Repository 'blastxml_to_top_descr'
hg clone https://toolshed.g2.bx.psu.edu/repos/peterjc/blastxml_to_top_descr

Changeset 4:34a0adda2770 (2013-02-20)
Previous changeset 3:60c2d6ce926d (2013-02-08) Next changeset 5:662fea0fe6b2 (2013-02-20)
Commit message:
Uploaded v0.0.3 which includes the test files required for the unit tests.
modified:
tools/ncbi_blast_plus/blastxml_to_top_descr.txt
added:
test-data/blastp_four_human_vs_rhodopsin.xml
test-data/blastp_four_human_vs_rhodopsin_top3.tabular
b
diff -r 60c2d6ce926d -r 34a0adda2770 test-data/blastp_four_human_vs_rhodopsin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastp_four_human_vs_rhodopsin.xml Wed Feb 20 13:18:07 2013 -0500
[
b'@@ -0,0 +1,646 @@\n+<?xml version="1.0"?>\n+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">\n+<BlastOutput>\n+  <BlastOutput_program>blastp</BlastOutput_program>\n+  <BlastOutput_version>BLASTP 2.2.26+</BlastOutput_version>\n+  <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, 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>\n+  <BlastOutput_db></BlastOutput_db>\n+  <BlastOutput_query-ID>sp|Q9BS26|ERP44_HUMAN</BlastOutput_query-ID>\n+  <BlastOutput_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</BlastOutput_query-def>\n+  <BlastOutput_query-len>406</BlastOutput_query-len>\n+  <BlastOutput_param>\n+    <Parameters>\n+      <Parameters_matrix>BLOSUM62</Parameters_matrix>\n+      <Parameters_expect>1e-08</Parameters_expect>\n+      <Parameters_gap-open>11</Parameters_gap-open>\n+      <Parameters_gap-extend>1</Parameters_gap-extend>\n+      <Parameters_filter>F</Parameters_filter>\n+    </Parameters>\n+  </BlastOutput_param>\n+  <BlastOutput_iterations>\n+    <Iteration>\n+      <Iteration_iter-num>1</Iteration_iter-num>\n+      <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>\n+      <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n+      <Iteration_query-len>406</Iteration_query-len>\n+      <Iteration_hits></Iteration_hits>\n+      <Iteration_stat>\n+        <Statistics>\n+          <Statistics_db-num>0</Statistics_db-num>\n+          <Statistics_db-len>0</Statistics_db-len>\n+          <Statistics_hsp-len>30</Statistics_hsp-len>\n+          <Statistics_eff-space>119568</Statistics_eff-space>\n+          <Statistics_kappa>0.041</Statistics_kappa>\n+          <Statistics_lambda>0.267</Statistics_lambda>\n+          <Statistics_entropy>0.14</Statistics_entropy>\n+        </Statistics>\n+      </Iteration_stat>\n+      <Iteration_message>No hits found</Iteration_message>\n+    </Iteration>\n+    <Iteration>\n+      <Iteration_iter-num>2</Iteration_iter-num>\n+      <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>\n+      <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n+      <Iteration_query-len>406</Iteration_query-len>\n+      <Iteration_hits></Iteration_hits>\n+      <Iteration_stat>\n+        <Statistics>\n+          <Statistics_db-num>0</Statistics_db-num>\n+          <Statistics_db-len>0</Statistics_db-len>\n+          <Statistics_hsp-len>30</Statistics_hsp-len>\n+          <Statistics_eff-space>119568</Statistics_eff-space>\n+          <Statistics_kappa>0.041</Statistics_kappa>\n+          <Statistics_lambda>0.267</Statistics_lambda>\n+          <Statistics_entropy>0.14</Statistics_entropy>\n+        </Statistics>\n+      </Iteration_stat>\n+      <Iteration_message>No hits found</Iteration_message>\n+    </Iteration>\n+    <Iteration>\n+      <Iteration_iter-num>3</Iteration_iter-num>\n+      <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>\n+      <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n+      <Iteration_query-len>406</Iteration_query-len>\n+      <Iteration_hits></Iteration_hits>\n+      <Iteration_stat>\n+        <Statistics>\n+          <Statistics_db-num>0</Statistics_db-num>\n+          <Statistics_db-len>0</Statistics_db-len>\n+          <Statistics_hsp-len>30</Statistics_hsp-len>\n+          <Statistics_eff-space>119568</Statistics_eff-space>\n+          <Statistics_kappa>0.041</Statistics_kappa>\n+          <Statistics_lambda>0.267</Statistics_lambda>\n+          <Statistics_entropy>0.14</Statistics_entropy>\n+        </Statistics>\n+      </Iteration_stat>\n+      <Iteration_message>No hits found</Iteratio'..b'VPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGID YT   E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline>\n+            </Hsp>\n+          </Hit_hsps>\n+        </Hit>\n+      </Iteration_hits>\n+      <Iteration_stat>\n+        <Statistics>\n+          <Statistics_db-num>0</Statistics_db-num>\n+          <Statistics_db-len>0</Statistics_db-len>\n+          <Statistics_hsp-len>29</Statistics_hsp-len>\n+          <Statistics_eff-space>101761</Statistics_eff-space>\n+          <Statistics_kappa>0.041</Statistics_kappa>\n+          <Statistics_lambda>0.267</Statistics_lambda>\n+          <Statistics_entropy>0.14</Statistics_entropy>\n+        </Statistics>\n+      </Iteration_stat>\n+    </Iteration>\n+    <Iteration>\n+      <Iteration_iter-num>24</Iteration_iter-num>\n+      <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>\n+      <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>\n+      <Iteration_query-len>348</Iteration_query-len>\n+      <Iteration_hits>\n+        <Hit>\n+          <Hit_num>1</Hit_num>\n+          <Hit_id>gi|12583665|dbj|BAB21486.1|</Hit_id>\n+          <Hit_def>fresh water form rod opsin [Conger myriaster]</Hit_def>\n+          <Hit_accession>BAB21486</Hit_accession>\n+          <Hit_len>354</Hit_len>\n+          <Hit_hsps>\n+            <Hsp>\n+              <Hsp_num>1</Hsp_num>\n+              <Hsp_bit-score>599.356</Hsp_bit-score>\n+              <Hsp_score>1544</Hsp_score>\n+              <Hsp_evalue>0</Hsp_evalue>\n+              <Hsp_query-from>1</Hsp_query-from>\n+              <Hsp_query-to>341</Hsp_query-to>\n+              <Hsp_hit-from>1</Hsp_hit-from>\n+              <Hsp_hit-to>342</Hsp_hit-to>\n+              <Hsp_query-frame>0</Hsp_query-frame>\n+              <Hsp_hit-frame>0</Hsp_hit-frame>\n+              <Hsp_identity>281</Hsp_identity>\n+              <Hsp_positive>314</Hsp_positive>\n+              <Hsp_gaps>1</Hsp_gaps>\n+              <Hsp_align-len>342</Hsp_align-len>\n+              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE</Hsp_qseq>\n+              <Hsp_hseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE</Hsp_hseq>\n+              <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE+HAIMGV  TW MALACA PPL GWSRYIPEGLQCSCGIDYYT  P +NNESFVIYMF  HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA+YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR+CM+TT+CCGKNP   +D ASAT SKTE</Hsp_midline>\n+            </Hsp>\n+          </Hit_hsps>\n+        </Hit>\n+      </Iteration_hits>\n+      <Iteration_stat>\n+        <Statistics>\n+          <Statistics_db-num>0</Statistics_db-num>\n+          <Statistics_db-len>0</Statistics_db-len>\n+          <Statistics_hsp-len>29</Statistics_hsp-len>\n+          <Statistics_eff-space>101761</Statistics_eff-space>\n+          <Statistics_kappa>0.041</Statistics_kappa>\n+          <Statistics_lambda>0.267</Statistics_lambda>\n+          <Statistics_entropy>0.14</Statistics_entropy>\n+        </Statistics>\n+      </Iteration_stat>\n+    </Iteration>\n+  </BlastOutput_iterations>\n+</BlastOutput>\n\\ No newline at end of file\n'
b
diff -r 60c2d6ce926d -r 34a0adda2770 test-data/blastp_four_human_vs_rhodopsin_top3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastp_four_human_vs_rhodopsin_top3.tabular Wed Feb 20 13:18:07 2013 -0500
[
@@ -0,0 +1,25 @@
+#Query BLAST hit 1 BLAST hit 2 BLAST hit 3
+sp|Q9BS26|ERP44_HUMAN
+sp|Q9BS26|ERP44_HUMAN
+sp|Q9BS26|ERP44_HUMAN
+sp|Q9BS26|ERP44_HUMAN
+sp|Q9BS26|ERP44_HUMAN
+sp|Q9BS26|ERP44_HUMAN
+sp|Q9NSY1|BMP2K_HUMAN
+sp|Q9NSY1|BMP2K_HUMAN
+sp|Q9NSY1|BMP2K_HUMAN
+sp|Q9NSY1|BMP2K_HUMAN
+sp|Q9NSY1|BMP2K_HUMAN
+sp|Q9NSY1|BMP2K_HUMAN
+sp|P06213|INSR_HUMAN
+sp|P06213|INSR_HUMAN
+sp|P06213|INSR_HUMAN
+sp|P06213|INSR_HUMAN
+sp|P06213|INSR_HUMAN
+sp|P06213|INSR_HUMAN
+sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]
+sp|P08100|OPSD_HUMAN gi|3024260|sp|P56514.1|OPSD_BUFBU RecName: Full=Rhodopsin
+sp|P08100|OPSD_HUMAN gi|283855846|gb|ADB45242.1| rhodopsin [Cynopterus brachyotis]
+sp|P08100|OPSD_HUMAN gi|283855823|gb|ADB45229.1| rhodopsin [Myotis pilosus]
+sp|P08100|OPSD_HUMAN gi|223523|prf||0811197A rhodopsin [Bos taurus]
+sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| fresh water form rod opsin [Conger myriaster]
b
diff -r 60c2d6ce926d -r 34a0adda2770 tools/ncbi_blast_plus/blastxml_to_top_descr.txt
--- a/tools/ncbi_blast_plus/blastxml_to_top_descr.txt Fri Feb 08 06:05:33 2013 -0500
+++ b/tools/ncbi_blast_plus/blastxml_to_top_descr.txt Wed Feb 20 13:18:07 2013 -0500
b
@@ -50,6 +50,7 @@
 v0.0.1 - Initial version.
 v0.0.2 - Since BLAST+ was moved out of the Galaxy core, now have a dependency
          on the 'blast_datatypes' repository in the Tool Shed.
+v0.0.3 - Include the test files required to run the unit tests
 
 
 Developers
@@ -61,7 +62,7 @@
 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
 the following command from the Galaxy root folder:
 
-$ tar -czf blastxml_to_top_descr.tar.gz tools/ncbi_blast_plus/blastxml_to_top_descr.* tools/ncbi_blast_plus/repository_dependencies.xml
+$ tar -czf blastxml_to_top_descr.tar.gz tools/ncbi_blast_plus/blastxml_to_top_descr.* tools/ncbi_blast_plus/repository_dependencies.xml test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_top3.tabular
 
 Check this worked:
 
@@ -70,6 +71,8 @@
 tools/ncbi_blast_plus/blastxml_to_top_descr.txt
 tools/ncbi_blast_plus/blastxml_to_top_descr.xml
 tools/ncbi_blast_plus/repository_dependencies.xml
+test-data/blastp_four_human_vs_rhodopsin.xml
+test-data/blastp_four_human_vs_rhodopsin_top3.tabular
 
 
 Licence (MIT/BSD style)