diff --git a/modules/bindings/tests/testfiles/raw_blastout.txt b/modules/bindings/tests/testfiles/raw_blastout.txt new file mode 100644 index 0000000000000000000000000000000000000000..95f567513d6584287e112cdb7e8796dad95b9a8d --- /dev/null +++ b/modules/bindings/tests/testfiles/raw_blastout.txt @@ -0,0 +1,167 @@ +<?xml version="1.0"?> +<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> +<BlastOutput> + <BlastOutput_program>blastp</BlastOutput_program> + <BlastOutput_version>blastp 2.2.16 [Mar-25-2007]</BlastOutput_version> + <BlastOutput_reference>~Reference: Altschul, Stephen F., 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.</BlastOutput_reference> + <BlastOutput_db>seqdb</BlastOutput_db> + <BlastOutput_query-ID>lcl|1_0</BlastOutput_query-ID> + <BlastOutput_query-def>A</BlastOutput_query-def> + <BlastOutput_query-len>101</BlastOutput_query-len> + <BlastOutput_param> + <Parameters> + <Parameters_matrix>BLOSUM62</Parameters_matrix> + <Parameters_expect>10</Parameters_expect> + <Parameters_gap-open>11</Parameters_gap-open> + <Parameters_gap-extend>1</Parameters_gap-extend> + <Parameters_filter>F</Parameters_filter> + </Parameters> + </BlastOutput_param> + <BlastOutput_iterations> + <Iteration> + <Iteration_iter-num>1</Iteration_iter-num> + <Iteration_query-ID>lcl|1_0</Iteration_query-ID> + <Iteration_query-def>A</Iteration_query-def> + <Iteration_query-len>101</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|1</Hit_id> + <Hit_def>1griA</Hit_def> + <Hit_accession>1</Hit_accession> + <Hit_len>211</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>210.305</Hsp_bit-score> + <Hsp_score>534</Hsp_score> + <Hsp_evalue>4.80893e-59</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>101</Hsp_query-to> + <Hsp_hit-from>49</Hsp_hit-from> + <Hsp_hit-to>149</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>101</Hsp_identity> + <Hsp_positive>101</Hsp_positive> + <Hsp_align-len>101</Hsp_align-len> + <Hsp_qseq>MKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVP</Hsp_qseq> + <Hsp_hseq>MKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVP</Hsp_hseq> + <Hsp_midline>MKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVP</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + <Hit> + <Hit_num>2</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>1fhsA</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>112</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>210.305</Hsp_bit-score> + <Hsp_score>534</Hsp_score> + <Hsp_evalue>4.80893e-59</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>101</Hsp_query-to> + <Hsp_hit-from>4</Hsp_hit-from> + <Hsp_hit-to>104</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>101</Hsp_identity> + <Hsp_positive>101</Hsp_positive> + <Hsp_align-len>101</Hsp_align-len> + <Hsp_qseq>MKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVP</Hsp_qseq> + <Hsp_hseq>MKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVP</Hsp_hseq> + <Hsp_midline>MKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVP</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + <Hit> + <Hit_num>3</Hit_num> + <Hit_id>gnl|BL_ORD_ID|2</Hit_id> + <Hit_def>3n84E</Hit_def> + <Hit_accession>2</Hit_accession> + <Hit_len>102</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>206.068</Hsp_bit-score> + <Hsp_score>523</Hsp_score> + <Hsp_evalue>9.06925e-58</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>99</Hsp_query-to> + <Hsp_hit-from>4</Hsp_hit-from> + <Hsp_hit-to>102</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>99</Hsp_identity> + <Hsp_positive>99</Hsp_positive> + <Hsp_align-len>99</Hsp_align-len> + <Hsp_qseq>MKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQ</Hsp_qseq> + <Hsp_hseq>MKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQ</Hsp_hseq> + <Hsp_midline>MKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQ</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + <Hit> + <Hit_num>4</Hit_num> + <Hit_id>gnl|BL_ORD_ID|5</Hit_id> + <Hit_def>1mw9X</Hit_def> + <Hit_accession>5</Hit_accession> + <Hit_len>556</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>15.0086</Hsp_bit-score> + <Hsp_score>27</Hsp_score> + <Hsp_evalue>2.96523</Hsp_evalue> + <Hsp_query-from>31</Hsp_query-from> + <Hsp_query-to>43</Hsp_query-to> + <Hsp_hit-from>123</Hsp_hit-from> + <Hsp_hit-to>135</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>4</Hsp_identity> + <Hsp_positive>10</Hsp_positive> + <Hsp_align-len>13</Hsp_align-len> + <Hsp_qseq>IRESESAPGDFSL</Hsp_qseq> + <Hsp_hseq>IRQAFNKPGELNI</Hsp_hseq> + <Hsp_midline>IR++ + PG+ ++</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>2</Hsp_num> + <Hsp_bit-score>13.853</Hsp_bit-score> + <Hsp_score>24</Hsp_score> + <Hsp_evalue>6.60584</Hsp_evalue> + <Hsp_query-from>9</Hsp_query-from> + <Hsp_query-to>33</Hsp_query-to> + <Hsp_hit-from>170</Hsp_hit-from> + <Hsp_hit-to>194</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>5</Hsp_identity> + <Hsp_positive>12</Hsp_positive> + <Hsp_align-len>25</Hsp_align-len> + <Hsp_qseq>GKIPRAKAEEMLSKQRHDGAFLIRE</Hsp_qseq> + <Hsp_hseq>GRVQSVAVRLVVEREREIKAFVPEE</Hsp_hseq> + <Hsp_midline>G++ ++ ++R AF+ E</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>6</Statistics_db-num> + <Statistics_db-len>1507</Statistics_db-len> + <Statistics_hsp-len>28</Statistics_hsp-len> + <Statistics_eff-space>97747</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> + </BlastOutput_iterations> +</BlastOutput>