Mercurial > repos > iuc > virannot_blast2tsv

diff test-data/rps_test.xml @ 1:0c7f6833f9ad draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
author iuc
date Sun, 08 Sep 2024 14:08:33 +0000
parents b82ce29791e7
children
line wrap: on
line diff
--- a/test-data/rps_test.xml	Wed Aug 21 13:12:59 2024 +0000
+++ b/test-data/rps_test.xml	Sun Sep 08 14:08:33 2024 +0000
@@ -194,6 +194,175 @@
   </Iteration_stat>
 </Iteration>
 <Iteration>
+  <Iteration_iter-num>4</Iteration_iter-num>
+  <Iteration_query-ID>Query_4</Iteration_query-ID>
+  <Iteration_query-def>ds2020-267_4</Iteration_query-def>
+  <Iteration_query-len>2297</Iteration_query-len>
+<Iteration_hits>
+<Hit>
+  <Hit_num>1</Hit_num>
+  <Hit_id>gnl|CDD|280316</Hit_id>
+  <Hit_def>pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase.  This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.</Hit_def>
+  <Hit_accession>280316</Hit_accession>
+  <Hit_len>465</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>187.283</Hsp_bit-score>
+      <Hsp_score>476</Hsp_score>
+      <Hsp_evalue>1.84305e-52</Hsp_evalue>
+      <Hsp_query-from>824</Hsp_query-from>
+      <Hsp_query-to>1858</Hsp_query-to>
+      <Hsp_hit-from>121</Hsp_hit-from>
+      <Hsp_hit-to>464</Hsp_hit-to>
+      <Hsp_query-frame>-2</Hsp_query-frame>
+      <Hsp_hit-frame>0</Hsp_hit-frame>
+      <Hsp_identity>94</Hsp_identity>
+      <Hsp_positive>136</Hsp_positive>
+      <Hsp_gaps>19</Hsp_gaps>
+      <Hsp_align-len>354</Hsp_align-len>
+      <Hsp_qseq>VRKSRLVNWEEEHKNRVSPNLAEMPEGLVYERASQLFSRSISAGKRPR-KFD-WREYWQSRWQWSAAGSIHSQYSEDDKYIFKDIYLKNKFISILAMPDMNMDSWRER----DPELHAWSSTKYEWSKLRAIYGTDVTSYVLAHFAFYNCEDVLPSPFPVGKAANDEN--VRSRVRSVLEGRTQYCVDFEDFNSQHSVQSMKAVIDAYRDTFGHFLTQEQLAAVEWTRLSLDRVIVHDNQGLKMEYNAKGTLLSGWRLTTFMNSVLNYIYTQLIVPDVVQSQNSLHNGDDVLLGSNSLEDVLLAGKNAKKHNIRLQMSK-CAYGAIAEFLRVDHKRGSKGQYLSRAMATLVHSR</Hsp_qseq>
+      <Hsp_hseq>GRGVTNVDWEEEAKNRVDLAVVCRLVLLPMEELRAHIDAVLDELVVRRGLCDPIRLFVKNEPLWCVNGHPDHKLRE---GRLRLLSSVSLVDQLVRR--MLFEPQNNNEIAWWGSVPSKPSMKLEHGKSRAIYACDTRSYLAFEYLLAPVEKAWANKSVILNPGEGDISGFDWSVQDWKRGGVSLMLDYDDFNSQHSTESMRAVFERLR----RRLPDEPAEAADWLVCSMDSMYQLSD-GTLLAQRVPGTLKSGHRATTFINSVLNCAYAELAGAPWADVPTSIHMGDDVLEGLRTPADATSLLDKYARLGFKVNPSKQSVGHTIAEFLRVAFCSHEVRGYLARAIASLVSGN</Hsp_hseq>
+      <Hsp_midline> R    V+WEEE KNRV   +      L  E         +      R   D  R + ++   W   G    +  E      + +   +    ++    M  +            + +  S K E  K RAIY  D  SY+   +     E    +   +      +       V+    G     +D++DFNSQHS +SM+AV +  R      L  E   A +W   S+D +    + G  +     GTL SG R TTF+NSVLN  Y +L          S+H GDDVL G  +  D         +   ++  SK      IAEFLRV         YL+RA+A+LV   </Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+<Hit>
+  <Hit_num>2</Hit_num>
+  <Hit_id>gnl|CDD|279070</Hit_id>
+  <Hit_def>pfam00680, RdRP_1, RNA dependent RNA polymerase.  </Hit_def>
+  <Hit_accession>279070</Hit_accession>
+  <Hit_len>475</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>45.0546</Hsp_bit-score>
+      <Hsp_score>107</Hsp_score>
+      <Hsp_evalue>3.12197e-05</Hsp_evalue>
+      <Hsp_query-from>995</Hsp_query-from>
+      <Hsp_query-to>1873</Hsp_query-to>
+      <Hsp_hit-from>4</Hsp_hit-from>
+      <Hsp_hit-to>344</Hsp_hit-to>
+      <Hsp_query-frame>-2</Hsp_query-frame>
+      <Hsp_hit-frame>0</Hsp_hit-frame>
+      <Hsp_identity>62</Hsp_identity>
+      <Hsp_positive>102</Hsp_positive>
+      <Hsp_gaps>96</Hsp_gaps>
+      <Hsp_align-len>365</Hsp_align-len>
+      <Hsp_qseq>SKEQHVRKSRLVNWEEEHKNRVSP-NLA----EMPEGLVYERASQL-----FSRSISAGKRPRKFDWREYWQSRWQWSAAGSIHSQYSEDDKYIFKDIYLKNKFISILAMPDMNMDS----------WRERDPE-------------LHAWSST----------------------KYEWSKLRAIYGTDVTSYVLAHFAFYNCEDVLPSPFPVGKAANDENVRSRVRSVLEGRTQ-----YCVDFEDFNSQHSVQSMKAVIDAYRDTFGHFLTQEQLAAVEW--TRLSL-DRVIVHDNQGLKMEYNAKGTLLSGWRLTTFMNSVLNYIYTQ--LI-------VPDVVQSQNSLHNGDDVLLGSN</Hsp_qseq>
+      <Hsp_hseq>MTKTALVPS-VIEGYIDTVEDYEPAALGFKDPRLDAYLGLSRVAISKDSLKPYGQEEVLGVPREF---------LHDAAKGLT----SMLEGADLGDLSVSEAINGADGFDALNMDTSPGFPYILNGGKKRDLVKDEEADKVLLKAAYEALRLAEGGEGLPGVYTTCLKDELRPLEKVLKGKTRLFWGCPVEVNLVARAAFGPFNNKIYANGIKLGIAVGINPFSRDWERLAALIRKGSDVLDVDYSAFDSTLSPFVFDLVIDIRSEFCEDKLKLTRLALLELLSNPIHIFNGTIIKVEGGLP----------SGQPATSVINSINNNIYVLYALIKHTGESELDDLFETIRFFSYGDDNLVAVN</Hsp_hseq>
+      <Hsp_midline>  +  +  S ++    +      P  L      +   L   R +                 PR+F            +A G      S  +     D+ +            +NMD+           ++RD                 A                          K    K R  +G  V   ++A  AF    + + +       A   N  SR    L    +       VD+  F+S  S      VID   +     L   +LA +E     + + +  I+    GL           SG   T+ +NS+ N IY    LI       + D+ ++      GDD L+  N</Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>16305</Statistics_db-num>
+      <Statistics_db-len>2821655</Statistics_db-len>
+      <Statistics_hsp-len>93</Statistics_hsp-len>
+      <Statistics_eff-space>877154880</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>5</Iteration_iter-num>
+  <Iteration_query-ID>Query_5</Iteration_query-ID>
+  <Iteration_query-def>ds2020-267_5</Iteration_query-def>
+  <Iteration_query-len>2029</Iteration_query-len>
+<Iteration_hits>
+<Hit>
+  <Hit_num>1</Hit_num>
+  <Hit_id>gnl|CDD|279070</Hit_id>
+  <Hit_def>pfam00680, RdRP_1, RNA dependent RNA polymerase.  </Hit_def>
+  <Hit_accession>279070</Hit_accession>
+  <Hit_len>475</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>46.5954</Hsp_bit-score>
+      <Hsp_score>111</Hsp_score>
+      <Hsp_evalue>8.86955e-06</Hsp_evalue>
+      <Hsp_query-from>840</Hsp_query-from>
+      <Hsp_query-to>1706</Hsp_query-to>
+      <Hsp_hit-from>166</Hsp_hit-from>
+      <Hsp_hit-to>437</Hsp_hit-to>
+      <Hsp_query-frame>3</Hsp_query-frame>
+      <Hsp_hit-frame>0</Hsp_hit-frame>
+      <Hsp_identity>55</Hsp_identity>
+      <Hsp_positive>99</Hsp_positive>
+      <Hsp_gaps>51</Hsp_gaps>
+      <Hsp_align-len>306</Hsp_align-len>
+      <Hsp_qseq>KDDPNKMRTIWGCSKPWIIADTMLWWEYVAYAKLQPGATPMLWSYETFTGGWLRLNHALFSSYIRHSYITLDWKRFDKKAYFCIIDKIFDGVETFLDFDNGYLPTKD-YPDTKSTWTQERSTRLKRLFDWTKENFYHAPIVLPNGHMYVRKFAGIPSGLFITQLIDSWYN-YTMLATILSAMGFDPRSCIIK-----VQGDDSIIRLSALIPPDAHDSFLTKVQELADYYFQSVVSVNKSEVRNELNGCEVLSYRHRHGLP----YRDEL---AMLAQLYHTKARNPSPEITMAQ---SIGFAYAS</Hsp_qseq>
+      <Hsp_hseq>KVLKGKTRLFWGCPVEVNLVARAAFGPFNNKIYANGIKLGIAVGINPFSRDWERL-AALIRKG--SDVLDVDYSAFDSTLSPFVFDLVIDIRSEF--CEDKLKLTRLALLELLSN-----------------------PIHIFNG-TIIKVEGGLPSGQPATSVINSINNNIYVLYALIKHTGESELDDLFETIRFFSYGDDNLVAVNPDVDSVGQKLK----EHLKDLG-LTPTRADKTSEFSPIKPIEEVVFLKRTFSRTEGGVRPRLDRKSIERQLYWIRAGNTSEEARGQQLENALGEAYHH</Hsp_hseq>
+      <Hsp_midline>K    K R  WGC     +     +  +            +      F+  W RL  AL         + +D+  FD      + D + D    F   ++    T+    +  S                        PI + NG   ++   G+PSG   T +I+S  N   +L  ++   G      + +       GDD+++ ++  +            + L D    +    +K+   + +   E + +  R         R  L   ++  QLY  +A N S E    Q   ++G AY  </Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>16305</Statistics_db-num>
+      <Statistics_db-len>2821655</Statistics_db-len>
+      <Statistics_hsp-len>92</Statistics_hsp-len>
+      <Statistics_eff-space>771811480</Statistics_eff-space>
+      <Statistics_kappa>0.0625983</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>6</Iteration_iter-num>
+  <Iteration_query-ID>Query_6</Iteration_query-ID>
+  <Iteration_query-def>ds2020-267_6</Iteration_query-def>
+  <Iteration_query-len>1860</Iteration_query-len>
+<Iteration_hits>
+<Hit>
+  <Hit_num>1</Hit_num>
+  <Hit_id>gnl|CDD|280316</Hit_id>
+  <Hit_def>pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase.  This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.</Hit_def>
+  <Hit_accession>280316</Hit_accession>
+  <Hit_len>465</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>83.6639</Hsp_bit-score>
+      <Hsp_score>207</Hsp_score>
+      <Hsp_evalue>1.27376e-17</Hsp_evalue>
+      <Hsp_query-from>1147</Hsp_query-from>
+      <Hsp_query-to>1764</Hsp_query-to>
+      <Hsp_hit-from>288</Hsp_hit-from>
+      <Hsp_hit-to>464</Hsp_hit-to>
+      <Hsp_query-frame>-1</Hsp_query-frame>
+      <Hsp_hit-frame>0</Hsp_hit-frame>
+      <Hsp_identity>49</Hsp_identity>
+      <Hsp_positive>81</Hsp_positive>
+      <Hsp_gaps>31</Hsp_gaps>
+      <Hsp_align-len>207</Hsp_align-len>
+      <Hsp_qseq>RRVMEMSTQGVVACIDARNFNILHTQEVMASILESASVMLGSRLSEEQHKCLKWLSKAELNQKVLVKKGEVTEELLSAGRQEGWINQMMKGDGTMVEAATVTVGMFSGTRFTMLYNTILNRAYYKVAEELAGIKTLSLHSGDDVYSAFASYIDVYKMKKAMAFIGYTLQLAK-CFLQGVREFLRISHKNANTSQYLARSAATAIHGR</Hsp_qseq>
+      <Hsp_hseq>WSVQDWKRGGVSLMLDYDDFNSQHSTESMRAVFER----LRRRLPDEPAEAADWLVCS--------------------------MDSMYQLSDGTLLAQRVPGTLKSGHRATTFINSVLNCAYAELAGAPWADVPTSIHMGDDVLEGLRTPADATSLLDKYARLGFKVNPSKQSVGHTIAEFLRVAFCSHEVRGYLARAIASLVSGN</Hsp_hseq>
+      <Hsp_midline>  V +    GV   +D  +FN  H+ E M ++ E     L  RL +E  +   WL  +                          ++ M +     + A  V   + SG R T   N++LN AY ++A         S+H GDDV     +  D   +    A +G+ +  +K      + EFLR++  +     YLAR+ A+ + G </Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>16305</Statistics_db-num>
+      <Statistics_db-len>2821655</Statistics_db-len>
+      <Statistics_hsp-len>92</Statistics_hsp-len>
+      <Statistics_eff-space>697802160</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+</Iteration>
+<Iteration>
   <Iteration_iter-num>7</Iteration_iter-num>
   <Iteration_query-ID>ds2020-267_374</Iteration_query-ID>
   <Iteration_query-def>No definition line</Iteration_query-def>