Test case for row of dashes in plain text BLAST

Based on GitHub issue #554 reported by @breviata

Tests/Blast/README.txt

@@ -5,6 +5,9 @@ This directory contains various data files for testing the
 BLAST-related code in Biopython. All files are grouped by BLAST
 release version, from the most recent first.
 
+BLAST+ 2.2.30
+-------------
+text_2230_blastp_001         single query, match with full line of dashes
 
 BLAST 2.2.28+
 -------------

Tests/Blast/text_2230_blastp_001.txt

@@ -0,0 +1,214 @@
+BLASTP 2.2.30+
+
+
+Reference: Stephen F. Altschul, 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.
+
+
+Reference for composition-based statistics: Alejandro A. Schaffer,
+L. Aravind, Thomas L. Madden, Sergei Shavirin, John L. Spouge, Yuri
+I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001),
+"Improving the accuracy of PSI-BLAST protein database searches with
+composition-based statistics and other refinements", Nucleic Acids
+Res. 29:2994-3005.
+
+
+
+Database: subject.fasta
+           1 sequences; 1,853 total letters
+
+
+
+Query= TR11080zzzc0_g2_i2_0
+
+Length=1691
+                                                                      Score     E
+Sequences producing significant alignments:                          (Bits)  Value
+
+  gi|308468219|ref|XP_003096353.1| CRE-AMA-1 protein [Caenorhabdi...   1901   0.0  
+
+
+> gi|308468219|ref|XP_003096353.1| CRE-AMA-1 protein [Caenorhabditis 
+remanei]
+Length=1853
+
+ Score =  1901 bits (4924),  Expect = 0.0, Method: Compositional matrix adjust.
+ Identities = 975/1817 (54%), Positives = 1275/1817 (70%), Gaps = 149/1817 (8%)
+
+Query  11    VKEVSYLQFGVLSPDEMKEMSVCKIEFPQTYENGVPKEGGLSDPRLGTMDRTQLCRTCNS  70
+             ++ V  +QFG+L P+E+K MSV  +EFP+ YENG PK GGL DPR G +DR   C TC  
+Sbjct  12    LRTVCRVQFGILGPEEIKRMSVAHVEFPEIYENGKPKLGGLMDPRQGVIDRRGRCMTCAG  71
+
+Query  71    DARECPGHFGHIVLAKPMYHVGFLPFVLKILRCVCFFCSKLLVDSNDPRLKSILAQ--NH  128
+             +  +CPGHF H+ LAKP++H+GFL   LKILRCVCF+C +LL+D ++PR+  IL +   +
+Sbjct  72    NLTDCPGHFAHLELAKPVFHIGFLTKSLKILRCVCFYCGRLLIDKSNPRVIDILKKTSGN  131
+
+Query  129   HRRRIQSMMNLCRTKKICE-AGDDADDLAEHETEP-EKQRKPHGGCGNFQPNITKDGLRL  186
+              ++R+  + +LC++K +CE A +  + L +   +P   ++K   GCG +QP+  + G+ +
+Sbjct  132   AKKRLALIYDLCKSKSVCEGAAEKEEGLPDDVDDPMSGEKKIPAGCGRYQPSYRRVGIDI  191
+
+Query  187   LAEFK-HVSDESIEKKQVLSAEKVYEILKKITDEDCRMMGLDPKFARPDWMVLTIFPVPP  245
+              AE+K +V++++ E+K +L+AE+V E+ K+ITDED  ++G+DP+FARP+WM+ T+ PVPP
+Sbjct  192   NAEWKKNVNEDTQERKIMLTAERVLEVFKQITDEDILVIGMDPQFARPEWMICTVLPVPP  251
+
+Query  246   PPVRPSILMDSSSRGEDDLTCKLADIIKSNHALRQQELSGSPAHIITEFTQILQYHVATY  305
+               VRP+++   S++ +DDLT KL+DIIK+N  L++ E +G+ AH++T+  ++LQYHVAT 
+Sbjct  252   LAVRPAVVTFGSAKNQDDLTHKLSDIIKTNQQLQRNEANGAAAHVLTDDVRLLQYHVATL  311
+
+Query  306   LDNELPGLPPAIQRSGRPLKSIRQRLRGKNGRVRGNLMGKRVDFSARTVITPDANIGIDE  365
+             +DN +PGLP A Q+ GRPLKSI+QRL+GK GR+RGNLMGKRVDFSARTVIT D N+ ID 
+Sbjct  312   VDNCIPGLPTATQKGGRPLKSIKQRLKGKEGRIRGNLMGKRVDFSARTVITADPNLPIDT  371
+
+Query  366   VGVPRSIALNLTFPDIVTPLNIDRMYEYVRNGPREYPGAKYIVRDDGSRLDLRYIRKPSD  425
+             VGVPR+IA NLTFP+IVTP N+D++ E V  G  +YPGAKYI+R++G+R+DLRY  + +D
+Sbjct  372   VGVPRTIAQNLTFPEIVTPFNVDKLQELVNRGDTQYPGAKYIIRENGARVDLRYHPRAAD  431
+
+Query  426   LHLDYGYKVERHLRDGDFVLFNRQPSLHKMSIMAHRVKLLPFSTFRLNLSVTSPYNADFD  485
+             LHL  GY+VERH++DGD ++FNRQP+LHKMS+M HRVK+LP+STFR+NLSVTSPYNADFD
+Sbjct  432   LHLQPGYRVERHMKDGDIIVFNRQPTLHKMSMMGHRVKILPWSTFRMNLSVTSPYNADFD  491
+
+Query  486   GDEMNLHVPQSLEAIAEAQELMLVPRQIISPQANKPVIGLVQDVLIGARNMTKRDTFIEL  545
+             GDEMNLH+PQSLE  AE +E+ +VPRQ+I+PQANKPV+G+VQD L   R MTKRD FI+ 
+Sbjct  492   GDEMNLHLPQSLETRAEIEEICMVPRQLITPQANKPVMGIVQDTLCAVRMMTKRDVFIDW  551
+
+Query  546   DTVMNILMCTENFDGRIPMPAILKPKKLWTGKQLFSLILP-NVNLIRFTSTHPDGE----  600
+               +M++LM    +DG++P PAILKPK LWTGKQLFSLI+P NVN++R  STHPD E    
+Sbjct  552   SFMMDLLMYLPTWDGKVPQPAILKPKPLWTGKQLFSLIIPGNVNVLRTHSTHPDSEDSGP  611
+
+Query  601   YTHISPGDTKVLIENGDLISGILCKRTLGTSGGSLIHIICNEHGHDTARLFLNQAQKVVN  660
+             Y  ISPGDTKVLIE+G+L+SGI+C +T+G S G+L+H++  E G++ A  F +  Q V+N
+Sbjct  612   YKWISPGDTKVLIEHGELLSGIVCSKTVGKSAGNLLHVVTLELGYEIAANFYSHIQTVIN  671
+
+Query  661   NWLVNIGFSIGIGDTIADEATMEQINKTIASAKNQVKELVLQAQQNILECQPGRTLHESF  720
+              WL+ +G +IGIGDTIAD AT   I  TI  AK  V +++ +A  + LE  PG TL ++F
+Sbjct  672   AWLLRVGHTIGIGDTIADHATYLDIQNTIKKAKQDVVDIIEKAHNDDLEPTPGNTLRQTF  731
+
+Query  721   ENKVNKVLNTARDTAGTSAQNSLKESNNVKSMVTAGSKGSFINISQMIACVGQQNVEGKR  780
+             ENKVN++LN ARD  G+SAQ SL E NN KSMV +GSKGS INISQ+IACVGQQNVEGKR
+Sbjct  732   ENKVNQILNDARDRTGSSAQKSLSEFNNFKSMVVSGSKGSKINISQVIACVGQQNVEGKR  791
+
+Query  781   IPYGFGHRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSET  840
+             IP+GF HRTLPHF KDDYGPES+GFVENSYL GLTP EFFFHAMGGREGLIDTAVKT+ET
+Sbjct  792   IPFGFRHRTLPHFIKDDYGPESKGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAET  851
+
+Query  841   GYIQRRLVKAMEDLMVRYDGTVRNSLGCIIQFSYGEDGMDGAFVESQKLEILRLGDKAFQ  900
+             GYIQRRL+KAME +MV YDGTVRNSL  ++Q  YGEDG+DG +VE Q +  ++  +  F+
+Sbjct  852   GYIQRRLIKAMESVMVNYDGTVRNSLAQMVQLRYGEDGLDGMWVEDQNMPTMKPNNAVFE  911
+
+Query  901   TLYFMDPTKANFGEDFLDQEVVEDVRNSSEAYELLSAEYEELKRCRRVLRQEVIPSGDDT  960
+               + MD T   F      ++VV +++ S +   L+ +E+ +L+  RR+LR+ + P GD  
+Sbjct  912   RDFRMDLTDNKFLRKNYSEDVVREIQESEDGISLVESEWSQLEEDRRLLRK-IFPRGDAK  970
+
+Query  961   WPLPVNLRRLIWNAQVIFRLDTRKSTDLSPVKIIKGVKTLLSRLIVVKGDDEVSLEAQES  1020
+               LP NL+RLIWNAQ IF++D RK  +LSP+ +I GV+ L  +LI+V G+DE+S +AQ +
+Sbjct  971   IVLPCNLQRLIWNAQKIFKVDLRKPVNLSPLHVINGVRELSKKLIIVSGNDEISKQAQYN  1030
+
+Query  1021  CTMLFGILLKSTLASKRVLKEFRLNTVAFDWVLGEIESRFMQAIVQPSEAVGAIAAQSIG  1080
+              T+L  ILL+STL +K++    +LNT AFDW+LGE+ESRF QAI QP E VGA+AAQS+G
+Sbjct  1031  ATLLMNILLRSTLCTKKMCTSAKLNTEAFDWLLGEVESRFQQAIAQPGEMVGALAAQSLG  1090
+
+Query  1081  EPATQMTLNTFHYAGVSSKNVTLGVPRLKELINVAKKVKTPSLTVYLLPHCAKDSERAKS  1140
+             EPATQMTLNTFHYAGVS+KNVTLGVPRLKE+INV+K++KTPSLTV+L    AKD+E+AK 
+Sbjct  1091  EPATQMTLNTFHYAGVSAKNVTLGVPRLKEIINVSKQLKTPSLTVFLTGAAAKDAEKAKD  1150
+
+Query  1141  VQCQLEHATLNTVTASTEIFYDPDPTTTVIEEDREFVQAYFEMPDEDISLEKISPWLLRI  1200
+             V C+LEH TL  VT +T I+YDPDP  TVI ED E+V  ++EMPD D+S  + SPWLLRI
+Sbjct  1151  VLCKLEHTTLKKVTLNTAIYYDPDPKNTVIAEDEEWVSIFYEMPDHDLS--RTSPWLLRI  1208
+
+Query  1201  VLNREMMTDKKLSMADIAEKINIEFGCDTLCIFNDDNAEKLVLHVRIMNDQD--PKHEET  1258
+              L+R+ M DKKL+M  IA++I+  FG D   I+ DDNAEKLV  +RI  +       EE 
+Sbjct  1209  ELDRKRMVDKKLTMEMIADRIHGGFGNDVHTIYTDDNAEKLVFRLRIAGEDKGADTQEEQ  1268
+
+Query  1259  ISEEATTTFLKQLEANMLSEMTLKGIDQIRKVYMRE-----ARKTFFDVDGRIATENEWI  1313
+             + +     FL+ +EANMLS++TL+GI  I KVYM +      ++     +G      +WI
+Sbjct  1269  VDKMEDDVFLRCIEANMLSDLTLQGIPAISKVYMNQPNTDDKKRIIITPEGGFKAVADWI  1328
+
+Query  1314  LETDGCNLLQVMSCPEVDFSRTTSNDIVEIIQVLGIEAARAALLKEIRDVISFDGSYVNY  1373
+             LETDG  LL+V++  ++D  RTTSNDI EI +VLGIEA R A+ +E+ +VISFDGSYVNY
+Sbjct  1329  LETDGTALLRVLAERQIDPVRTTSNDICEIFEVLGIEAVRKAIEREMDNVISFDGSYVNY  1388
+
+Query  1374  RHLAILVDFMTYRGYLMSITRHGINRNVTGPLMRCSFEETVEILMESAAFAEADHLRGVT  1433
+             RHLA+L D MT +G+LM+ITRHGINR   G LMRCSFEETV+ILME++  AE D ++GV+
+Sbjct  1389  RHLALLCDVMTAKGHLMAITRHGINRQEVGALMRCSFEETVDILMEASVHAEVDPVKGVS  1448
+
+Query  1434  ENIILGQLGKFGTGSFDVFLNEKMLREAVDIPLPDGLEGQELFG--------DTSPTHQM  1485
+             ENI+LGQL + GTG FD+ L+ +  +  ++IP    +      G        + SP+H  
+Sbjct  1449  ENIMLGQLARCGTGCFDLVLDVEKCKYGMEIPQNVVMGAGYYGGFAGSPNAHEFSPSH--  1506
+
+Query  1486  TPFETMGTP--GGA--------------FSPSTPNDGAMFSPFN--GYSNEATFSPSG--  1525
+             +P+ +  TP  GGA              FSP+   DG   SPFN  G+S  +   P G  
+Sbjct  1507  SPWNSGVTPSYGGASWSPGAGGMSPSAGFSPAGNMDGGA-SPFNEGGWSPASPGDPLGAL  1565
+
+Query  1526  SPSSP----FSP--YTPASPGYSPSSPAYSPSSPAYSPTSP-------------------  1560
+             SP +P     SP  Y+P SP +S +SP YSP+SP+YSPTSP                   
+Sbjct  1566  SPRTPAYGGMSPGAYSPTSPQFSMTSPHYSPTSPSYSPTSPAAGQSPASPSYSPTSPSYS  1625
+
+Query        ------------------------------------------------------------  
+
+Sbjct  1626  PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPSSPRYSPTSP  1685
+
+Query  1561  AYSPTSPAYSPTSPAYSPTSPAYSPTSPAYS----------PTSPAYSPTSPAYSPTSPA  1610
+              YSPTSP YSPTSP YSPTSP YSPTSP+Y           P+SP YSPTSP+YSPTSP 
+Sbjct  1686  TYSPTSPTYSPTSPTYSPTSPTYSPTSPSYEGYSPSSPKYSPSSPTYSPTSPSYSPTSPQ  1745
+
+Query  1611  YSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYTPTSPAYTPTSPAYTPT  1670
+             YSPTSP YSP+SP Y+P+SP Y+PTSP     SP YSPTSP Y+PTSP+YTP+SP Y+PT
+Sbjct  1746  YSPTSPQYSPSSPTYTPSSPTYNPTSP--RAFSPQYSPTSPTYSPTSPSYTPSSPQYSPT  1803
+
+Query  1671  SPAYTPTSPAYTPTSPA  1687
+             SP YTP SP+  P + A
+Sbjct  1804  SPTYTP-SPSDQPGTSA  1819
+
+
+ Score =   166 bits (419),  Expect = 1e-44, Method: Compositional matrix adjust.
+ Identities = 88/133 (66%), Positives = 101/133 (76%), Gaps = 13/133 (10%)
+
+Query  1568  AYSPTSPAYSPTSPAYSPTSPAYSPTSPAYS----------PTSPAYSPTSPAYSPTSPA  1617
+              YSPTSP YSPTSP YSPTSP YSPTSP+Y           P+SP YSPTSP+YSPTSP 
+Sbjct  1686  TYSPTSPTYSPTSPTYSPTSPTYSPTSPSYEGYSPSSPKYSPSSPTYSPTSPSYSPTSPQ  1745
+
+Query  1618  YSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYTPTSPAYTPTSPAYTPTSPAYTPT  1677
+             YSPTSP YSP+SP Y+P+SP Y+PTSP     SP Y+PTSP Y+PTSP+YTP+SP Y+PT
+Sbjct  1746  YSPTSPQYSPSSPTYTPSSPTYNPTSP--RAFSPQYSPTSPTYSPTSPSYTPSSPQYSPT  1803
+
+Query  1678  SPAYTPTSPAYTP  1690
+             SP YTP SP+  P
+Sbjct  1804  SPTYTP-SPSDQP  1815
+
+
+ Score =   140 bits (352),  Expect = 9e-37, Method: Compositional matrix adjust.
+ Identities = 73/110 (66%), Positives = 83/110 (75%), Gaps = 15/110 (14%)
+
+Query  1597  YSPTSPAYSPTSPAYSPTSPAYSPTSPAYS----------PTSPAYSPTSPAYSPTSPAY  1646
+             YSPTSP YSPTSP YSPTSP YSPTSP+Y           P+SP YSPTSP+YSPTSP Y
+Sbjct  1687  YSPTSPTYSPTSPTYSPTSPTYSPTSPSYEGYSPSSPKYSPSSPTYSPTSPSYSPTSPQY  1746
+
+Query  1647  SPTSPAYTPTSPAYTPTSPAYTPT-----SPAYTPTSPAYTPTSPAYTPT  1691
+             SPTSP Y+P+SP YTP+SP Y PT     SP Y+PTSP Y+PTSP+YTP+
+Sbjct  1747  SPTSPQYSPSSPTYTPSSPTYNPTSPRAFSPQYSPTSPTYSPTSPSYTPS  1796
+
+
+
+Lambda      K        H        a         alpha
+   0.317    0.134    0.394    0.792     4.96 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.267   0.0410    0.140     1.90     42.6     43.6 
+
+Effective search space used: 2948400
+
+
+  Database: subject.fasta
+    Posted date:  Jun 3, 2015  4:53 PM
+  Number of letters in database: 1,853
+  Number of sequences in database:  1
+
+
+
+Matrix: BLOSUM62
+Gap Penalties: Existence: 11, Extension: 1
+Neighboring words threshold: 11
+Window for multiple hits: 40