAHFFGVYDGHGGSQVANYCRERMHLAL------AEEI-AKEKPMLCDGDTWLE 1076
+
+Query: 115 RSFLESIDDALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGAMAVVAVLL 174
+ + + L + ++S PE V G+ +VVAV+
+Sbjct: 1077 KWKKALFNSFLRVDSEIESVAPETV-------------------------GSTSVVAVVF 1181
+
+Query: 175 NNKLYVANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKIKQ---- 230
+ + ++VAN G +RA+LC+ G L+VDH + EDE R+ G GK+ Q
+Sbjct: 1182 PSHIFVANCGDSRAVLCR----GKTALPLSVDHKPDREDEAARIEAAG---GKVIQWNGA 1340
+
+Query: 231 --VGIICGQESTRRIGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVTGFLVLM 288
+ G++ +R IGD +K II +PE+ + + L+L
+Sbjct: 1341 RVFGVLA---MSRSIGDRYLK--------------PSIIPDPEVTAVKRVK-EDDCLILA 1466
+
+Query: 289 SEGLYKAL 296
+ S+G++ +
+Sbjct: 1467 SDGVWDVM 1490
+
+
+>gb|U12856|ATU12856 Arabidopsis thaliana Col-0 abscisic acid insensitive protein (ABI1)
+ mRNA, complete cds.
+ Length = 2000
+
+ Score = 52.7 bits (124), Expect = 1e-05
+ Identities = 59/242 (24%), Positives = 105/242 (43%), Gaps = 6/242 (2%)
+
+Query: 55 KFRSENNCFLYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVE 114
+ +F ++ +GV++G+ G++V N+ +R+ L AE A + +L +E
+Sbjct: 918 RFDPQSAAHFFGVYDGHGGSQVANYCRERMHLAL------AEEI-AKEKPMLCDGDTWLE 1076
+
+Query: 115 RSFLESIDDALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGAMAVVAVLL 174
+ + + L + ++S PE V G+ +VVAV+
+Sbjct: 1077 KWKKALFNSFLRVDSEIESVAPETV-------------------------GSTSVVAVVF 1181
+
+Query: 175 NNKLYVANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKIKQ---- 230
+ + ++VAN G +RA+LC+ G L+VDH + EDE R+ G GK+ Q
+Sbjct: 1182 PSHIFVANCGDSRAVLCR----GKTALPLSVDHKPDREDEAARIEAAG---GKVIQWNGA 1340
+
+Query: 231 --VGIICGQESTRRIGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVTGFLVLM 288
+ G++ +R IGD +K II +PE+ + + L+L
+Sbjct: 1341 RVFGVLA---MSRSIGDRYLK--------------PSIIPDPEVTAVKRVK-EDDCLILA 1466
+
+Query: 289 SEGLYKAL 296
+ S+G++ +
+Sbjct: 1467 SDGVWDVM 1490
+
+
+>dbj|D38109|ATHPP2CA Arabidopsis thaliana mRNA for protein phosphatase 2C
+ Length = 1371
+
+ Score = 51.5 bits (121), Expect = 3e-05
+ Identities = 73/290 (25%), Positives = 132/290 (45%), Gaps = 13/290 (4%)
+
+Query: 47 HPPEDSWLKFRSENNCFLYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVL 106
+ HP S+L+ SEN+ F YGVF+G+ + V +RL +++ ++ A + +
+Sbjct: 447 HP---SFLQRNSENHHF-YGVFDGHGCSHVAEKCRERLH-DIVKKEVEVM-ASDEWTETM 608
+
+Query: 107 LQAFDVVERSFLESIDDALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGA 166
+ +++F +++ + + + A+ + PQ + G+
+Sbjct: 609 VKSFQKMDKEVSQRECNLVVNGAT--RSMKNSCRCELQSPQCDAV-------------GS 743
+
+Query: 167 MAVVAVLLNNKLYVANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAG 226
+ AVV+V+ K+ V+N G +RA+LC++ V L+VDH + DEL R+ Q G G
+Sbjct: 744 TAVVSVVTPEKIIVSNCGDSRAVLCRNGV----AIPLSVDHKPDRPDELIRIQQAG---G 902
+
+Query: 227 KI------KQVGIICGQESTRRIGD-YKVKYGYTDIDLLSAAKSKP----IIAEPEIHGA 275
+ ++ + +G++ +R IGD Y Y D ++ ++ I+A +
+Sbjct: 903 RVIYWDGARVLGVLA---MSRAIGDNYLKPYVIPDPEVTVTDRTDEDECLILASDGLWDV 1073
+
+Query: 276 QPLDGVTGF--LVLMSEGLYKALEAAHGPGQANQEIAAMIDTEFAKQTSLDAVAQAVVDR 333
+ P + G + L G +AAH A + A ++ + S D V+ VVD
+Sbjct: 1074VPNETACGVARMCLRGAGAGDDSDAAH---NACSDAALLLTKLALARQSSDNVSVVVVDL 1244
+
+Query: 334 VKR 336
+ KR
+Sbjct: 1245RKR 1253
+
+
+>emb|Y08965|ATABI2RNA A.thaliana mRNA for ABI2 protein
+ Length = 1470
+
+ Score = 46.9 bits (109), Expect = 8e-04
+ Identities = 55/241 (22%), Positives = 100/241 (40%), Gaps = 7/241 (2%)
+
+Query: 56 FRSENNCFLYGVFNGYDGNRVTNFVAQRLSAELL--LGQLNAEHAEADV-----RRVLLQ 108
+ F + +GV++G+ G++V N+ +R+ L + + E + D ++ L
+Sbjct: 504 FNPHLSAHFFGVYDGHGGSQVANYCRERMHLALTEEIVKEKPEFCDGDTWQEKWKKALFN 683
+
+Query: 109 AFDVVERSFLESIDDALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGAMA 168
+ +F V+ S +E++ A PE V G+ +
+Sbjct: 684 SFMRVD-SEIETVAHA-----------PETV-------------------------GSTS 752
+
+Query: 169 VVAVLLNNKLYVANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKI 228
+ VVAV+ ++VAN G +RA+LC+ G L+VDH + +DE R+ G +
+Sbjct: 753 VVAVVFPTHIFVANCGDSRAVLCR----GKTPLALSVDHKPDRDDEAARIEAAGGKVIRW 920
+
+Query: 229 KQVGIICGQESTRRIGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVTGFLVLM 288
+ + +R IGD +K +I +PE+ + + L+L
+Sbjct: 921 NGARVFGVLAMSRSIGDRYLK--------------PSVIPDPEVTSVRRVK-EDDCLILA 1055
+
+Query: 289 SEGLYKAL 296
+ S+GL+ +
+Sbjct: 1056SDGLWDVM 1079
+
+
+>emb|AL010222|PFSC04009 Plasmodium falciparum DNA *** SEQUENCING IN PROGRESS *** from contig
+ 4-9, complete sequence [Plasmodium falciparum]
+ Length = 5332
+
+ Score = 44.5 bits (103), Expect = 0.004
+ Identities = 48/183 (26%), Positives = 83/183 (45%), Gaps = 15/183 (8%)
+
+Query: 163 SGGAMAVVAVLLNNKLYVANVGTNRALLCKSTVDGLQVTQLNVDHTTE-NEDELFRLSQL 221
+ S G A V+V+ N LYVAN+G +R ++ K+ + L VDH N+ E R+ +
+Sbjct: 2760 SSGTTACVSVIFKNMLYVANIGDSRCIISKNG----RAIVLTVDHRASINKKEQDRILKS 2593
+
+Query: 222 GLDAGKIKQVGIICGQESTRRIGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGV 281
+ G G + G + G R G+ + K K +I EP++ + D
+Sbjct: 2592 G---GILDDEGYLGGCLGVCR--------GFGSFHKKTKEKLKGLICEPDLFHIKLTDD- 2449
+
+Query: 282 TGFLVLMSEGLYKALEAAHGPGQANQEIAAMIDTEFA---------KQTSLDAVAQAVV- 331
+ FL++ +G++ + + + D + A K+ SLD ++ VV
+Sbjct: 2448 DEFLIICCDGIFDVITSQEAVNTVKNSLIQSRDAKTAAEALCQLAYKKKSLDNLSVLVVI 2269
+
+Query: 332 ----DRVKRIHSDTFASG 345
+ D+ ++ S +SG
+Sbjct: 2268 FQNPDKNNKVSSINESSG 2215
+
+
+>gb|AC002409|ATAC002409 Arabidopsis thaliana chromosome II BAC T20B5 genomic sequence, complete
+ sequence [Arabidopsis thaliana]
+ Length = 72839
+
+ Score = 43.0 bits (99), Expect = 0.012
+ Identities = 21/57 (36%), Positives = 38/57 (65%)
+
+Query: 165 GAMAVVAVLLNNKLYVANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQL 221
+ G A+ ++L+ NKL+VANVG +RA+LC++ ++++ D+ TE+E L+ + L
+Sbjct: 24355 GCTAIASLLVENKLFVANVGDSRAILCRAG-HPFALSKVR*DYHTESELSLYSIGAL 24188
+
+
+>emb|Z98762|SPAC4A8 S.pombe chromosome I cosmid c4A8
+ Length = 43895
+
+ Score = 42.2 bits (97), Expect = 0.020
+ Identities = 56/230 (24%), Positives = 104/230 (44%), Gaps = 20/230 (8%)
+
+Query: 63 FLYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVERSFLESID 122
+ F YG+F+G+ G + F++ L + LN D ++L + V ++ +
+Sbjct: 3939 FFYGLFDGHGGTECSEFLSTNLGKIIENQDLN------DTEKILKEVHSV--GGYMAGLK 3784
+
+Query: 123 DALAEKASLQSQLPEGVPQHQLPPQY-QKILERLKTLER----EISGGAMAVVAVLLNNK 177
+ + + LQS+ + + + +L + Q ++ L R GA+ VA++ +
+Sbjct: 3783 PPFSLRTVLQSRDEDLLWRARLYYSFLQADMDYLTNYARPSPDSAVPGAVGTVAIITSKN 3604
+
+Query: 178 -----------LYVANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGL--- 223
+ +++A+VG RALLC S + +L H + +E RL + +
+Sbjct: 3603 NLSYWESDSYIIHLAHVGDTRALLCDSRTG--RAHRLTFQHHPADVEEARRLRRYNMGFS 3430
+
+Query: 224 -DAGKIKQVGIICGQESTRRIGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVT 282
+ D+ K+ + +TR GD GY K ++AEP++ L
+Sbjct: 3429 RDSFGQKRFAWVA---NTRSFGD-----GY-------KLKKLGVVAEPQLTSIHSLRDDW 3295
+
+Query: 283 GFLVLMSEGL 292
+ FL L+S+G+
+Sbjct: 3294 SFLTLLSDGI 3265
+
+
+>gb|AF006827|AF006827 Magnaporthe grisea adenylate cyclase (MAC1) gene, complete cds
+ Length = 8678
+
+ Score = 41.0 bits (94), Expect = 0.045
+ Identities = 63/259 (24%), Positives = 111/259 (42%), Gaps = 8/259 (3%)
+
+Query: 14 QPSWTDDLPLCHLSGVGSASNR-SYS-ADGKGTESHPPEDSWL--KFRSENNCFLYGVFN 69
+ QPS + C + GS++ Y+ AD G H + +F + L G+F+
+Sbjct: 5314 QPSIPEQSEDCRVRTSGSSAGYLPYAMADTLGKNEHLSTVDLVVPRFNASETETLLGLFD 5493
+
+Query: 70 GY----DGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVERSFLESIDDAL 125
+ G G+++ ++ + GQ+ A A + D + R+FL +++ L
+Sbjct: 5494 GQALSSGGSKIAKYLHENF------GQILATELRALKTGLKETPEDALRRAFL-ALNKEL 5652
+
+Query: 126 AEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGAMAVVAVLLNNKLYVANVGT 185
+ A S+ VP H+ Q IL + +++ G +A V L LYVANVG
+Sbjct: 5653 VTIAIQHSEDRPSVP-HRSGSQAHVILNK-----EDLNSGGVATVVYLQGQDLYVANVGD 5814
+
+Query: 186 NRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKIKQVGIICGQESTRRIGD 245
+ +A++ +S +T+ H E R+ + G G + + G + Q R
+Sbjct: 5815 AQAMIIQSDQTHKMLTR---KHDPAEPTERSRIREAG---GWVSRNGKLNDQLGVSR--- 5967
+
+Query: 246 YKVKYGYTDIDLLSAAKSKPIIAEPEI 272
+ +GY +DL+ A ++ P ++ I
+Sbjct: 5968 ---AFGY--VDLMPAVQAAPHVSHVAI 6033
+
+
+CPU time: 78.72 user secs. 0.85 sys. secs 79.57 total secs.
+
+ Database: Non-redundant GenBank+EMBL+DDBJ+PDB sequences
+ Posted date: Apr 16, 1998 9:38 AM
+ Number of letters in database: 677,679,054
+ Number of sequences in database: 336,723
+
+Lambda K H
+ 0.313 0.130 0.370
+
+Gapped
+Lambda K H
+ 0.270 0.0470 0.230
+
+
+Matrix: BLOSUM62
+Gap Penalties: Existence: 11, Extension: 1
+Number of Hits to DB: 374080624
+Number of Sequences: 336723
+Number of extensions: 5779396
+Number of successful extensions: 37522
+Number of sequences better than 10: 214
+Number of HSP's better than 10.0 without gapping: 32
+Number of HSP's successfully gapped in prelim test: 85
+Number of HSP's that attempted gapping in prelim test: 35679
+Number of HSP's gapped (non-prelim): 445
+length of query: 504
+length of database: 225893018
+effective HSP length: 62
+effective length of query: 442
+effective length of database: 205016192
+effective search space: 90617156864
+frameshift window, decay const: 50, 0.1
+T: 13
+A: 40
+X1: 16 ( 7.2 bits)
+X2: 38 (14.8 bits)
+X3: 64 (24.9 bits)
+S1: 42 (21.9 bits)
+S2: 74 (33.2 bits)
diff --git a/modules/t/converter.t b/modules/t/converter.t
index 85fecca2c8..f57f5c9448 100644
--- a/modules/t/converter.t
+++ b/modules/t/converter.t
@@ -4,11 +4,9 @@ use strict;
BEGIN {
$| = 1;
use Test;
- plan tests => 22;
+ plan tests => 36;
}
-use Bio::EnsEMBL::Utils::Converter;
-
END {
}
@@ -49,6 +47,8 @@ my $featurePair1 = new Bio::SeqFeature::FeaturePair(
-feature2 => $seqFeature2
);
+use Bio::EnsEMBL::Utils::Converter;
+
&test_SeqFeature;
&test_FeaturePair;
&test_hit;
@@ -125,9 +125,48 @@ sub test_FeaturePair{
}
-
+# 14 OKs
sub test_hit {
+ my $converter = new Bio::EnsEMBL::Utils::Converter(
+ -in => 'Bio::Search::HSP::GenericHSP',
+ -out => 'Bio::EnsEMBL::BaseAlignFeature',
+ -analysis => $ens_analysis,
+ -contig => $ens_contig
+ );
+
+ use Bio::SearchIO;
+ my $searchio = new Bio::SearchIO(
+ -format => 'blast',
+ -file => 't/converter.blast'
+ );
+ my @hsps = ();
+ while(my $result = $searchio->next_result){
+ while(my $hit = $result->next_hit){
+ while(my $hsp = $hit->next_hsp){
+ push @hsps, $hsp;
+ }
+ }
+ }
+ my @align_features = @{$converter->convert(\@hsps)};
+ my $align_feature = shift @align_features;
+ ok $align_feature->isa('Bio::EnsEMBL::BaseAlignFeature');
+ ok $align_feature->start, 1;
+ ok $align_feature->end, 504;
+ ok $align_feature->strand, 0;
+ ok $align_feature->hstart, 21;
+ ok $align_feature->hend, 1532;
+ ok $align_feature->cigar_string, '504M';
+
+ $align_feature = shift @align_features;
+ ok $align_feature->isa('Bio::EnsEMBL::BaseAlignFeature');
+ ok $align_feature->start, 64;
+ ok $align_feature->end, 324;
+ ok $align_feature->strand, 0;
+ ok $align_feature->hstart, 182;
+ ok $align_feature->hend, 844;
+ ok $align_feature->cigar_string, '29M18I22M11I20MD33M4I22M3I25M5I21MI33MD14M';
+
}
--
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