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Add hmmer2-text tests for hmmpfam multiple queries and hmmsearch

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commit 9d9bc22d91718023f0e11ae9896b8d15f065adcf 1 parent 1cdea7a
@bow bow authored
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1  Tests/Hmmer/README.txt
@@ -40,5 +40,6 @@ text_21_hmmpfam_001.out single query, two matches, bioperl's hmmpfam.out fil
text_22_hmmpfam_001.out single query, one match, bioperl's L77119.hmmer file
text_23_hmmpfam_001.out single query, multiple matches, bioperl's hmmpfam_cs.out file
text_23_hmmpfam_002.out single query, no match
+text_24_hmmpfam_001.out multiple queries
text_20_hmmsearch_001.out single query, multiple matches, bioperl's hmmsearch.out file
text_22_hmmsearch_001.out single query, multiple matches, bioperl's cysprot1b.hmmsearch file
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489 Tests/Hmmer/text_24_hmmpfam_001.out
@@ -0,0 +1,489 @@
+hmmpfam - search one or more sequences against HMM database
+HMMER 2.4i (December 2006)
+Copyright (C) 1992-2006 HHMI Janelia Farm
+Freely distributed under the GNU General Public License (GPL)
+- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+HMM file: /home/bow/db/hmmer/Pfam_fs
+Sequence file: mult.fasta
+- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+
+Query sequence: random_s00
+Accession: [none]
+Description: [none]
+
+Scores for sequence family classification (score includes all domains):
+Model Description Score E-value N
+-------- ----------- ----- ------- ---
+ [no hits above thresholds]
+
+Parsed for domains:
+Model Domain seq-f seq-t hmm-f hmm-t score E-value
+-------- ------- ----- ----- ----- ----- ----- -------
+ [no hits above thresholds]
+
+Alignments of top-scoring domains:
+ [no hits above thresholds]
+//
+
+Query sequence: gi|4885477|ref|NP_005359.1|
+Accession: [none]
+Description: myoglobin [Homo sapiens]
+
+Scores for sequence family classification (score includes all domains):
+Model Description Score E-value N
+-------- ----------- ----- ------- ---
+Globin Globin 129.8 5.8e-37 1
+tRNA-synt_1b tRNA synthetases class I (W and Y) 1.8 2.2 1
+Rotavirus_VP3 Rotavirus VP3 protein -1.2 7.9 1
+DTHCT DTHCT (NUC029) region 1.5 9.8 1
+
+Parsed for domains:
+Model Domain seq-f seq-t hmm-f hmm-t score E-value
+-------- ------- ----- ----- ----- ----- ----- -------
+Globin 1/1 7 143 .. 1 148 [] 129.8 5.8e-37
+DTHCT 1/1 101 106 .. 101 106 .] 1.5 9.8
+tRNA-synt_1b 1/1 120 137 .. 320 337 .] 1.8 2.2
+Rotavirus_VP3 1/1 134 147 .. 1 15 [. -1.2 7.9
+
+Alignments of top-scoring domains:
+Globin: domain 1 of 1, from 7 to 143: score 129.8, E = 5.8e-37
+ *->dkalvkasWgkvkgtdnreelGaealarlFkayPdtktyFpkfgdls
+ +++lv+ Wgkv++ +++ +G+e+l rlFk +P+t ++F kf+ l+
+ gi|4885477 7 EWQLVLNVWGKVEA--DIPGHGQEVLIRLFKGHPETLEKFDKFKHLK 51
+
+ sadaikgspkfkaHgkkVlaalgeavkhLgnddddgnlkaalkkLaarHa
+ s d++k s+++k+Hg++Vl alg ++k +g + a +k La +Ha
+ gi|4885477 52 SEDEMKASEDLKKHGATVLTALGGILKK------KGHHEAEIKPLAQSHA 95
+
+ erghvdpanFkllgeallIvvLaahlggeveftpevkaAWdkaldvvada
+ ++++++ ++ + ++e+++ +vL+++ +g +f +++++A++kal + +
+ gi|4885477 96 TKHKIPVKYLEFISECII-QVLQSKHPG--DFGADAQGAMNKALELFRKD 142
+
+ l<-*
+ +
+ gi|4885477 143 M 143
+
+DTHCT: domain 1 of 1, from 101 to 106: score 1.5, E = 9.8
+ *->pvKYLe<-*
+ pvKYLe
+ gi|4885477 101 PVKYLE 106
+
+tRNA-synt_1b: domain 1 of 1, from 120 to 137: score 1.8, E = 2.2
+ *->hggelKkaaaeavnalls<-*
+ h+g++ +a+ a+n++l+
+ gi|4885477 120 HPGDFGADAQGAMNKALE 137
+
+Rotavirus_VP3: domain 1 of 1, from 134 to 147: score -1.2, E = 7.9
+ *->MkVLaLFrrgvalnY<-*
+ k L LFr+++a+nY
+ gi|4885477 134 -KALELFRKDMASNY 147
+
+//
+
+Query sequence: gi|126362951:116-221
+Accession: [none]
+Description: leukocyte immunoglobulin-like receptor subfamily B member 1 isoform 2 precursor [Homo sapiens]
+
+Scores for sequence family classification (score includes all domains):
+Model Description Score E-value N
+-------- ----------- ----- ------- ---
+Pro-NT_NN Neurotensin/neuromedin N precursor 1.9 1.9 1
+ig Immunoglobulin domain 4.1 2.3 1
+
+Parsed for domains:
+Model Domain seq-f seq-t hmm-f hmm-t score E-value
+-------- ------- ----- ----- ----- ----- ----- -------
+Pro-NT_NN 1/1 22 48 .. 1 28 [. 1.9 1.9
+ig 1/1 23 84 .. 1 65 [] 4.1 2.3
+
+Alignments of top-scoring domains:
+Pro-NT_NN: domain 1 of 1, from 22 to 48: score 1.9, E = 1.9
+ *->maGmnlqLvCliLLAFssWsLCsDsEEd<-*
+ G n+ L C +AF +sLC + E++
+ gi|1263629 22 -SGGNVILQCDSQVAFDGFSLCKEGEDE 48
+
+ig: domain 1 of 1, from 23 to 84: score 4.1, E = 2.3
+ *->GesvtLtCsvsgfgppdvtvtWlrngk.lt.gvlvtssenngdstyq
+ G+ v L+C + ++++++g + ++ l + + +g+s +
+ gi|1263629 23 GGNVILQCDS---QVAFDGFSLCKEGEdEHpQCLNSQPHARGSSRAI 66
+
+ tsLtitnvtpeDggtYtCvv<-*
+ +++ +v+p+ Y+C++
+ gi|1263629 67 --FSVGPVSPSRRWWYRCYA 84
+
+//
+
+Query sequence: gi|22748937|ref|NP_065801.1|
+Accession: [none]
+Description: exportin-5 [Homo sapiens]
+
+Scores for sequence family classification (score includes all domains):
+Model Description Score E-value N
+-------- ----------- ----- ------- ---
+Xpo1 Exportin 1-like protein 170.1 5.1e-48 1
+Ssl1 Ssl1-like 8.7 0.00012 1
+IBN_N Importin-beta N-terminal domain 9.7 0.053 1
+XH XH domain 4.8 0.56 1
+Ni_hydr_CYTB Cytochrome b561 family 4.5 1.1 1
+Mic1 Colon cancer-associated protein Mic1- 3.3 1.7 1
+DNA_ligase_aden NAD-dependent DNA ligase adenylation 1.6 1.7 1
+FGGY_N FGGY family of carbohydrate kinases, 2.2 1.9 1
+DUF1098 Protein of unknown function (DUF1098) 3.3 2 1
+Pox_L5 Poxvirus L5 protein family 3.8 2 1
+Phage_holin_4 Holin family 3.0 2.3 1
+PTR2 POT family 1.1 3 1
+EAV_GS Equine arteritis virus small envelope 0.4 3.5 1
+VIRB2 VIRB2 type IV secretion protein 1.6 3.5 1
+SapB_1 Saposin-like type B, region 1 3.2 3.7 1
+DUF1177 Protein of unknown function (DUF1177) 0.3 3.7 1
+Trehalase Trehalase 0.4 3.8 1
+DUF1019 Protein of unknown function (DUF1019) 1.4 3.9 1
+Peptidase_S13 D-Ala-D-Ala carboxypeptidase 3 (S13) 0.5 4 1
+LCM Leucine carboxyl methyltransferase -0.4 5.1 1
+RRN3 RNA polymerase I specific transcripti -0.7 5.5 1
+dNK Deoxynucleoside kinase 1.1 6.1 1
+Transposase_5 Transposase 2.1 6.3 1
+ATP-grasp ATP-grasp domain 0.1 6.7 1
+Lys C-type lysozyme/alpha-lactalbumin fam 1.2 7.1 1
+Plant_TF Plant transcription factor 0.9 7.2 1
+Hydantoinase_B Hydantoinase B/oxoprolinase -1.4 7.6 1
+DUF1116 Protein of unknown function (DUF1116) -1.1 7.8 1
+Herpes_teg_N Herpesvirus tegument protein, N-termi 0.1 8.7 1
+KE2 KE2 family protein 1.6 9.1 1
+RVP_2 Retroviral aspartyl protease 0.1 9.1 1
+Rad50_zn_hook Rad50 zinc hook motif 2.2 9.2 2
+V-ATPase_H V-ATPase subunit H -1.3 9.6 1
+
+Parsed for domains:
+Model Domain seq-f seq-t hmm-f hmm-t score E-value
+-------- ------- ----- ----- ----- ----- ----- -------
+DUF1116 1/1 6 15 .. 405 414 .] -1.1 7.8
+SapB_1 1/1 9 27 .. 6 24 .. 3.2 3.7
+Rad50_zn_hook 1/2 21 47 .. 1 28 [. 0.8 22
+IBN_N 1/1 33 100 .. 1 85 [] 9.7 0.053
+dNK 1/1 103 120 .. 153 170 .] 1.1 6.1
+Xpo1 1/1 109 271 .. 1 178 [] 170.1 5.1e-48
+Peptidase_S13 1/1 186 195 .. 390 399 .] 0.5 4
+DUF1098 1/1 193 213 .. 32 54 .. 3.3 2
+KE2 1/1 198 213 .. 1 16 [. 1.6 9.1
+RRN3 1/1 198 211 .. 656 669 .] -0.7 5.5
+LCM 1/1 297 305 .. 322 330 .] -0.4 5.1
+FGGY_N 1/1 325 338 .. 249 262 .] 2.2 1.9
+Ni_hydr_CYTB 1/1 376 396 .. 197 218 .] 4.5 1.1
+Ssl1 1/1 404 411 .. 257 264 .] 8.7 0.00012
+DUF1177 1/1 445 465 .. 292 312 .] 0.3 3.7
+V-ATPase_H 1/1 491 517 .. 144 170 .. -1.3 9.6
+PTR2 1/1 497 513 .. 414 430 .] 1.1 3
+Mic1 1/1 502 528 .. 1 27 [. 3.3 1.7
+Hydantoinase_B 1/1 512 532 .. 308 328 .. -1.4 7.6
+Transposase_5 1/1 605 617 .. 1 13 [. 2.1 6.3
+Lys 1/1 641 652 .. 1 12 [. 1.2 7.1
+XH 1/1 645 666 .. 133 156 .] 4.8 0.56
+Trehalase 1/1 660 673 .. 1 14 [. 0.4 3.8
+ATP-grasp 1/1 661 677 .. 1 18 [. 0.1 6.7
+DNA_ligase_aden 1/1 767 787 .. 1 21 [. 1.6 1.7
+Phage_holin_4 1/1 789 810 .. 124 146 .] 3.0 2.3
+Rad50_zn_hook 2/2 790 811 .. 1 22 [. 1.3 16
+RVP_2 1/1 873 894 .. 46 67 .. 0.1 9.1
+VIRB2 1/1 956 991 .. 1 32 [. 1.6 3.5
+DUF1019 1/1 1019 1028 .. 1 12 [. 1.4 3.9
+Plant_TF 1/1 1027 1034 .. 132 139 .] 0.9 7.2
+EAV_GS 1/1 1049 1071 .. 1 27 [. 0.4 3.5
+Pox_L5 1/1 1110 1134 .. 1 26 [. 3.8 2
+Herpes_teg_N 1/1 1125 1133 .. 1 10 [. 0.1 8.7
+
+Alignments of top-scoring domains:
+DUF1116: domain 1 of 1, from 6 to 15: score -1.1, E = 7.8
+ *->leALAErvgv<-*
+ + AL+E+ ++
+ gi|2274893 6 VNALCEQLVK 15
+
+SapB_1: domain 1 of 1, from 9 to 27: score 3.2, E = 3.7
+ *->lCemvVkevenlLkdnkTq<-*
+ lCe++Vk v + n Tq
+ gi|2274893 9 LCEQLVKAVTVMMDPNSTQ 27
+
+Rad50_zn_hook: domain 1 of 2, from 21 to 47: score 0.8, E = 22
+ *->galesekaelkkaieeleeeesscCPvC<-*
+ + +s+ +++++a++ +ee + +CP+C
+ gi|2274893 21 MDPNSTQRYRLEALKFCEEFKE-KCPIC 47
+
+IBN_N: domain 1 of 1, from 33 to 100: score 9.7, E = 0.053
+ *->AEkqLeqlekqklPgFllaLlqIlansdtssdlqvRqlAalyLKNlI
+ A k +e++++ k P ++++ l+++ +t+ vR++++++L++ +
+ gi|2274893 33 ALKFCEEFKE-KCPICVPCGLRLA--EKTQ-VAIVRHFGLQILEHVV 75
+
+ trhWnshrkqggyeqrwlslpeeekeqIknnllnllgs<-*
+ + +Wn ++ ek ++kn++ +l++
+ gi|2274893 76 KFRWN-------------GMSRLEKVYLKNSVMELIAN 100
+
+dNK: domain 1 of 1, from 103 to 120: score 1.1, E = 6.1
+ *->lDfvedeediknkreeil<-*
+ l++ e+e++ik+++ +i+
+ gi|2274893 103 LNILEEENHIKDALSRIV 120
+
+Xpo1: domain 1 of 1, from 109 to 271: score 170.1, E = 5.1e-48
+ *->pkflrnKLalalaelakqewPsnWpsffpdlvsllsssssqkspnps
+ +++++ L+++++e++k+ewP++Wp+ + +l l++++ ++
+ gi|2274893 109 ENHIKDALSRIVVEMIKREWPQHWPDMLIELDTLSKQG-------ET 148
+
+ vcellLriLkvLpEEvfdqdfsrtrltqdrfnnrlkdllrsqDcmpqile
+ ++el++ iL++L E+v+ f ++l +r +++++++l+++ m++i++
+ gi|2274893 149 QTELVMFILLRLAEDVVT--F--QTLPPQR-RRDIQQTLTQN--MERIFS 191
+
+ lllqiLessrsthss.e.t.q.e.kAkqssellsatLkclgswlslgWip
+ +ll+ L+ +++++++ ++++++e+kA++++++ +a+L++l+++++ W++
+ gi|2274893 192 FLLNTLQENVNKYQQvKtDtSqEsKAQANCRVGVAALNTLAGYID--WVS 239
+
+ iglianvnpi.llnllfslLsgpesdpdlreaAveCL<-*
+ +++i + ++++ll++l+ lL + +l++ A+eCL
+ gi|2274893 240 MSHITA-ENCkLLEILCLLL----NEQELQLGAAECL 271
+
+Peptidase_S13: domain 1 of 1, from 186 to 195: score 0.5, E = 4
+ *->rklaFsfisN<-*
+ ++++Fsf++N
+ gi|2274893 186 MERIFSFLLN 195
+
+DUF1098: domain 1 of 1, from 193 to 213: score 3.3, E = 2
+ *->llnsLNalLsdTvAslIlnDtSe<-*
+ lln+L+++ ++ ++++++DtS+
+ gi|2274893 193 LLNTLQEN--VNKYQQVKTDTSQ 213
+
+KE2: domain 1 of 1, from 198 to 213: score 1.6, E = 9.1
+ *->QelinkfqqLqqqlek<-*
+ Qe++nk+qq + + ++
+ gi|2274893 198 QENVNKYQQVKTDTSQ 213
+
+RRN3: domain 1 of 1, from 198 to 211: score -0.7, E = 5.5
+ *->spnyiewSevkgdy<-*
+ ++n +++++vk+d
+ gi|2274893 198 QENVNKYQQVKTDT 211
+
+LCM: domain 1 of 1, from 297 to 305: score -0.4, E = 5.1
+ *->HYcLvhAss<-*
+ HY+L +A++
+ gi|2274893 297 HYILSAAQT 305
+
+FGGY_N: domain 1 of 1, from 325 to 338: score 2.2, E = 1.9
+ *->VvgGggDnaaaalG<-*
+ V +++g++ +a+lG
+ gi|2274893 325 VLCALGNQLCALLG 338
+
+Ni_hydr_CYTB: domain 1 of 1, from 376 to 396: score 4.5, E = 1.1
+ *->aAWAlfHhfvrkDnvllrMlpg<-*
+ +A ++H + ++D++ll+ +p+
+ gi|2274893 376 GA-LFRHEILSRDPLLLAIIPK 396
+
+Ssl1: domain 1 of 1, from 404 to 411: score 8.7, E = 0.00012
+ *->sLIkMGFP<-*
+ +L+kMGFP
+ gi|2274893 404 NLVKMGFP 411
+
+DUF1177: domain 1 of 1, from 445 to 465: score 0.3, E = 3.7
+ *->ElkeLeeklGPksnLqklkre<-*
+ E ++L +l Pk++ q ++ +
+ gi|2274893 445 EVMRLACRLDPKTSFQMAGEW 465
+
+V-ATPase_H: domain 1 of 1, from 491 to 517: score -1.3, E = 9.6
+ *->AKLAcfGpelvegsdLtyylnwLkeqL<-*
+ +++++f+p v + t++l++ ++q+
+ gi|2274893 491 SLCSVFSPSFVQWEAMTLFLESVITQM 517
+
+PTR2: domain 1 of 1, from 497 to 513: score 1.1, E = 3
+ *->lpssmkslwtllsaaas<-*
+ +ps++++++++l++ ++
+ gi|2274893 497 SPSFVQWEAMTLFLESV 513
+
+Mic1: domain 1 of 1, from 502 to 528: score 3.3, E = 1.7
+ *->emiapekYviaIlmeYLRSLnkaeiaa<-*
+ + +a ++++++++ R Ln++ei +
+ gi|2274893 502 QWEAMTLFLESVITQMFRTLNREEIPV 528
+
+Hydantoinase_B: domain 1 of 1, from 512 to 532: score -1.4, E = 7.6
+ *->savlYvlrtlvgpDiPlNdGc<-*
+ s++ ++rtl + iP+NdG+
+ gi|2274893 512 SVITQMFRTLNREEIPVNDGI 532
+
+Transposase_5: domain 1 of 1, from 605 to 617: score 2.1, E = 6.3
+ *->dRrIlrvvredPr<-*
+ ++ I++++r +P+
+ gi|2274893 605 CSSIIKMCRDYPQ 617
+
+Lys: domain 1 of 1, from 641 to 652: score 1.2, E = 7.1
+ *->KvftRCeLareL<-*
+ +++++C+L ++L
+ gi|2274893 641 TQMEKCALMEAL 652
+
+XH: domain 1 of 1, from 645 to 666: score 4.8, E = 0.56
+ *->KATLkEvvdfllniRqlkalkRkR<-*
+ K+ L+E ++ ++n q k+ R++
+ gi|2274893 645 KCALMEALVLISN--QFKNYERQK 666
+
+Trehalase: domain 1 of 1, from 660 to 673: score 0.4, E = 3.8
+ *->klfpDsKtFVDmal<-*
+ k + ++K F+++ +
+ gi|2274893 660 KNYERQKVFLEELM 673
+
+ATP-grasp: domain 1 of 1, from 661 to 677: score 0.1, E = 6.7
+ *->DRlvqkellAkelGlptp<-*
+ + ++qk +l +el +p++
+ gi|2274893 661 NYERQKVFL-EELMAPVA 677
+
+DNA_ligase_aden: domain 1 of 1, from 767 to 787: score 1.6, E = 1.7
+ *->eeaqqeieeLrelirkydyeY<-*
+ e++ +++++L +lir+++ +Y
+ gi|2274893 767 EQILKLLDNLLALIRTHNTLY 787
+
+Phage_holin_4: domain 1 of 1, from 789 to 810: score 3.0, E = 2.3
+ *->PkemlldiletLknktkqlkked<-*
+ P eml+++ e + ++++ l++e+
+ gi|2274893 789 P-EMLAKMAEPFTKALDMLDAEK 810
+
+Rad50_zn_hook: domain 2 of 2, from 790 to 811: score 1.3, E = 16
+ *->galesekaelkkaieeleeees<-*
+ ++l+ + + + ka+++l+ e+s
+ gi|2274893 790 EMLAKMAEPFTKALDMLDAEKS 811
+
+RVP_2: domain 1 of 1, from 873 to 894: score 0.1, E = 9.1
+ *->ISqaFVgrHglpleaLrtPllV<-*
+ +S aFV +++p ++Lr l+V
+ gi|2274893 873 LSSAFVNLNNIPDYRLRPMLRV 894
+
+VIRB2: domain 1 of 1, from 956 to 991: score 1.6, E = 3.5
+ *->msknklrriiaivlmalataivls....efsyapaA<-*
+ m++++l r+ +m l t+ ++s+++ + s+ap+A
+ gi|2274893 956 MLEEQLVRMLTREVMDLITVCCVSkkgaDHSSAPPA 991
+
+DUF1019: domain 1 of 1, from 1019 to 1028: score 1.4, E = 3.9
+ *->MKIkhEhIreaL<-*
+ M khE ++ aL
+ gi|2274893 1019 M--KHEDVCTAL 1028
+
+Plant_TF: domain 1 of 1, from 1027 to 1034: score 0.9, E = 7.2
+ *->AVlvsAFn<-*
+ A l++AFn
+ gi|2274893 1027 ALLITAFN 1034
+
+EAV_GS: domain 1 of 1, from 1049 to 1071: score 0.4, E = 3.5
+ *->FsflCylHWLLLLcfFsGsLLPsavAW<-*
+ s lC W LL + sG LL av W
+ gi|2274893 1049 -SQLC---WPLLKQVLSGTLLADAVTW 1071
+
+Pox_L5: domain 1 of 1, from 1110 to 1134: score 3.8, E = 2
+ *->ElnmaFsptkkvpnDPIdqlvartrL<-*
+ E+++ + + +D++dq+ + + L
+ gi|2274893 1110 EIRAVMEQIPEIQKDSLDQF-DCKLL 1134
+
+Herpes_teg_N: domain 1 of 1, from 1125 to 1133: score 0.1, E = 8.7
+ *->StnQadDckf<-*
+ S +Q+ Dck+
+ gi|2274893 1125 SLDQF-DCKL 1133
+
+//
+
+Query sequence: gi|125490392|ref|NP_038661.2|
+Accession: [none]
+Description: POU domain, class 5, transcription factor 1 isoform 1 [Mus musculus]
+
+Scores for sequence family classification (score includes all domains):
+Model Description Score E-value N
+-------- ----------- ----- ------- ---
+Pou Pou domain - N-terminal to homeobox d 171.2 2.4e-48 1
+Homeobox Homeobox domain 86.7 6.5e-23 1
+HTH_3 Helix-turn-helix 7.5 0.33 1
+WSC WSC domain 2.1 1.5 1
+ComC COMC family 3.4 2.3 1
+CBM_1 Fungal cellulose binding domain 3.3 3.6 1
+Peptidase_M29 Thermophilic metalloprotease (M29) -2.1 4.4 1
+DUF1690 Protein of Unknown function (DUF1690) 1.1 4.5 1
+DUF137 Protein of unknown function DUF137 1.0 4.7 1
+DASH_Duo1 DASH complex subunit Duo1 2.3 5.7 1
+TFIIB Transcription factor TFIIB repeat 2.6 6.1 1
+DUF1392 Protein of unknown function (DUF1392) 0.8 6.7 1
+
+Parsed for domains:
+Model Domain seq-f seq-t hmm-f hmm-t score E-value
+-------- ------- ----- ----- ----- ----- ----- -------
+WSC 1/1 59 67 .. 80 87 .] 2.1 1.5
+CBM_1 1/1 61 73 .. 1 13 [. 3.3 3.6
+Pou 1/1 131 205 .. 1 78 [] 171.2 2.4e-48
+ComC 1/1 132 145 .. 1 20 [. 3.4 2.3
+Peptidase_M29 1/1 132 145 .. 1 14 [. -2.1 4.4
+DASH_Duo1 1/1 133 141 .. 1 9 [. 2.3 5.7
+DUF1690 1/1 137 147 .. 151 161 .] 1.1 4.5
+HTH_3 1/1 146 166 .. 1 25 [. 7.5 0.33
+DUF137 1/1 197 213 .. 164 180 .. 1.0 4.7
+Homeobox 1/1 224 280 .. 1 57 [] 86.7 6.5e-23
+DUF1392 1/1 248 269 .. 127 164 .] 0.8 6.7
+TFIIB 1/1 253 268 .. 1 19 [. 2.6 6.1
+
+Alignments of top-scoring domains:
+WSC: domain 1 of 1, from 59 to 67: score 2.1, E = 1.5
+ *->p.pseiCGG<-*
+ p+++e CGG
+ gi|1254903 59 PpAYEFCGG 67
+
+CBM_1: domain 1 of 1, from 61 to 73: score 3.3, E = 3.6
+ *->vygQCGGigysGp<-*
+ +y+ CGG+ y Gp
+ gi|1254903 61 AYEFCGGMAYCGP 73
+
+Pou: domain 1 of 1, from 131 to 205: score 171.2, E = 2.4e-48
+ *->deatdleeLEkFAkeFKqRRIkLGyTQadVGlALgalygPGvnafSQ
+ d+++ ++eLE+FAk +Kq+RI+LGyTQadVGl+Lg l+g ++fSQ
+ gi|1254903 131 DMKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFG---KVFSQ 174
+
+ tTICRFEaLqLSfKNmcKLKPlLekWLeeAE<-*
+ tTICRFEaLqLS KNmcKL+PlLekW+eeA+
+ gi|1254903 175 TTICRFEALQLSLKNMCKLRPLLEKWVEEAD 205
+
+ComC: domain 1 of 1, from 132 to 145: score 3.4, E = 2.3
+ *->MKntvkkkllkkeLeqFkeL<-*
+ MK ++k eLeqF L
+ gi|1254903 132 MKALQK------ELEQFAKL 145
+
+Peptidase_M29: domain 1 of 1, from 132 to 145: score -2.1, E = 4.4
+ *->MdaFkkeLekyAeL<-*
+ M a +keLe +A L
+ gi|1254903 132 MKALQKELEQFAKL 145
+
+DASH_Duo1: domain 1 of 1, from 133 to 141: score 2.3, E = 5.7
+ *->aaLqkELeq<-*
+ +aLqkELeq
+ gi|1254903 133 KALQKELEQ 141
+
+DUF1690: domain 1 of 1, from 137 to 147: score 1.1, E = 4.5
+ *->eEvEqFKklvr<-*
+ +E EqF+kl++
+ gi|1254903 137 KELEQFAKLLK 147
+
+HTH_3: domain 1 of 1, from 146 to 166: score 7.5, E = 0.33
+ *->lkelRkkkelglsqeeLAeklGskv<-*
+ lk++R lg++q+++ lG v
+ gi|1254903 146 LKQKRI--TLGYTQADVGLTLG--V 166
+
+DUF137: domain 1 of 1, from 197 to 213: score 1.0, E = 4.7
+ *->LeeIVEnyDNkKnLkEv<-*
+ Le+ VE+ DN++nL+E+
+ gi|1254903 197 LEKWVEEADNNENLQEI 213
+
+Homeobox: domain 1 of 1, from 224 to 280: score 86.7, E = 6.5e-23
+ *->rrkRTtftpeQleeLEkeFqknrYPsreeReeLAkkLgLterqVkvW
+ +rkRT++ + + LE +F k+++Ps +++ ++A++LgL++++V+vW
+ gi|1254903 224 KRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVW 270
+
+ FQNRRaKwKk<-*
+ F+NRR+K K+
+ gi|1254903 271 FCNRRQKGKR 280
+
+DUF1392: domain 1 of 1, from 248 to 269: score 0.8, E = 6.7
+ *->PtLsqtttEGlCIFPrssqGnkmpnRfsLvrerDLVrV<-*
+ P+L q+t +n++ L e+D VrV
+ gi|1254903 248 PSLQQITH--------------IANQLGL--EKDVVRV 269
+
+TFIIB: domain 1 of 1, from 253 to 268: score 2.6, E = 6.1
+ *->ikrfadaLeLpeKkikVad<-*
+ i+++a +L+L + V++
+ gi|1254903 253 ITHIANQLGLEK---DVVR 268
+
+//
View
265 Tests/test_SearchIO_hmmer2_text.py
@@ -1,16 +1,22 @@
# Copyright 2012 by Kai Blin.
+# Revisions copyright 2012 by Wibowo Arindrarto
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import unittest
from os import path
-from Bio.SearchIO import parse
+
+from Bio.SearchIO import parse, read
+
class HmmpfamTests(unittest.TestCase):
+
+ fmt = 'hmmer2-text'
+
def test_hmmpfam_21(self):
"""Test parsing hmmpfam 2.1 file (text_21_hmmpfam_001.out)"""
- results = parse(path.join("Hmmer", "text_21_hmmpfam_001.out"), "hmmer2-text")
+ results = parse(path.join("Hmmer", "text_21_hmmpfam_001.out"), self.fmt)
res = results.next()
self.assertEqual('roa1_drome', res.id)
self.assertEqual('<unknown description>', res.description)
@@ -59,7 +65,7 @@ def test_hmmpfam_21(self):
def test_hmmpfam_22(self):
"""Test parsing hmmpfam 2.2 file (text_22_hmmpfam_001.out)"""
- results = parse(path.join("Hmmer", "text_22_hmmpfam_001.out"), "hmmer2-text")
+ results = parse(path.join("Hmmer", "text_22_hmmpfam_001.out"), self.fmt)
res = results.next()
self.assertEqual('gi|1522636|gb|AAC37060.1|', res.id)
self.assertEqual('M. jannaschii predicted coding region MJECS02 [Methanococcus jannaschii]', res.description)
@@ -95,7 +101,7 @@ def test_hmmpfam_22(self):
def test_hmmpfam_23(self):
"""Test parsing hmmpfam 2.3 file (text_23_hmmpfam_001.out)"""
- results = parse(path.join("Hmmer", "text_23_hmmpfam_001.out"), "hmmer2-text")
+ results = parse(path.join("Hmmer", "text_23_hmmpfam_001.out"), self.fmt)
res = results.next()
self.assertEqual('gi|90819130|dbj|BAE92499.1|', res.id)
self.assertEqual('glutamate synthase [Porphyra yezoensis]', res.description)
@@ -140,7 +146,8 @@ def test_hmmpfam_23(self):
self.assertAlmostEqual(9e-255, hsp.evalue)
def test_hmmpfam_23_no_match(self):
- results = parse(path.join("Hmmer", "text_23_hmmpfam_002.out"), "hmmer2-text")
+ """Test parsing hmmpfam 2.3 file (text_23_hmmpfam_002.out)"""
+ results = parse(path.join("Hmmer", "text_23_hmmpfam_002.out"), self.fmt)
res = results.next()
self.assertEqual('SEQ0001', res.id)
@@ -151,6 +158,254 @@ def test_hmmpfam_23_no_match(self):
self.assertEqual('SEQ0002', res.id)
self.assertEqual(0, len(res.hits))
+ def test_hmmpfam_24(self):
+ """Test parsing hmmpfam 2.4 file (text_24_hmmpfam_001.out)"""
+ results = list(parse(path.join("Hmmer", "text_24_hmmpfam_001.out"), self.fmt))
+ self.assertEqual(3, len(results))
+
+ # first qresult
+ res = results[0]
+ self.assertEqual('random_s00', res.id)
+ self.assertEqual('[none]', res.accession)
+ self.assertEqual('[none]', res.description)
+ self.assertEqual('hmmpfam', res.program)
+ self.assertEqual('2.4i', res.version)
+ self.assertEqual('/home/bow/db/hmmer/Pfam_fs', res.target)
+ self.assertEqual(0, len(res))
+
+ # last qresult
+ res = results[-1]
+ self.assertEqual('gi|22748937|ref|NP_065801.1|', res.id)
+ self.assertEqual('[none]', res.accession)
+ self.assertEqual('exportin-5 [Homo sapiens]', res.description)
+ self.assertEqual('hmmpfam', res.program)
+ self.assertEqual('2.4i', res.version)
+ self.assertEqual('/home/bow/db/hmmer/Pfam_fs', res.target)
+ self.assertEqual(33, len(res))
+
+ # last qresult, first hit
+ hit = res[0]
+ self.assertEqual('Xpo1', hit.id)
+ self.assertEqual('Exportin 1-like protein', hit.description)
+ self.assertAlmostEqual(170.1, hit.bitscore)
+ self.assertAlmostEqual(5.1e-48, hit.evalue)
+ self.assertEqual(1, hit.domain_obs_num)
+ self.assertEqual(1, len(hit))
+
+ # last qresult, first hit, first hsp
+ hsp = hit[0]
+ self.assertEqual(1, hsp.domain_index)
+ self.assertAlmostEqual(170.1, hsp.bitscore)
+ self.assertAlmostEqual(5.1e-148, hsp.evalue)
+ self.assertEqual(108, hsp.query_start)
+ self.assertEqual(271, hsp.query_end)
+ self.assertEqual('..', hsp.query_endtype)
+ self.assertEqual('ENHIKDALSRIVVEMIKREWPQHWPDMLIELDTLSKQG--',
+ str(hsp.query.seq)[:40])
+ self.assertEqual('WVSMSHITA-ENCkLLEILCLLL----NEQELQLGAAECL',
+ str(hsp.query.seq)[-40:])
+ self.assertEqual(0, hsp.hit_start)
+ self.assertEqual(178, hsp.hit_end)
+ self.assertEqual('[]', hsp.hit_endtype)
+ self.assertEqual('pkflrnKLalalaelakqewPsnWpsffpdlvsllsssss',
+ str(hsp.hit.seq)[:40])
+ self.assertEqual('Wipiglianvnpi.llnllfslLsgpesdpdlreaAveCL',
+ str(hsp.hit.seq)[-40:])
+
+ # last qresult, second from last hit
+ hit = res[-2]
+ self.assertEqual('Rad50_zn_hook', hit.id)
+ self.assertEqual('Rad50 zinc hook motif', hit.description)
+ self.assertAlmostEqual(2.2, hit.bitscore)
+ self.assertAlmostEqual(9.2, hit.evalue)
+ self.assertEqual(2, hit.domain_obs_num)
+ self.assertEqual(2, len(hit))
+
+ # last qresult, second from last hit, first hsp
+ hsp = hit[0]
+ self.assertEqual(1, hsp.domain_index)
+ self.assertAlmostEqual(0.8, hsp.bitscore)
+ self.assertAlmostEqual(22, hsp.evalue)
+ self.assertEqual(20, hsp.query_start)
+ self.assertEqual(47, hsp.query_end)
+ self.assertEqual('..', hsp.query_endtype)
+ self.assertEqual('MDPNSTQRYRLEALKFCEEFKE-KCPIC', str(hsp.query.seq))
+ self.assertEqual(0, hsp.hit_start)
+ self.assertEqual(28, hsp.hit_end)
+ self.assertEqual('[.', hsp.hit_endtype)
+ self.assertEqual('galesekaelkkaieeleeeesscCPvC', str(hsp.hit.seq))
+
+ # last qresult, second from last hit, last hsp
+ hsp = hit[-1]
+ self.assertEqual(2, hsp.domain_index)
+ self.assertAlmostEqual(1.3, hsp.bitscore)
+ self.assertAlmostEqual(16, hsp.evalue)
+ self.assertEqual(789, hsp.query_start)
+ self.assertEqual(811, hsp.query_end)
+ self.assertEqual('..', hsp.query_endtype)
+ self.assertEqual('EMLAKMAEPFTKALDMLDAEKS', str(hsp.query.seq))
+ self.assertEqual(0, hsp.hit_start)
+ self.assertEqual(22, hsp.hit_end)
+ self.assertEqual('[.', hsp.hit_endtype)
+ self.assertEqual('galesekaelkkaieeleeees', str(hsp.hit.seq))
+
+
+class HmmsearchTests(unittest.TestCase):
+
+ fmt = 'hmmer2-text'
+
+ def test_hmmsearch_20(self):
+ """Test parsing hmmsearch 2.0 file (text_20_hmmsearch_001.out)"""
+ res = read(path.join("Hmmer", "text_20_hmmsearch_001.out"), self.fmt)
+
+ # first query
+ self.assertEqual('SEED', res.id)
+ self.assertEqual('<unknown description>', res.description)
+ self.assertEqual('hmmsearch', res.program)
+ self.assertEqual('2.0', res.version)
+ self.assertEqual('HMM.dbtemp.29591', res.target)
+ self.assertEqual(751, len(res))
+
+ # first hit
+ hit = res[0]
+ self.assertEqual('PAB2_ARATH', hit.id)
+ self.assertEqual('P42731 POLYADENYLATE-BINDING PROTEIN 2 (PO', hit.description)
+ self.assertAlmostEqual(393.8, hit.bitscore)
+ self.assertAlmostEqual(6.1e-114, hit.evalue)
+ self.assertEqual(4, hit.domain_obs_num)
+ self.assertEqual(4, len(hit))
+
+ # first hit, first hsp
+ hsp = hit[0]
+ self.assertEqual('SEED', hsp.query_id)
+ self.assertEqual('<unknown description>', hsp.query_description)
+ self.assertEqual('PAB2_ARATH', hsp.hit_id)
+ self.assertEqual('P42731 POLYADENYLATE-BINDING PROTEIN 2 (PO', hsp.hit_description)
+ self.assertEqual(3, hsp.domain_index)
+ self.assertAlmostEqual(109.1, hsp.bitscore)
+ self.assertAlmostEqual(3e-28, hsp.evalue)
+ self.assertEqual(0, hsp.query_start)
+ self.assertEqual(77, hsp.query_end)
+ self.assertEqual('[]', hsp.query_endtype)
+ self.assertEqual(216, hsp.hit_start)
+ self.assertEqual(287, hsp.hit_end)
+ self.assertEqual('..', hsp.hit_endtype)
+
+ # first hit, last hsp
+ hsp = hit[-1]
+ self.assertEqual('SEED', hsp.query_id)
+ self.assertEqual('<unknown description>', hsp.query_description)
+ self.assertEqual('PAB2_ARATH', hsp.hit_id)
+ self.assertEqual('P42731 POLYADENYLATE-BINDING PROTEIN 2 (PO', hsp.hit_description)
+ self.assertEqual(1, hsp.domain_index)
+ self.assertAlmostEqual(92.1, hsp.bitscore)
+ self.assertAlmostEqual(3.9e-23, hsp.evalue)
+ self.assertEqual(0, hsp.query_start)
+ self.assertEqual(77, hsp.query_end)
+ self.assertEqual('[]', hsp.query_endtype)
+ self.assertEqual(37, hsp.hit_start)
+ self.assertEqual(109, hsp.hit_end)
+ self.assertEqual('..', hsp.hit_endtype)
+
+ # last hit
+ hit = res[-1]
+ self.assertEqual('O00369', hit.id)
+ self.assertEqual('O00369 L1 ELEMENT L1.20 P40 AND PUTATIVE P', hit.description)
+ self.assertAlmostEqual(-23.8, hit.bitscore)
+ self.assertAlmostEqual(9.9e+02, hit.evalue)
+ self.assertEqual(1, hit.domain_obs_num)
+ self.assertEqual(1, len(hit))
+
+ # last hit, first hsp
+ hsp = hit[0]
+ self.assertEqual('SEED', hsp.query_id)
+ self.assertEqual('<unknown description>', hsp.query_description)
+ self.assertEqual('O00369', hsp.hit_id)
+ self.assertEqual('O00369 L1 ELEMENT L1.20 P40 AND PUTATIVE P', hsp.hit_description)
+ self.assertEqual(1, hsp.domain_index)
+ self.assertAlmostEqual(-23.8, hsp.bitscore)
+ self.assertAlmostEqual(9.9e+02, hsp.evalue)
+ self.assertEqual(0, hsp.query_start)
+ self.assertEqual(77, hsp.query_end)
+ self.assertEqual('[]', hsp.query_endtype)
+ self.assertEqual(180, hsp.hit_start)
+ self.assertEqual(249, hsp.hit_end)
+ self.assertEqual('..', hsp.hit_endtype)
+
+ def test_hmmsearch_22(self):
+ """Test parsing hmmsearch 2.2 file (text_22_hmmsearch_001.out)"""
+ res = read(path.join("Hmmer", "text_22_hmmsearch_001.out"), self.fmt)
+
+ # first query
+ self.assertEqual('Peptidase_C1', res.id)
+ self.assertEqual('Papain family cysteine protease', res.description)
+ self.assertEqual('hmmsearch', res.program)
+ self.assertEqual('2.2g', res.version)
+ self.assertEqual('cysprot1b.fa', res.target)
+ self.assertEqual(4, len(res))
+
+ # first hit
+ hit = res[0]
+ self.assertEqual('CATL_RAT', hit.id)
+ self.assertEqual('<unknown description>', hit.description)
+ self.assertAlmostEqual(449.4, hit.bitscore)
+ self.assertAlmostEqual(2e-135, hit.evalue)
+ self.assertEqual(1, hit.domain_obs_num)
+ self.assertEqual(1, len(hit))
+
+ # first hit, first hsp
+ hsp = hit[0]
+ self.assertEqual('Peptidase_C1', hsp.query_id)
+ self.assertEqual('Papain family cysteine protease', hsp.query_description)
+ self.assertEqual('CATL_RAT', hit.id)
+ self.assertEqual('<unknown description>', hit.description)
+ self.assertEqual(1, hsp.domain_index)
+ self.assertAlmostEqual(449.4, hsp.bitscore)
+ self.assertAlmostEqual(2e-135, hsp.evalue)
+ self.assertEqual(0, hsp.query_start)
+ self.assertEqual(337, hsp.query_end)
+ self.assertEqual('[]', hsp.query_endtype)
+ self.assertEqual('lPesfDWReWkggaVtpVKdQGiqCGSCWAFSavgalEgr', str(hsp.query.seq)[:40])
+ self.assertEqual('IVKNSWGtdWGEnGYfriaRgknksgkneCGIaseasypi',str(hsp.query.seq)[-40:])
+ self.assertEqual(337, len(hsp.query.seq))
+ self.assertEqual(113, hsp.hit_start)
+ self.assertEqual(332, hsp.hit_end)
+ self.assertEqual('..', hsp.hit_endtype)
+ self.assertEqual('IPKTVDWRE-KG-CVTPVKNQG-QCGSCWAFSASGCLEGQ', str(hsp.hit.seq)[:40])
+ self.assertEqual('LVKNSWGKEWGMDGYIKIAKDRN----NHCGLATAASYPI',str(hsp.hit.seq)[-40:])
+ self.assertEqual(337, len(hsp.hit.seq))
+
+ # last hit
+ hit = res[-1]
+ self.assertEqual('PAPA_CARPA', hit.id)
+ self.assertEqual('<unknown description>', hit.description)
+ self.assertAlmostEqual(337.7, hit.bitscore)
+ self.assertAlmostEqual(9e-102, hit.evalue)
+ self.assertEqual(1, hit.domain_obs_num)
+ self.assertEqual(1, len(hit))
+
+ # last hit, last hsp
+ hsp = hit[-1]
+ self.assertEqual('Peptidase_C1', hsp.query_id)
+ self.assertEqual('Papain family cysteine protease', hsp.query_description)
+ self.assertEqual('PAPA_CARPA', hit.id)
+ self.assertEqual('<unknown description>', hit.description)
+ self.assertEqual(1, hsp.domain_index)
+ self.assertAlmostEqual(337.7, hsp.bitscore)
+ self.assertAlmostEqual(9e-102, hsp.evalue)
+ self.assertEqual(0, hsp.query_start)
+ self.assertEqual(337, hsp.query_end)
+ self.assertEqual('[]', hsp.query_endtype)
+ self.assertEqual('lPesfDWReWkggaVtpVKdQGiqCGSCWAFSavgalEgr', str(hsp.query.seq)[:40])
+ self.assertEqual('IVKNSWGtdWGEnGYfriaRgknksgkneCGIaseasypi',str(hsp.query.seq)[-40:])
+ self.assertEqual(337, len(hsp.query.seq))
+ self.assertEqual(133, hsp.hit_start)
+ self.assertEqual(343, hsp.hit_end)
+ self.assertEqual('..', hsp.hit_endtype)
+ self.assertEqual('IPEYVDWRQ-KG-AVTPVKNQG-SCGSCWAFSAVVTIEGI', str(hsp.hit.seq)[:40])
+ self.assertEqual('LIKNSWGTGWGENGYIRIKRGTGNS-YGVCGLYTSSFYPV',str(hsp.hit.seq)[-40:])
+ self.assertEqual(337, len(hsp.hit.seq))
+
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
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