wwood-bioruby 1.2.11

data/test/data/blast/b0002.faa

@@ -0,0 +1,15 @@
+>eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal) [EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928 aspartate kinase (A)
+MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA
+LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA
+ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP
+ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV
+PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD
+EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF
+CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL
+ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGAL
+LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL
+VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR
+RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA
+REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA
+NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF
+YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV

data/test/data/blast/b0002.faa.m0

@@ -0,0 +1,128 @@
+BLASTP 2.2.10 [Oct-19-2004]
+
+
+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.
+
+Query= eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional:
+aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal)
+[EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928
+aspartate kinase (A)
+         (820 letters)
+
+Database: b0002.faa 
+           1 sequences; 820 total letters
+
+Searching.done
+
+                                                                 Score    E
+Sequences producing significant alignments:                      (bits) Value
+
+eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokin...  1567   0.0  
+
+>eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase
+           I (N-terminal); homoserine dehydrogenase I (C-terminal)
+           [EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase;
+           K00928 aspartate kinase (A)
+          Length = 820
+
+ Score = 1567 bits (4058), Expect = 0.0
+ Identities = 806/820 (98%), Positives = 806/820 (98%)
+
+Query: 1   MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60
+           MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA
+Sbjct: 1   MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60
+
+Query: 61  LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA 120
+           LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA
+Sbjct: 61  LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA 120
+
+Query: 121 ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP 180
+           ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP
+Sbjct: 121 ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP 180
+
+Query: 181 ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 240
+           ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV
+Sbjct: 181 ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 240
+
+Query: 241 PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD 300
+           PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD
+Sbjct: 241 PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD 300
+
+Query: 301 EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF 360
+           EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF
+Sbjct: 301 EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF 360
+
+Query: 361 CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL 420
+           CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL
+Sbjct: 361 CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL 420
+
+Query: 421 ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQXXXXXXXXXXXXXXAL 480
+           ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQ              AL
+Sbjct: 421 ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGAL 480
+
+Query: 481 LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL 540
+           LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL
+Sbjct: 481 LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL 540
+
+Query: 541 VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR 600
+           VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR
+Sbjct: 541 VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR 600
+
+Query: 601 RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA 660
+           RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA
+Sbjct: 601 RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA 660
+
+Query: 661 REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA 720
+           REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA
+Sbjct: 661 REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA 720
+
+Query: 721 NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF 780
+           NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF
+Sbjct: 721 NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF 780
+
+Query: 781 YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV 820
+           YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV
+Sbjct: 781 YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV 820
+
+
+  Database: b0002.faa
+    Posted date:  Aug 7, 2005  7:29 AM
+  Number of letters in database: 820
+  Number of sequences in database:  1
+  
+Lambda     K      H
+   0.319    0.134    0.383 
+
+Gapped
+Lambda     K      H
+   0.267   0.0410    0.140 
+
+
+Matrix: BLOSUM62
+Gap Penalties: Existence: 11, Extension: 1
+Number of Hits to DB: 1986
+Number of Sequences: 1
+Number of extensions: 52
+Number of successful extensions: 8
+Number of sequences better than 10.0: 1
+Number of HSP's better than 10.0 without gapping: 1
+Number of HSP's successfully gapped in prelim test: 0
+Number of HSP's that attempted gapping in prelim test: 0
+Number of HSP's gapped (non-prelim): 1
+length of query: 820
+length of database: 820
+effective HSP length: 42
+effective length of query: 778
+effective length of database: 778
+effective search space:   605284
+effective search space used:   605284
+T: 11
+A: 40
+X1: 16 ( 7.4 bits)
+X2: 38 (14.6 bits)
+X3: 64 (24.7 bits)
+S1: 30 (16.7 bits)
+S2: 30 (16.2 bits)

data/test/data/blast/b0002.faa.m7

@@ -0,0 +1,65 @@
+<?xml version="1.0"?>
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
+<BlastOutput>
+  <BlastOutput_program>blastp</BlastOutput_program>
+  <BlastOutput_version>blastp 2.2.10 [Oct-19-2004]</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), ~&quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs&quot;,  Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
+  <BlastOutput_db>b0002.faa</BlastOutput_db>
+  <BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
+  <BlastOutput_query-def>eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal) [EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928 aspartate kinase (A)</BlastOutput_query-def>
+  <BlastOutput_query-len>820</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>S</Parameters_filter>
+    </Parameters>
+  </BlastOutput_param>
+  <BlastOutput_iterations>
+    <Iteration>
+      <Iteration_iter-num>1</Iteration_iter-num>
+      <Iteration_hits>
+        <Hit>
+          <Hit_num>1</Hit_num>
+          <Hit_id>gnl|BL_ORD_ID|0</Hit_id>
+          <Hit_def>eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal) [EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928 aspartate kinase (A)</Hit_def>
+          <Hit_accession>0</Hit_accession>
+          <Hit_len>820</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>1567.75</Hsp_bit-score>
+              <Hsp_score>4058</Hsp_score>
+              <Hsp_evalue>0</Hsp_evalue>
+              <Hsp_query-from>1</Hsp_query-from>
+              <Hsp_query-to>820</Hsp_query-to>
+              <Hsp_hit-from>1</Hsp_hit-from>
+              <Hsp_hit-to>820</Hsp_hit-to>
+              <Hsp_query-frame>1</Hsp_query-frame>
+              <Hsp_hit-frame>1</Hsp_hit-frame>
+              <Hsp_identity>820</Hsp_identity>
+              <Hsp_positive>820</Hsp_positive>
+              <Hsp_align-len>820</Hsp_align-len>
+              <Hsp_qseq>MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV</Hsp_qseq>
+              <Hsp_hseq>MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV</Hsp_hseq>
+              <Hsp_midline>MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+      </Iteration_hits>
+      <Iteration_stat>
+        <Statistics>
+          <Statistics_db-num>1</Statistics_db-num>
+          <Statistics_db-len>820</Statistics_db-len>
+          <Statistics_hsp-len>42</Statistics_hsp-len>
+          <Statistics_eff-space>605284</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>

data/test/data/blast/b0002.faa.m8

@@ -0,0 +1 @@
+eco:b0002	eco:b0002	100.00	820	0	0	1	820	1	820	0.0	1567

data/test/data/blast/blastp-multi.m7

@@ -0,0 +1,188 @@
+<?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 2.2.18 [Mar-02-2008]</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), ~&quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs&quot;,  Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
+  <BlastOutput_db>BA000007.faa</BlastOutput_db>
+  <BlastOutput_query-ID>lcl|1_0</BlastOutput_query-ID>
+  <BlastOutput_query-def>gi|1790845|gb|AAC77338.1| predicted DNA-binding transcriptional regulator [Escherichia coli str. K-12 substr. MG1655]</BlastOutput_query-def>
+  <BlastOutput_query-len>443</BlastOutput_query-len>
+  <BlastOutput_param>
+    <Parameters>
+      <Parameters_matrix>BLOSUM62</Parameters_matrix>
+      <Parameters_expect>0.001</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>2</Iteration_iter-num>
+      <Iteration_query-ID>lcl|2_0</Iteration_query-ID>
+      <Iteration_query-def>gi|1790846|gb|AAC77339.1| lipoate-protein ligase A [Escherichia coli str. K-12</Iteration_query-def>
+      <Iteration_query-len>346</Iteration_query-len>
+      <Iteration_hits>
+        <Hit>
+          <Hit_num>1</Hit_num>
+          <Hit_id>gi|13364823|dbj|BAB38768.1|</Hit_id>
+          <Hit_def>putative lipoate-protein ligase A [Escherichia coli O157:H7 str. Sakai]</Hit_def>
+          <Hit_accession>BAB38768</Hit_accession>
+          <Hit_len>562</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>697.197</Hsp_bit-score>
+              <Hsp_score>1798</Hsp_score>
+              <Hsp_evalue>0</Hsp_evalue>
+              <Hsp_query-from>9</Hsp_query-from>
+              <Hsp_query-to>346</Hsp_query-to>
+              <Hsp_hit-from>225</Hsp_hit-from>
+              <Hsp_hit-to>562</Hsp_hit-to>
+              <Hsp_query-frame>1</Hsp_query-frame>
+              <Hsp_hit-frame>1</Hsp_hit-frame>
+              <Hsp_identity>331</Hsp_identity>
+              <Hsp_positive>335</Hsp_positive>
+              <Hsp_align-len>338</Hsp_align-len>
+              <Hsp_qseq>MSTLRLLISDSYDPWFNLAVEECIFRQMPATQRVLFLWRNADTVVIGRAQNPWKECNTRRMEEDNVRLARRSSGGGAVFHDLGNTCFTFMAGKPEYDKTISTSIVLNALNALGVSAEASGRNDLVVKTVEGDRKVSGSAYRETKDRGFHHGTLLLNADLSRLANYLNPDKKKLAAKGITSVRSRVTNLTELLPGITHEQVCEAITEAFFAHYGERVEAEIISPNKTPDLPNFAETFARQSSWEWNFGQAPAFSHLLDERFTWGGVELHFDVEKGHITRAQVFTDSLNPAPLEALAGRLQGCLYRADMLQQECEALLVDFPEQEKELRELSAWMAGAVR</Hsp_qseq>
+              <Hsp_hseq>MSTLRLLISDSYDPWFNLAVEECIFRQMPATQRVLFLWRNADTVVIGRAQNPWKECNTRRMEEDNVRLARRSSGGGAVFHDLGNTCFTFMAGKPEYDKTISTSIVLNALNALGVSAEASGRNDLVVKTAEGDRKVSGSAYRETKDRGFHHGTLLLNADLSRLANYLNPDKKKLAAKGITSVRSRVTNLTELLPGIPHEQVCEAITEAFFAHYGERVEAEIISPDKTPDLPNFAETFARQSSWEWNFGQAPAFSHLLDERFSWGGVELHFDVEKGHITRAQVFTDSLNPAPLEALAGRLQGCLYRADMLQQECEALLVDFPDQEKELRELSTWIAGAVR</Hsp_hseq>
+              <Hsp_midline>MSTLRLLISDSYDPWFNLAVEECIFRQMPATQRVLFLWRNADTVVIGRAQNPWKECNTRRMEEDNVRLARRSSGGGAVFHDLGNTCFTFMAGKPEYDKTISTSIVLNALNALGVSAEASGRNDLVVKT EGDRKVSGSAYRETKDRGFHHGTLLLNADLSRLANYLNPDKKKLAAKGITSVRSRVTNLTELLPGI HEQVCEAITEAFFAHYGERVEAEIISP+KTPDLPNFAETFARQSSWEWNFGQAPAFSHLLDERF+WGGVELHFDVEKGHITRAQVFTDSLNPAPLEALAGRLQGCLYRADMLQQECEALLVDFP+QEKELRELS W+AGAVR</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+      </Iteration_hits>
+      <Iteration_stat>
+        <Statistics>
+          <Statistics_db-num>5361</Statistics_db-num>
+          <Statistics_db-len>1609188</Statistics_db-len>
+          <Statistics_hsp-len>0</Statistics_hsp-len>
+          <Statistics_eff-space>0</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>3</Iteration_iter-num>
+      <Iteration_query-ID>lcl|3_0</Iteration_query-ID>
+      <Iteration_query-def>gi|1790847|gb|AAC77340.1| conserved protein [Escherichia coli str. K-12 substr. MG1655]</Iteration_query-def>
+      <Iteration_query-len>214</Iteration_query-len>
+      <Iteration_hits>
+        <Hit>
+          <Hit_num>1</Hit_num>
+          <Hit_id>gi|13364823|dbj|BAB38768.1|</Hit_id>
+          <Hit_def>putative lipoate-protein ligase A [Escherichia coli O157:H7 str. Sakai]</Hit_def>
+          <Hit_accession>BAB38768</Hit_accession>
+          <Hit_len>562</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>432.95</Hsp_bit-score>
+              <Hsp_score>1112</Hsp_score>
+              <Hsp_evalue>7.66702e-123</Hsp_evalue>
+              <Hsp_query-from>1</Hsp_query-from>
+              <Hsp_query-to>214</Hsp_query-to>
+              <Hsp_hit-from>1</Hsp_hit-from>
+              <Hsp_hit-to>214</Hsp_hit-to>
+              <Hsp_query-frame>1</Hsp_query-frame>
+              <Hsp_hit-frame>1</Hsp_hit-frame>
+              <Hsp_identity>214</Hsp_identity>
+              <Hsp_positive>214</Hsp_positive>
+              <Hsp_align-len>214</Hsp_align-len>
+              <Hsp_qseq>MARTKLKFRLHRAVIVLFCLALLVALMQGASWFSQNHQRQRNPQLEELARTLARQVTLNVAPLMRTDSPDEKRIQAILDQLTDESRILDAGVYDEQGDLIARSGESVEVRDRLALDGKKAGGYFNQQIVEPIAGKNGPLGYLRLTLDTHTLATEAQQVDNTTNILRLMLLLSLAIGVVLTRTLLQGKRTRWQQSPFLLTASKPVPEEEESEKKE</Hsp_qseq>
+              <Hsp_hseq>MARTKLKFRLHRAVIVLFCLALLVALMQGASWFSQNHQRQRNPQLEELARTLARQVTLNVAPLMRTDSPDEKRIQAILDQLTDESRILDAGVYDEQGDLIARSGESVEVRDRLALDGKKAGGYFNQQIVEPIAGKNGPLGYLRLTLDTHTLATEAQQVDNTTNILRLMLLLSLAIGVVLTRTLLQGKRTRWQQSPFLLTASKPVPEEEESEKKE</Hsp_hseq>
+              <Hsp_midline>MARTKLKFRLHRAVIVLFCLALLVALMQGASWFSQNHQRQRNPQLEELARTLARQVTLNVAPLMRTDSPDEKRIQAILDQLTDESRILDAGVYDEQGDLIARSGESVEVRDRLALDGKKAGGYFNQQIVEPIAGKNGPLGYLRLTLDTHTLATEAQQVDNTTNILRLMLLLSLAIGVVLTRTLLQGKRTRWQQSPFLLTASKPVPEEEESEKKE</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+      </Iteration_hits>
+      <Iteration_stat>
+        <Statistics>
+          <Statistics_db-num>5361</Statistics_db-num>
+          <Statistics_db-len>1609188</Statistics_db-len>
+          <Statistics_hsp-len>0</Statistics_hsp-len>
+          <Statistics_eff-space>0</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>lcl|5_0</Iteration_query-ID>
+      <Iteration_query-def>gi|1790849|gb|AAC77341.1| 3-phosphoserine phosphatase [Escherichia coli str. K-12 substr. MG1655]</Iteration_query-def>
+      <Iteration_query-len>322</Iteration_query-len>
+      <Iteration_hits>
+        <Hit>
+          <Hit_num>1</Hit_num>
+          <Hit_id>gi|13364824|dbj|BAB38769.1|</Hit_id>
+          <Hit_def>3-phosphoserine phosphatase [Escherichia coli O157:H7 str. Sakai]</Hit_def>
+          <Hit_accession>BAB38769</Hit_accession>
+          <Hit_len>322</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>657.907</Hsp_bit-score>
+              <Hsp_score>1696</Hsp_score>
+              <Hsp_evalue>0</Hsp_evalue>
+              <Hsp_query-from>1</Hsp_query-from>
+              <Hsp_query-to>322</Hsp_query-to>
+              <Hsp_hit-from>1</Hsp_hit-from>
+              <Hsp_hit-to>322</Hsp_hit-to>
+              <Hsp_query-frame>1</Hsp_query-frame>
+              <Hsp_hit-frame>1</Hsp_hit-frame>
+              <Hsp_identity>322</Hsp_identity>
+              <Hsp_positive>322</Hsp_positive>
+              <Hsp_align-len>322</Hsp_align-len>
+              <Hsp_qseq>MPNITWCDLPEDVSLWPGLPLSLSGDEVMPLDYHAGRSGWLLYGRGLDKQRLTQYQSKLGAAMVIVAAWCVEDYQVIRLAGSLTARATRLAHEAQLDVAPLGKIPHLRTPGLLVMDMDSTAIQIECIDEIAKLAGTGEMVAEVTERAMRGELDFTASLRSRVATLKGADANILQQVRENLPLMPGLTQLVLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVIGDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNEKAEVTIRHADLMGVFCILSGSLNQK</Hsp_qseq>
+              <Hsp_hseq>MPNITWCDLPEDVSLWPGLPLSLSGDEVMPLDYHAGRSGWLLYGRGLDKQRLTQYQSKLGAAMVIVAAWCVEDYQVIRLAGSLTARATRLAHEAQLDVAPLGKIPHLRTPGLLVMDMDSTAIQIECIDEIAKLAGTGEMVAEVTERAMRGELDFTASLRSRVATLKGADANILQQVRENLPLMPGLTQLVLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVIGDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNEKAEVTIRHADLMGVFCILSGSLNQK</Hsp_hseq>
+              <Hsp_midline>MPNITWCDLPEDVSLWPGLPLSLSGDEVMPLDYHAGRSGWLLYGRGLDKQRLTQYQSKLGAAMVIVAAWCVEDYQVIRLAGSLTARATRLAHEAQLDVAPLGKIPHLRTPGLLVMDMDSTAIQIECIDEIAKLAGTGEMVAEVTERAMRGELDFTASLRSRVATLKGADANILQQVRENLPLMPGLTQLVLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVIGDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNEKAEVTIRHADLMGVFCILSGSLNQK</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+        <Hit>
+          <Hit_num>2</Hit_num>
+          <Hit_id>gi|13363792|dbj|BAB37741.1|</Hit_id>
+          <Hit_def>zinc-transporting ATPase [Escherichia coli O157:H7 str. Sakai]</Hit_def>
+          <Hit_accession>BAB37741</Hit_accession>
+          <Hit_len>732</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>38.1206</Hsp_bit-score>
+              <Hsp_score>87</Hsp_score>
+              <Hsp_evalue>0.000899657</Hsp_evalue>
+              <Hsp_query-from>190</Hsp_query-from>
+              <Hsp_query-to>311</Hsp_query-to>
+              <Hsp_hit-from>569</Hsp_hit-from>
+              <Hsp_hit-to>668</Hsp_hit-to>
+              <Hsp_query-frame>1</Hsp_query-frame>
+              <Hsp_hit-frame>1</Hsp_hit-frame>
+              <Hsp_identity>39</Hsp_identity>
+              <Hsp_positive>56</Hsp_positive>
+              <Hsp_gaps>24</Hsp_gaps>
+              <Hsp_align-len>123</Hsp_align-len>
+              <Hsp_qseq>VLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVIGDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVN-EKAEVTIRHADLMGV</Hsp_qseq>
+              <Hsp_hseq>ISELNALGVKGVILTG----------DNPRAAAAIAGELGL---EFKAGLL-----PEDKVKAVTELNQHA--PLAM---VGDGINDAPAMKAAAIGIAMGSGTDVALETADAALTHNHLRGL</Hsp_hseq>
+              <Hsp_midline>+ +L  LG K  I +G          D  R  A +A EL +   +F   ++      + K K +T L Q    PLA    +GDG ND P +KAA +GIA  +   V  E A+  + H  L G+</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+      </Iteration_hits>
+      <Iteration_stat>
+        <Statistics>
+          <Statistics_db-num>5361</Statistics_db-num>
+          <Statistics_db-len>1609188</Statistics_db-len>
+          <Statistics_hsp-len>0</Statistics_hsp-len>
+          <Statistics_eff-space>0</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>

data/test/data/command/echoarg2.bat

@@ -0,0 +1 @@
+@echo %2

data/test/data/embl/AB090716.embl

@@ -0,0 +1,65 @@
+ID   AB090716   standard; genomic DNA; VRT; 166 BP.
+XX
+AC   AB090716;
+XX
+SV   AB090716.1
+XX
+DT   25-OCT-2002 (Rel. 73, Created)
+DT   29-NOV-2002 (Rel. 73, Last updated, Version 2)
+XX
+DE   Haplochromis sp. 'muzu, rukwa' LWS gene for long wavelength-sensitive
+DE   opsin, partial cds, specimen_voucher:specimen No. HT-9361.
+XX
+KW   .
+XX
+OS   Haplochromis sp. 'muzu, rukwa'
+OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
+OC   Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei;
+OC   Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Labroidei;
+OC   Cichlidae; Haplochromis.
+XX
+RN   [1]
+RP   1-166
+RA   Terai Y., Mayer W.E., Klein J., Tichy H., Okada N.;
+RT   ;
+RL   Submitted (26-AUG-2002) to the EMBL/GenBank/DDBJ databases.
+RL   Yohey Terai, Tokyo Institute of Technology, Graduate School of Bioscience
+RL   and Biotechnology; 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa
+RL   226-8501, Japan (E-mail:yterai@bio.titech.ac.jp, Tel:81-45-924-5744,
+RL   Fax:81-45-924-5835)
+XX
+RN   [2]
+RX   DOI; 10.1073/pnas.232561099.
+RX   MEDLINE; 22342723.
+RX   PUBMED; 12438648.
+RA   Terai Y., Mayer W.E., Klein J., Tichy H., Okada N.;
+RT   "The effect of selection on a long wavelength-sensitive (LWS) opsin gene of
+RT   Lake Victoria cichlid fishes";
+RL   Proc. Natl. Acad. Sci. U.S.A. 99(24):15501-15506(2002).
+XX
+FH   Key             Location/Qualifiers
+FH
+FT   source          1..166
+FT                   /db_xref="taxon:205497"
+FT                   /mol_type="genomic DNA"
+FT                   /organism="Haplochromis sp. 'muzu, rukwa'"
+FT                   /specimen_voucher="specimen No. HT-9361"
+FT                   /tissue_type="piece of fin"
+FT   CDS             <1..>166
+FT                   /codon_start=2
+FT                   /db_xref="UniProt/TrEMBL:Q8AUS6"
+FT                   /gene="LWS"
+FT                   /product="long wavelength-sensitive opsin"
+FT                   /protein_id="BAC22028.1"
+FT                   /translation="FWPHGLKTSCGPDVFSGSEDPGVQSYMIVLMITCCFIPLAIIILC
+FT                   YLAVWMAIRA"
+FT   exon            1..166
+FT                   /number=4
+FT                   /gene="LWS"
+FT                   /product="long wavelength-sensitive opsin"
+XX
+SQ   Sequence 166 BP; 29 A; 42 C; 41 G; 54 T; 0 other;
+     gttctggcct catggactga agacttcctg tggacctgat gtgttcagtg gaagtgaaga        60
+     ccctggagta cagtcctaca tgattgttct catgattact tgctgtttca tccccctggc       120
+     tatcatcatc ctgtgctacc ttgctgtgtg gatggccatc cgtgct                      166
+//