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[hg] galaxy 1692: Fix for my last commit.
by Greg Von Kuster 07 Jan '09

07 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/93b946a7d8cb changeset: 1692:93b946a7d8cb user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Jan 07 15:33:35 2009 -0500 description: Fix for my last commit. 1 file(s) affected in this change: test/functional/test_sniffing_and_metadata_settings.py diffs (13 lines): diff -r 6e9dd26f782f -r 93b946a7d8cb test/functional/test_sniffing_and_metadata_settings.py --- a/test/functional/test_sniffing_and_metadata_settings.py Wed Jan 07 12:20:35 2009 -0500 +++ b/test/functional/test_sniffing_and_metadata_settings.py Wed Jan 07 15:33:35 2009 -0500 @@ -110,8 +110,7 @@ self.delete_history_item( 1 ) def test_60_blastxml_datatype( self ): """Testing correctly sniffing blastxml data type upon upload""" - self.upload_file( 'megablast_xml_parser_test1.blastxml' ) - self.verify_dataset_correctness( 'megablast_xml_parser_test1.blastxml' ) + self.upload_file( 'megablast_xml_parser_test1.gz' ) self.check_history_for_string( 'NCBI Blast XML data' ) self.check_history_for_string( 'format: <span class="blastxml">blastxml</span>' ) self.delete_history_item( 1 )

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[hg] galaxy 1691: Add support for NCBI Blast XML data format.
by Greg Von Kuster 07 Jan '09

07 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/6e9dd26f782f changeset: 1691:6e9dd26f782f user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Jan 07 12:20:35 2009 -0500 description: Add support for NCBI Blast XML data format. 8 file(s) affected in this change: datatypes_conf.xml.sample lib/galaxy/datatypes/registry.py lib/galaxy/datatypes/sniff.py lib/galaxy/datatypes/test/megablast_xml_parser_test1.blastxml lib/galaxy/datatypes/xml.py lib/galaxy/tools/actions/upload.py test/functional/test_sniffing_and_metadata_settings.py tools/metag_tools/megablast_xml_parser.xml diffs (truncated from 4398 to 3000 lines): diff -r 317d5f454dfd -r 6e9dd26f782f datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Tue Jan 06 13:29:03 2009 -0500 +++ b/datatypes_conf.xml.sample Wed Jan 07 12:20:35 2009 -0500 @@ -41,6 +41,7 @@ <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/> <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/> <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/> + <datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" display_in_upload="true"/> <datatype extension="txtseq.zip" type="galaxy.datatypes.images:Txtseq" mimetype="application/zip" display_in_upload="true"/> <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true"/>  @@ -147,17 +148,18 @@ important because some formats are much more loosely defined than others. --> - <sniffer order="05" type="galaxy.datatypes.sequence:Maf"/> - <sniffer order="10" type="galaxy.datatypes.sequence:Lav"/> - <sniffer order="15" type="galaxy.datatypes.sequence:Fasta"/> - <sniffer order="25" type="galaxy.datatypes.sequence:FastqSolexa"/> - <sniffer order="30" type="galaxy.datatypes.interval:Wiggle"/> - <sniffer order="35" type="galaxy.datatypes.images:Html"/> - <sniffer order="40" type="galaxy.datatypes.sequence:Axt"/> - <sniffer order="45" type="galaxy.datatypes.interval:Bed"/> - <sniffer order="50" type="galaxy.datatypes.interval:CustomTrack"/> - <sniffer order="55" type="galaxy.datatypes.interval:Gff"/> - <sniffer order="60" type="galaxy.datatypes.interval:Gff3"/> - <sniffer order="65" type="galaxy.datatypes.interval:Interval"/> + <sniffer order="005" type="galaxy.datatypes.xml:BlastXml"/> + <sniffer order="010" type="galaxy.datatypes.sequence:Maf"/> + <sniffer order="015" type="galaxy.datatypes.sequence:Lav"/> + <sniffer order="020" type="galaxy.datatypes.sequence:Fasta"/> + <sniffer order="025" type="galaxy.datatypes.sequence:FastqSolexa"/> + <sniffer order="030" type="galaxy.datatypes.interval:Wiggle"/> + <sniffer order="035" type="galaxy.datatypes.images:Html"/> + <sniffer order="040" type="galaxy.datatypes.sequence:Axt"/> + <sniffer order="045" type="galaxy.datatypes.interval:Bed"/> + <sniffer order="050" type="galaxy.datatypes.interval:CustomTrack"/> + <sniffer order="055" type="galaxy.datatypes.interval:Gff"/> + <sniffer order="060" type="galaxy.datatypes.interval:Gff3"/> + <sniffer order="065" type="galaxy.datatypes.interval:Interval"/> </sniffers> </datatypes> diff -r 317d5f454dfd -r 6e9dd26f782f lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Tue Jan 06 13:29:03 2009 -0500 +++ b/lib/galaxy/datatypes/registry.py Wed Jan 07 12:20:35 2009 -0500 @@ -3,7 +3,7 @@ """ import os import logging -import data, tabular, interval, images, sequence, qualityscore, genetics +import data, tabular, interval, images, sequence, qualityscore, genetics, xml import galaxy.util from galaxy.util.odict import odict @@ -96,6 +96,7 @@ 'axt' : sequence.Axt(), 'bed' : interval.Bed(), 'binseq.zip' : images.Binseq(), + 'blastxml' : xml.BlastXml(), 'customtrack' : interval.CustomTrack(), 'csfasta' : sequence.csFasta(), 'fasta' : sequence.Fasta(), @@ -119,6 +120,7 @@ 'axt' : 'text/plain', 'bed' : 'text/plain', 'binseq.zip' : 'application/zip', + 'blastxml' : 'text/plain', 'customtrack' : 'text/plain', 'csfasta' : 'text/plain', 'fasta' : 'text/plain', @@ -141,6 +143,7 @@ # because some formats are much more flexibly defined than others. if len(self.sniff_order) < 1: self.sniff_order = [ + xml.BlastXml(), sequence.Maf(), sequence.Lav(), sequence.Fasta(), diff -r 317d5f454dfd -r 6e9dd26f782f lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py Tue Jan 06 13:29:03 2009 -0500 +++ b/lib/galaxy/datatypes/sniff.py Wed Jan 07 12:20:35 2009 -0500 @@ -160,6 +160,9 @@ Returns an extension that can be used in the datatype factory to generate a data for the 'fname' file + >>> fname = get_test_fname('megablast_xml_parser_test1.blastxml') + >>> guess_ext(fname) + 'blastxml' >>> fname = get_test_fname('interval.interval') >>> guess_ext(fname) 'interval' diff -r 317d5f454dfd -r 6e9dd26f782f lib/galaxy/datatypes/test/megablast_xml_parser_test1.blastxml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/test/megablast_xml_parser_test1.blastxml Wed Jan 07 12:20:35 2009 -0500 @@ -0,0 +1,4117 @@ +<?xml version="1.0"?> +<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> +<BlastOutput> + <BlastOutput_program>blastn</BlastOutput_program> + <BlastOutput_version>blastn 2.2.17 [Aug-26-2007]</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>Ecoli.fa</BlastOutput_db> + <BlastOutput_query-ID>lcl|1_0</BlastOutput_query-ID> + <BlastOutput_query-def>0_0.666667</BlastOutput_query-def> + <BlastOutput_query-len>30</BlastOutput_query-len> + <BlastOutput_param> + <Parameters> + <Parameters_expect>10</Parameters_expect> + <Parameters_sc-match>1</Parameters_sc-match> + <Parameters_sc-mismatch>-3</Parameters_sc-mismatch> + <Parameters_gap-open>0</Parameters_gap-open> + <Parameters_gap-extend>0</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>0_0.666667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>5436010</Hsp_hit-from> + <Hsp_hit-to>5436039</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>CGGACAGCGCCGCCACCAACAAAGCCACCA</Hsp_qseq> + <Hsp_hseq>CGGACAGCGCCGCCACCAACAAAGCCACCA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>2</Iteration_iter-num> + <Iteration_query-ID>lcl|2_0</Iteration_query-ID> + <Iteration_query-def>1_0.600000</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>696993</Hsp_hit-from> + <Hsp_hit-to>697022</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>AAAACACCGGATGCTCCGGCGCTGGCAGAT</Hsp_qseq> + <Hsp_hseq>AAAACACCGGATGCTCCGGCGCTGGCAGAT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</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>2_0.400000</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>4100018</Hsp_hit-from> + <Hsp_hit-to>4100047</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TTTGCTTTTAGTACACCGGATTCAGAACCA</Hsp_qseq> + <Hsp_hseq>TTTGCTTTTAGTACACCGGATTCAGAACCA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>4</Iteration_iter-num> + <Iteration_query-ID>lcl|4_0</Iteration_query-ID> + <Iteration_query-def>3_0.566667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>2305844</Hsp_hit-from> + <Hsp_hit-to>2305873</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>-1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>CCGTCCAGAAAGGTGTATTCATGGGGACGG</Hsp_qseq> + <Hsp_hseq>CCGTCCAGAAAGGTGTATTCATGGGGACGG</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</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>4_0.766667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>3457901</Hsp_hit-from> + <Hsp_hit-to>3457930</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>CACGCTACGTGCGCCCCCGCCCAGAAGGCG</Hsp_qseq> + <Hsp_hseq>CACGCTACGTGCGCCCCCGCCCAGAAGGCG</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>6</Iteration_iter-num> + <Iteration_query-ID>lcl|6_0</Iteration_query-ID> + <Iteration_query-def>5_0.533333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>1264131</Hsp_hit-from> + <Hsp_hit-to>1264160</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>-1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GCACTTAACCCGCTTCGGCGGGTTTTGTTT</Hsp_qseq> + <Hsp_hseq>GCACTTAACCCGCTTCGGCGGGTTTTGTTT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>2</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>1636485</Hsp_hit-from> + <Hsp_hit-to>1636514</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>-1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GCACTTAACCCGCTTCGGCGGGTTTTGTTT</Hsp_qseq> + <Hsp_hseq>GCACTTAACCCGCTTCGGCGGGTTTTGTTT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>3</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2318694</Hsp_hit-from> + <Hsp_hit-to>2318723</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>AAACAAAACCCGCCGAAGCGGGTTAAGTGC</Hsp_qseq> + <Hsp_hseq>AAACAAAACCCGCCGAAGCGGGTTAAGTGC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>4</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2777043</Hsp_hit-from> + <Hsp_hit-to>2777072</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>AAACAAAACCCGCCGAAGCGGGTTAAGTGC</Hsp_qseq> + <Hsp_hseq>AAACAAAACCCGCCGAAGCGGGTTAAGTGC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>7</Iteration_iter-num> + <Iteration_query-ID>lcl|7_0</Iteration_query-ID> + <Iteration_query-def>6_0.533333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1185124</Hsp_hit-from> + <Hsp_hit-to>1185153</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TAAGCCGTTACTGGCAGCAAGTGCAGGCAA</Hsp_qseq> + <Hsp_hseq>TAAGCCGTTACTGGCAGCAAGTGCAGGCAA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>8</Iteration_iter-num> + <Iteration_query-ID>lcl|8_0</Iteration_query-ID> + <Iteration_query-def>7_0.400000</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2458203</Hsp_hit-from> + <Hsp_hit-to>2458232</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TGAATTTACCGTTATCTATCTTGCCTGCCT</Hsp_qseq> + <Hsp_hseq>TGAATTTACCGTTATCTATCTTGCCTGCCT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>10</Iteration_iter-num> + <Iteration_query-ID>lcl|10_0</Iteration_query-ID> + <Iteration_query-def>9_0.400000</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>5286666</Hsp_hit-from> + <Hsp_hit-to>5286695</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GCGTTTTGCTAAACTTCTGCCGGAATATAA</Hsp_qseq> + <Hsp_hseq>GCGTTTTGCTAAACTTCTGCCGGAATATAA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>11</Iteration_iter-num> + <Iteration_query-ID>lcl|11_0</Iteration_query-ID> + <Iteration_query-def>10_0.500000</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2787672</Hsp_hit-from> + <Hsp_hit-to>2787701</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>AAAGAGGCGAGCAGAGTAAAACGCAGGCAA</Hsp_qseq> + <Hsp_hseq>AAAGAGGCGAGCAGAGTAAAACGCAGGCAA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>13</Iteration_iter-num> + <Iteration_query-ID>lcl|13_0</Iteration_query-ID> + <Iteration_query-def>12_0.700000</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>4116145</Hsp_hit-from> + <Hsp_hit-to>4116174</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GCGGACGATCTTCACGGTCGCCACGCGGAC</Hsp_qseq> + <Hsp_hseq>GCGGACGATCTTCACGGTCGCCACGCGGAC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>14</Iteration_iter-num> + <Iteration_query-ID>lcl|14_0</Iteration_query-ID> + <Iteration_query-def>13_0.533333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>5442351</Hsp_hit-from> + <Hsp_hit-to>5442380</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TTCTTGTTGGATGGCATACTCCGGCAGCCA</Hsp_qseq> + <Hsp_hseq>TTCTTGTTGGATGGCATACTCCGGCAGCCA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>15</Iteration_iter-num> + <Iteration_query-ID>lcl|15_0</Iteration_query-ID> + <Iteration_query-def>14_0.666667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>4626492</Hsp_hit-from> + <Hsp_hit-to>4626521</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>ACCCCGATATCGTCGCAGGCGTTGCCGCAC</Hsp_qseq> + <Hsp_hseq>ACCCCGATATCGTCGCAGGCGTTGCCGCAC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>16</Iteration_iter-num> + <Iteration_query-ID>lcl|16_0</Iteration_query-ID> + <Iteration_query-def>15_0.666667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>346897</Hsp_hit-from> + <Hsp_hit-to>346926</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_qseq> + <Hsp_hseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>2</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>1466536</Hsp_hit-from> + <Hsp_hit-to>1466565</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>-1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GAAGCGCCTCTTCCAGCGGAGACAGCAGCC</Hsp_qseq> + <Hsp_hseq>GAAGCGCCTCTTCCAGCGGAGACAGCAGCC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>3</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1750132</Hsp_hit-from> + <Hsp_hit-to>1750161</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_qseq> + <Hsp_hseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>4</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1908046</Hsp_hit-from> + <Hsp_hit-to>1908075</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_qseq> + <Hsp_hseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>5</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2279107</Hsp_hit-from> + <Hsp_hit-to>2279136</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_qseq> + <Hsp_hseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>6</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2813407</Hsp_hit-from> + <Hsp_hit-to>2813436</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_qseq> + <Hsp_hseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>7</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>3939162</Hsp_hit-from> + <Hsp_hit-to>3939191</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_qseq> + <Hsp_hseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>8</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>4656510</Hsp_hit-from> + <Hsp_hit-to>4656539</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_qseq> + <Hsp_hseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>17</Iteration_iter-num> + <Iteration_query-ID>lcl|17_0</Iteration_query-ID> + <Iteration_query-def>16_0.566667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2595157</Hsp_hit-from> + <Hsp_hit-to>2595186</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>ATGTCCTGATCGAGCGGCGTTTTACCGACC</Hsp_qseq> + <Hsp_hseq>ATGTCCTGATCGAGCGGCGTTTTACCGACC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>18</Iteration_iter-num> + <Iteration_query-ID>lcl|18_0</Iteration_query-ID> + <Iteration_query-def>17_0.533333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>717743</Hsp_hit-from> + <Hsp_hit-to>717772</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GGTGTTGAGTGTCCAGGTAATACGCTCTCG</Hsp_qseq> + <Hsp_hseq>GGTGTTGAGTGTCCAGGTAATACGCTCTCG</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>20</Iteration_iter-num> + <Iteration_query-ID>lcl|20_0</Iteration_query-ID> + <Iteration_query-def>19_0.566667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1237938</Hsp_hit-from> + <Hsp_hit-to>1237967</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GTTGTAAGCGTCAGAACCGATGCGGTCGGT</Hsp_qseq> + <Hsp_hseq>GTTGTAAGCGTCAGAACCGATGCGGTCGGT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>21</Iteration_iter-num> + <Iteration_query-ID>lcl|21_0</Iteration_query-ID> + <Iteration_query-def>20_0.566667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>4792054</Hsp_hit-from> + <Hsp_hit-to>4792083</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>CGACATCCTGTAGGCTGGCTTCAATGCGAC</Hsp_qseq> + <Hsp_hseq>CGACATCCTGTAGGCTGGCTTCAATGCGAC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>22</Iteration_iter-num> + <Iteration_query-ID>lcl|22_0</Iteration_query-ID> + <Iteration_query-def>21_0.733333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>269757</Hsp_hit-from> + <Hsp_hit-to>269786</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GGGAAGGCTGACGGGCGTCCACACCACGGC</Hsp_qseq> + <Hsp_hseq>GGGAAGGCTGACGGGCGTCCACACCACGGC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>2</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>274007</Hsp_hit-from> + <Hsp_hit-to>274036</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GGGAAGGCTGACGGGCGTCCACACCACGGC</Hsp_qseq> + <Hsp_hseq>GGGAAGGCTGACGGGCGTCCACACCACGGC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>23</Iteration_iter-num> + <Iteration_query-ID>lcl|23_0</Iteration_query-ID> + <Iteration_query-def>22_0.566667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2706426</Hsp_hit-from> + <Hsp_hit-to>2706455</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>CGGTATTCCTCAGTTCTCGCTGCATGCCTG</Hsp_qseq> + <Hsp_hseq>CGGTATTCCTCAGTTCTCGCTGCATGCCTG</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>24</Iteration_iter-num> + <Iteration_query-ID>lcl|24_0</Iteration_query-ID> + <Iteration_query-def>23_0.600000</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1512107</Hsp_hit-from> + <Hsp_hit-to>1512136</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TTGCCGTTACGCACCACGCCTTCAGTAGCG</Hsp_qseq> + <Hsp_hseq>TTGCCGTTACGCACCACGCCTTCAGTAGCG</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>25</Iteration_iter-num> + <Iteration_query-ID>lcl|25_0</Iteration_query-ID> + <Iteration_query-def>24_0.733333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + 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</Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>42</Iteration_iter-num> + <Iteration_query-ID>lcl|42_0</Iteration_query-ID> + <Iteration_query-def>41_0.566667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + 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</Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>43</Iteration_iter-num> + <Iteration_query-ID>lcl|43_0</Iteration_query-ID> + <Iteration_query-def>42_0.566667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1714771</Hsp_hit-from> + <Hsp_hit-to>1714800</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + 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<Hsp> + <Hsp_num>2</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>1357952</Hsp_hit-from> + <Hsp_hit-to>1357981</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>-1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>ATCCGCGATAAGGTCATCCGGTATCAGGAA</Hsp_qseq> + <Hsp_hseq>ATCCGCGATAAGGTCATCCGGTATCAGGAA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>3</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2310674</Hsp_hit-from> + <Hsp_hit-to>2310703</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TTCCTGATACCGGATGACCTTATCGCGGAT</Hsp_qseq> + <Hsp_hseq>TTCCTGATACCGGATGACCTTATCGCGGAT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>4</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2769319</Hsp_hit-from> + <Hsp_hit-to>2769348</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TTCCTGATACCGGATGACCTTATCGCGGAT</Hsp_qseq> + <Hsp_hseq>TTCCTGATACCGGATGACCTTATCGCGGAT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>5</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2991293</Hsp_hit-from> + <Hsp_hit-to>2991322</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TTCCTGATACCGGATGACCTTATCGCGGAT</Hsp_qseq> + <Hsp_hseq>TTCCTGATACCGGATGACCTTATCGCGGAT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>47</Iteration_iter-num> + <Iteration_query-ID>lcl|47_0</Iteration_query-ID> + <Iteration_query-def>46_0.466667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1080570</Hsp_hit-from> + <Hsp_hit-to>1080599</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>ACCTGTACCCCAGGACCATGGTACATTTAT</Hsp_qseq> + <Hsp_hseq>ACCTGTACCCCAGGACCATGGTACATTTAT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>2</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1476177</Hsp_hit-from> + <Hsp_hit-to>1476206</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>ACCTGTACCCCAGGACCATGGTACATTTAT</Hsp_qseq> + <Hsp_hseq>ACCTGTACCCCAGGACCATGGTACATTTAT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>48</Iteration_iter-num> + <Iteration_query-ID>lcl|48_0</Iteration_query-ID> + <Iteration_query-def>47_0.533333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2887871</Hsp_hit-from> + <Hsp_hit-to>2887900</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>ACAATGCAACCAGACCAGCCCGGATCGATA</Hsp_qseq> + <Hsp_hseq>ACAATGCAACCAGACCAGCCCGGATCGATA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>50</Iteration_iter-num> + <Iteration_query-ID>lcl|50_0</Iteration_query-ID> + <Iteration_query-def>49_0.433333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>4152853</Hsp_hit-from> + <Hsp_hit-to>4152882</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>CGTTATACGGAACAACATTTAACTCCAGCG</Hsp_qseq> + <Hsp_hseq>CGTTATACGGAACAACATTTAACTCCAGCG</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>51</Iteration_iter-num> + <Iteration_query-ID>lcl|51_0</Iteration_query-ID> + <Iteration_query-def>50_0.466667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>3568677</Hsp_hit-from> + <Hsp_hit-to>3568706</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TTGCTGTTGCCATCGCTTTTCAGGACATAC</Hsp_qseq> + <Hsp_hseq>TTGCTGTTGCCATCGCTTTTCAGGACATAC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>52</Iteration_iter-num> + <Iteration_query-ID>lcl|52_0</Iteration_query-ID> + <Iteration_query-def>51_0.533333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>3739788</Hsp_hit-from> + <Hsp_hit-to>3739817</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>CGACGGTATCGGTACGCAGATTGTGATGGA</Hsp_qseq> + <Hsp_hseq>CGACGGTATCGGTACGCAGATTGTGATGGA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>53</Iteration_iter-num> + <Iteration_query-ID>lcl|53_0</Iteration_query-ID> + <Iteration_query-def>52_0.366667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>3789407</Hsp_hit-from> + <Hsp_hit-to>3789436</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>ATGAGCATCAACATCGAAATCTCAAACCAA</Hsp_qseq> + <Hsp_hseq>ATGAGCATCAACATCGAAATCTCAAACCAA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>55</Iteration_iter-num> + <Iteration_query-ID>lcl|55_0</Iteration_query-ID> + <Iteration_query-def>54_0.400000</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>3161991</Hsp_hit-from> + <Hsp_hit-to>3162020</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GTATTCTTCATTGATTTGTAAGCGGGTACC</Hsp_qseq> + <Hsp_hseq>GTATTCTTCATTGATTTGTAAGCGGGTACC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>56</Iteration_iter-num> + <Iteration_query-ID>lcl|56_0</Iteration_query-ID> + <Iteration_query-def>55_0.466667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>4384753</Hsp_hit-from> + <Hsp_hit-to>4384782</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>AAGCGCTGTTCAACATAAATTGGCTGACGG</Hsp_qseq> + <Hsp_hseq>AAGCGCTGTTCAACATAAATTGGCTGACGG</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>57</Iteration_iter-num> + <Iteration_query-ID>lcl|57_0</Iteration_query-ID> + <Iteration_query-def>56_0.433333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2915787</Hsp_hit-from> + <Hsp_hit-to>2915816</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>AACCGTCAGCTCTTTACGCAATATTTTGCC</Hsp_qseq> + <Hsp_hseq>AACCGTCAGCTCTTTACGCAATATTTTGCC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>58</Iteration_iter-num> + <Iteration_query-ID>lcl|58_0</Iteration_query-ID> + <Iteration_query-def>57_0.566667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>294604</Hsp_hit-from> + <Hsp_hit-to>294633</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>CGCGAAATCCTCGACGTCCAGGCACGTATT</Hsp_qseq> + <Hsp_hseq>CGCGAAATCCTCGACGTCCAGGCACGTATT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>59</Iteration_iter-num> + <Iteration_query-ID>lcl|59_0</Iteration_query-ID> + <Iteration_query-def>58_0.300000</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1553483</Hsp_hit-from> + <Hsp_hit-to>1553512</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GTTATCCATTAAAATAGATCGGATCGATAT</Hsp_qseq> + <Hsp_hseq>GTTATCCATTAAAATAGATCGGATCGATAT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>60</Iteration_iter-num> + <Iteration_query-ID>lcl|60_0</Iteration_query-ID> + <Iteration_query-def>59_0.300000</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1351506</Hsp_hit-from> + <Hsp_hit-to>1351535</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>AAAATCTGCATATCATGATAAGAGTGGTTA</Hsp_qseq> + <Hsp_hseq>AAAATCTGCATATCATGATAAGAGTGGTTA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>2</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>2997458</Hsp_hit-from> + <Hsp_hit-to>2997487</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>-1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TAACCACTCTTATCATGATATGCAGATTTT</Hsp_qseq> + <Hsp_hseq>TAACCACTCTTATCATGATATGCAGATTTT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>62</Iteration_iter-num> + <Iteration_query-ID>lcl|62_0</Iteration_query-ID> + <Iteration_query-def>61_0.366667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1987157</Hsp_hit-from> + <Hsp_hit-to>1987186</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TCAGTTTGAAAGCTTTGTCAGCCGTTTTTT</Hsp_qseq> + <Hsp_hseq>TCAGTTTGAAAGCTTTGTCAGCCGTTTTTT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>63</Iteration_iter-num> + <Iteration_query-ID>lcl|63_0</Iteration_query-ID> + <Iteration_query-def>62_0.366667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1667830</Hsp_hit-from> + <Hsp_hit-to>1667859</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>AATCCTAAACCTAGGAATGCCAGAATATCT</Hsp_qseq> + <Hsp_hseq>AATCCTAAACCTAGGAATGCCAGAATATCT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>64</Iteration_iter-num> + <Iteration_query-ID>lcl|64_0</Iteration_query-ID> + <Iteration_query-def>63_0.566667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>231418</Hsp_hit-from> + <Hsp_hit-to>231447</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>-1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_qseq> + <Hsp_hseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>2</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>3516862</Hsp_hit-from> + <Hsp_hit-to>3516891</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TCACGCTCGCAGTCAAGCTGGCTTATGCCA</Hsp_qseq> + <Hsp_hseq>TCACGCTCGCAGTCAAGCTGGCTTATGCCA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>3</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>4226650</Hsp_hit-from> + <Hsp_hit-to>4226679</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TCACGCTCGCAGTCAAGCTGGCTTATGCCA</Hsp_qseq> + <Hsp_hseq>TCACGCTCGCAGTCAAGCTGGCTTATGCCA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>4</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>4808457</Hsp_hit-from> + <Hsp_hit-to>4808486</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>-1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_qseq> + <Hsp_hseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>5</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>4904735</Hsp_hit-from> + <Hsp_hit-to>4904764</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>-1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_qseq> + <Hsp_hseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>6</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>5048915</Hsp_hit-from> + <Hsp_hit-to>5048944</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>-1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_qseq> + <Hsp_hseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>7</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>5089922</Hsp_hit-from> + <Hsp_hit-to>5089951</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>-1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_qseq> + <Hsp_hseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>65</Iteration_iter-num> + <Iteration_query-ID>lcl|65_0</Iteration_query-ID> + <Iteration_query-def>64_0.500000</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>5440369</Hsp_hit-from> + <Hsp_hit-to>5440398</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GAGATGACGGTTGCAGAGTCATGCGTTTGA</Hsp_qseq> + <Hsp_hseq>GAGATGACGGTTGCAGAGTCATGCGTTTGA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps>

1 0

[hg] galaxy 1689: Better exception handling, messaging for uploa...
by Greg Von Kuster 06 Jan '09

06 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/cf3c6da6f552 changeset: 1689:cf3c6da6f552 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Jan 06 11:35:49 2009 -0500 description: Better exception handling, messaging for upload utility. 3 file(s) affected in this change: lib/galaxy/datatypes/sniff.py lib/galaxy/tools/actions/upload.py test/functional/test_toolbox.py diffs (140 lines): diff -r e0162b7bf0ba -r cf3c6da6f552 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py Tue Jan 06 11:11:24 2009 -0500 +++ b/lib/galaxy/datatypes/sniff.py Tue Jan 06 11:35:49 2009 -0500 @@ -12,11 +12,11 @@ full_path = os.path.join(path, 'test', fname) return full_path -def stream_to_file(stream): +def stream_to_file( stream, suffix='', prefix='', dir=None, text=False ): """ Writes a stream to a temporary file, returns the temporary file's name """ - fd, temp_name = tempfile.mkstemp() + fd, temp_name = tempfile.mkstemp( suffix=suffix, prefix=prefix, dir=dir, text=text ) while 1: chunk = stream.read(1048576) if not chunk: diff -r e0162b7bf0ba -r cf3c6da6f552 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Tue Jan 06 11:11:24 2009 -0500 +++ b/lib/galaxy/tools/actions/upload.py Tue Jan 06 11:35:49 2009 -0500 @@ -44,22 +44,33 @@ trans.log_event( 'created job id %d' % job.id, tool_id=tool.id ) if 'local_filename' in dir( data_file ): # Use the existing file + file_name = data_file.filename + file_name = file_name.split( '\\' )[-1] + file_name = file_name.split( '/' )[-1] try: - file_name = data_file.filename - file_name = file_name.split( '\\' )[-1] - file_name = file_name.split( '/' )[-1] data_list.append( self.add_file( trans, data_file.local_filename, file_name, file_type, dbkey, space_to_tab=space_to_tab ) ) except Exception, e: - return self.upload_empty( trans, job, "Error:", str( e ) ) + errmsg = 'exception in add_file using datafile.local_filename %s: %s' % ( data_file.local_filename, str( e ) ) + return self.upload_empty( trans, job, "Error:", errmsg ) elif 'filename' in dir( data_file ): + file_name = data_file.filename + file_name = file_name.split( '\\' )[-1] + file_name = file_name.split( '/' )[-1] try: - file_name = data_file.filename - file_name = file_name.split( '\\' )[-1] - file_name = file_name.split( '/' )[-1] - temp_name = sniff.stream_to_file( data_file.file ) + temp_name = sniff.stream_to_file( data_file.file, prefix='upload' ) + except Exception, e: + try: + # Attempt to remove temporary file + os.unlink( temp_name ) + except: + pass + errmsg = 'exception in sniff.stream_to_file using file %s: %s' % ( data_file.filename, str( e ) ) + return self.upload_empty( trans, job, "Error:", errmsg ) + try: data_list.append( self.add_file( trans, temp_name, file_name, file_type, dbkey, space_to_tab=space_to_tab ) ) except Exception, e: - return self.upload_empty( trans, job, "Error:", str( e ) ) + errmsg = 'exception in add_file using file temp_name %s: %s' % ( str( temp_name ), str( e ) ) + return self.upload_empty( trans, job, "Error:", errmsg ) if url_paste not in [ None, "" ]: if url_paste.lower().find( 'http://' ) >= 0 or url_paste.lower().find( 'ftp://' ) >= 0: url_paste = url_paste.replace( '\r', '' ).split( '\n' ) @@ -67,10 +78,20 @@ line = line.rstrip( '\r\n' ) if line: try: - temp_name = sniff.stream_to_file( urllib.urlopen( line ) ) + temp_name = sniff.stream_to_file( urllib.urlopen( line ), prefix='url_paste' ) + except Exception, e: + try: + # Attempt to remove temporary file + os.unlink( temp_name ) + except: + pass + errmsg = 'exception in sniff.stream_to_file using url_paste %s: %s' % ( url_paste, str( e ) ) + return self.upload_empty( trans, job, "Error:", errmsg ) + try: data_list.append( self.add_file( trans, temp_name, line, file_type, dbkey, info="uploaded url", space_to_tab=space_to_tab ) ) except Exception, e: - return self.upload_empty( trans, job, "Error:", str( e ) ) + errmsg = 'exception in add_file using url_paste temp_name %s: %s' % ( str( temp_name ), str( e ) ) + return self.upload_empty( trans, job, "Error:", errmsg ) else: is_valid = False for line in url_paste: @@ -80,10 +101,20 @@ break if is_valid: try: - temp_name = sniff.stream_to_file( StringIO.StringIO( url_paste ) ) + temp_name = sniff.stream_to_file( StringIO.StringIO( url_paste ), prefix='strio_url_paste' ) + except Exception, e: + try: + # Attempt to remove temporary file + os.unlink( temp_name ) + except: + pass + errmsg = 'exception in sniff.stream_to_file using StringIO.StringIO( url_paste ) %s: %s' % ( url_paste, str( e ) ) + return self.upload_empty( trans, job, "Error:", errmsg ) + try: data_list.append( self.add_file( trans, temp_name, 'Pasted Entry', file_type, dbkey, info="pasted entry", space_to_tab=space_to_tab ) ) except Exception, e: - return self.upload_empty( trans, job, "Error:", str( e ) ) + errmsg = 'exception in add_file using StringIO.StringIO( url_paste ) temp_name %s: %s' % ( str( temp_name ), str( e ) ) + return self.upload_empty( trans, job, "Error:", errmsg ) else: return self.upload_empty( trans, job, "No data error:", "you pasted no data." ) if self.empty: @@ -103,7 +134,7 @@ log.info("End of tool %s execution for job id %d, memory used increased by %s" % ( tool.id, job.id, m1 ) ) return dict( output=hda ) - def upload_empty(self, trans, job, err_code, err_msg): + def upload_empty( self, trans, job, err_code, err_msg ): data = trans.app.model.HistoryDatasetAssociation( create_dataset = True ) data.name = err_code data.extension = "txt" @@ -119,8 +150,8 @@ job.info = err_msg job.add_output_dataset( data.name, data ) job.flush() - log.info( 'job id %d ended with errors' % job.id ) - trans.log_event( 'job id %d ended with errors' % job.id, tool_id=job.tool_id ) + log.info( 'job id %d ended with errors, err_msg: %s' % ( job.id, err_msg ) ) + trans.log_event( 'job id %d ended with errors, err_msg: %s' % ( job.id, err_msg ), tool_id=job.tool_id ) return dict( output=data ) def add_file( self, trans, temp_name, file_name, file_type, dbkey, info=None, space_to_tab=False ): diff -r e0162b7bf0ba -r cf3c6da6f552 test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Tue Jan 06 11:11:24 2009 -0500 +++ b/test/functional/test_toolbox.py Tue Jan 06 11:35:49 2009 -0500 @@ -8,7 +8,6 @@ class ToolTestCase( TwillTestCase ): """Abstract test case that runs tests based on a `galaxy.tools.test.ToolTest`""" def do_it( self ): - print "###self.testdef: ", self.testdef # If the test generation had an error, raise if self.testdef.error: if self.testdef.exception:

1 0

[hg] galaxy 1690: log exceptions when removing temporary files w...
by Greg Von Kuster 06 Jan '09

06 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/317d5f454dfd changeset: 1690:317d5f454dfd user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Jan 06 13:29:03 2009 -0500 description: log exceptions when removing temporary files when upload fails. 1 file(s) affected in this change: lib/galaxy/tools/actions/upload.py diffs (30 lines): diff -r cf3c6da6f552 -r 317d5f454dfd lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Tue Jan 06 11:35:49 2009 -0500 +++ b/lib/galaxy/tools/actions/upload.py Tue Jan 06 13:29:03 2009 -0500 @@ -63,7 +63,7 @@ # Attempt to remove temporary file os.unlink( temp_name ) except: - pass + log.exception( 'failure removing temporary file: %s' % temp_name ) errmsg = 'exception in sniff.stream_to_file using file %s: %s' % ( data_file.filename, str( e ) ) return self.upload_empty( trans, job, "Error:", errmsg ) try: @@ -84,7 +84,7 @@ # Attempt to remove temporary file os.unlink( temp_name ) except: - pass + log.exception( 'failure removing temporary file: %s' % temp_name ) errmsg = 'exception in sniff.stream_to_file using url_paste %s: %s' % ( url_paste, str( e ) ) return self.upload_empty( trans, job, "Error:", errmsg ) try: @@ -107,7 +107,7 @@ # Attempt to remove temporary file os.unlink( temp_name ) except: - pass + log.exception( 'failure removing temporary file: %s' % temp_name ) errmsg = 'exception in sniff.stream_to_file using StringIO.StringIO( url_paste ) %s: %s' % ( url_paste, str( e ) ) return self.upload_empty( trans, job, "Error:", errmsg ) try:

1 0

[hg] galaxy 1688: Added a new option to the grouping tool to fac...
by Greg Von Kuster 06 Jan '09

06 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e0162b7bf0ba changeset: 1688:e0162b7bf0ba user: guru date: Tue Jan 06 11:11:24 2009 -0500 description: Added a new option to the grouping tool to facilitate picking of random entries from columns not chosen for either grouping or aggregate operations. 2 file(s) affected in this change: tools/stats/grouping.py tools/stats/grouping.xml diffs (230 lines): diff -r 091573fd6e27 -r e0162b7bf0ba tools/stats/grouping.py --- a/tools/stats/grouping.py Mon Jan 05 15:26:17 2009 -0500 +++ b/tools/stats/grouping.py Tue Jan 06 11:11:24 2009 -0500 @@ -12,13 +12,15 @@ def main(): inputfile = sys.argv[2] + in_columns = int( sys.argv[5] ) + show_remaining_cols = sys.argv[4] ops = [] cols = [] rounds = [] elems = [] - for var in sys.argv[4:]: + for var in sys.argv[6:]: ops.append(var.split()[0]) cols.append(var.split()[1]) rounds.append(var.split()[2]) @@ -79,9 +81,19 @@ if error_code != 0: stop_err( "Sorting input dataset resulted in error: %s: %s" %( error_code, stdout )) - + + if show_remaining_cols == 'yes': + show_cols_list = [1]*in_columns + show_cols_list[group_col] = 0 + for c in cols: + c = int(c)-1 + show_cols_list[c] = 0 + #at the end of this, only the indices of the remaining columns will be set to 1 + remaining_cols = [j for j,k in enumerate(show_cols_list) if k==1] #this is the list of remaining column indices + prev_item = "" prev_vals = [] + remaining_vals = [] skipped_lines = 0 first_invalid_line = 0 invalid_line = '' @@ -116,22 +128,30 @@ invalid_column = col+1 if valid: prev_vals[i].append(fields[col].strip()) + #Store values from all the remaning columns + if show_remaining_cols == 'yes': + for j, index in enumerate(remaining_cols): + remaining_vals[j].append(fields[index].strip()) else: """ When a new value is encountered, write the previous value and the corresponding aggregate values into the output file. This works due to the sort on group_col we've applied to the data above. """ - out_str = prev_item - + out_list = ['']*in_columns + out_list[group_col] = str(prev_item) + for i, op in enumerate( ops ): rfunc = "r." + op if op not in ['c','length','unique','random']: for j, elem in enumerate( prev_vals[i] ): prev_vals[i][j] = float( elem ) - rout = "%g" %( eval( rfunc )( prev_vals[i] )) if rounds[i] == 'yes': + rout = "%f" %( eval( rfunc )( prev_vals[i] )) rout = int(round(float(rout))) + else: + rout = "%g" %( eval( rfunc )( prev_vals[i] )) + else: if op != 'random': rout = eval( rfunc )( prev_vals[i] ) @@ -142,9 +162,21 @@ if op == 'unique': rfunc = "r.length" rout = eval( rfunc )( rout ) - out_str += "\t" + str(rout) - - print >>fout, out_str + + out_list[int(cols[i])-1] = str(rout) + + if show_remaining_cols == 'yes': + for index,el in enumerate(remaining_cols): + if index == 0: + try: + random_index = random.randint(0,len(remaining_vals[index])-1) + except: + random_index = 0 + #pick a random value from each of the remaning columns + rand_out = remaining_vals[index][random_index] + out_list[el] = str(rand_out) + + print >>fout, '\t'.join([elem for elem in out_list if elem != '']) prev_item = item prev_vals = [] @@ -153,6 +185,14 @@ val_list = [] val_list.append(fields[col].strip()) prev_vals.append(val_list) + + if show_remaining_cols == 'yes': + remaining_vals = [] + for index in remaining_cols: + remaining_val_list = [] + remaining_val_list.append(fields[index].strip()) + remaining_vals.append(remaining_val_list) + else: # This only occurs once, right at the start of the iteration. prev_item = item @@ -161,8 +201,15 @@ val_list = [] val_list.append(fields[col].strip()) prev_vals.append(val_list) + + if show_remaining_cols == 'yes': + remaining_vals = [] + for index in remaining_cols: + remaining_val_list = [] + remaining_val_list.append(fields[index].strip()) + remaining_vals.append(remaining_val_list) - except Exception, exc: + except Exception: skipped_lines += 1 if not first_invalid_line: first_invalid_line = ii+1 @@ -172,7 +219,8 @@ first_invalid_line = ii+1 # Handle the last grouped value - out_str = prev_item + out_list = ['']*in_columns + out_list[group_col] = str(prev_item) for i, op in enumerate(ops): rfunc = "r." + op @@ -180,9 +228,11 @@ if op not in ['c','length','unique','random']: for j, elem in enumerate( prev_vals[i] ): prev_vals[i][j] = float( elem ) - rout = '%g' %( eval( rfunc )( prev_vals[i] )) if rounds[i] == 'yes': + rout = '%f' %( eval( rfunc )( prev_vals[i] )) rout = int(round(float(rout))) + else: + rout = '%g' %( eval( rfunc )( prev_vals[i] )) else: if op != 'random': rout = eval( rfunc )( prev_vals[i] ) @@ -193,13 +243,22 @@ if op == 'unique': rfunc = "r.length" rout = eval( rfunc )( rout ) - out_str += "\t" + str( rout ) + out_list[int(cols[i])-1] = str(rout) except: skipped_lines += 1 if not first_invalid_line: first_invalid_line = ii+1 + if show_remaining_cols == 'yes': + for index,el in enumerate(remaining_cols): + if index == 0: + try: + random_index = random.randint(0,len(remaining_vals[index])-1) + except: + random_index = 0 + rand_out = remaining_vals[index][random_index] + out_list[el] = str(rand_out) - print >>fout, out_str + print >>fout, '\t'.join([elem for elem in out_list if elem != '']) # Generate a useful info message. msg = "--Group by c%d: " %(group_col+1) diff -r 091573fd6e27 -r e0162b7bf0ba tools/stats/grouping.xml --- a/tools/stats/grouping.xml Mon Jan 05 15:26:17 2009 -0500 +++ b/tools/stats/grouping.xml Tue Jan 06 11:11:24 2009 -0500 @@ -1,10 +1,12 @@ -<tool id="Grouping1" name="Group" version="1.4.0"> +<tool id="Grouping1" name="Group" version="1.5.0"> <description>data by a column and perform aggregate operation on other columns.</description> <command interpreter="python"> grouping.py $out_file1 $input1 - $groupcol + $groupcol + $othercols + ${input1.metadata.columns} #for $op in $operations '${op.optype} ${op.opcol} @@ -30,7 +32,11 @@ <option value="no">NO</option> <option value="yes">YES</option> </param> - </repeat> + </repeat> + <param name="othercols" type="select" label="Randomly pick an entry from each of the remaining columns (besides the columns chosen for group and aggregate operations above) ?"> + <option value="no">NO</option> + <option value="yes">YES</option> + </param> </inputs> <outputs> <data format="input" name="out_file1" metadata_source="input1" /> @@ -46,9 +52,9 @@ <param name="optype" value="mean"/> <param name="opcol" value="2"/> <param name="opround" value="no"/> + <param name="othercols" value="no"/> <output name="out_file1" file="groupby_out1.dat"/> </test> -  <test> <param name="input1" value="1.tabular"/> @@ -56,6 +62,7 @@ <param name="optype" value="mean"/> <param name="opcol" value="2"/> <param name="opround" value="no"/> + <param name="othercols" value="no"/> <output name="out_file1" file="groupby_out2.dat"/> </test> </tests>

1 0

[hg] galaxy 1687: megablast fix from Anton
by Nate Coraor 05 Jan '09

05 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/091573fd6e27 changeset: 1687:091573fd6e27 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Jan 05 15:26:17 2009 -0500 description: megablast fix from Anton 1 file(s) affected in this change: tools/metag_tools/megablast_xml_parser.py diffs (20 lines): diff -r 696fc4c02a0c -r 091573fd6e27 tools/metag_tools/megablast_xml_parser.py --- a/tools/metag_tools/megablast_xml_parser.py Tue Dec 23 13:28:27 2008 -0500 +++ b/tools/metag_tools/megablast_xml_parser.py Mon Jan 05 15:26:17 2009 -0500 @@ -1,6 +1,6 @@ #! /usr/bin/python -import sys, os +import sys, os, re assert sys.version_info[:2] >= ( 2, 4 ) @@ -55,6 +55,8 @@ # for every <Hit> within <Iteration> for hit in elem.findall( "Iteration_hits/Hit/" ): subject = hit.findtext( "Hit_id" ) + if re.search( '^gi', subject ): + subject = subject.split('|')[1] sLen = hit.findtext( "Hit_len" ) # for every <Hsp> within <Hit> for hsp in hit.findall( "Hit_hsps/Hsp" ):

1 0

Storing/Peeking/Downloading compressed files
by Assaf Gordon 27 Dec '08

27 Dec '08

Hello, I'd like to request/suggest a feature: Semi-Transparent support for compressed files. The feature requires four (tiny) patches (detailed below). With this feature, dataset files (/database/files/NNN/dataset_NNNN.dat) can be stored compressed, and their content will be automatically 'peeked' in the preview window. Additionally, when a user clicks 'save' or 'eye icon', they will be uncompressed on-the-fly - so the user doesn't need to know/care they are compressed. Of course, there's the whole issue of making the different tools read and write compressed files - but that's another story. It's actually not too complicated story: In Python, just call gzip.open instead of open. In shell scripts, pipe the input file through "zcat -f FILE | program". In Perl, use PerlIO::Gzip module. Comments are welcomed, Regards, Gordon. First Patch - Adding a function to "util" module, which returns a Gzip/Bzip2/Zip File object (or a plain File object) based on the file type. File type detection is done using the 'magic' module - I think it is quite standard (in ubuntu I got it with "apt-get install python-magic"). However, to get galaxy to find this module I had to remove the "-ES" from "run.sh" - I'm sure there's a better way to do it. ==================================================================== --- ./lib/galaxy/util/__init__.orig.py 2008-12-26 23:48:40.000000000 -0500 +++ ./lib/galaxy/util/__init__.py 2008-12-27 00:31:44.000000000 -0500 @@ -14,11 +14,41 @@ from galaxy.util.docutils_ext.htmlfrag i pkg_resources.require( 'elementtree' ) from elementtree import ElementTree +import magic # file detection +import gzip # allow peeking into compressed files +import bz2 +import zipfile + log = logging.getLogger(__name__) _lock = threading.RLock() gzip_magic = '\037\213' +# Magic file detection +magic_file = magic.open(magic.MAGIC_MIME) +try: + magic_file.load() +except: + magic_file = None + +def open_file_wrapper(filename): + file_mime = "" + if magic_file is not None: + try: + file_mime = magic_file.file(filename) + except: + file_mime = "" + if file_mime == "application/x-gzip": + return gzip.open(filename) + if file_mime == "application/x-bzip2": + return bz2.BZ2File(filename) + if file_mime == "appication/x-zip": + return zipfile.ZipFile(filename) + + #for all other mime types, return the raw file + return file(filename) + + def synchronized(func): """This wrapper will serialize access to 'func' to a single thread. Use it as a decorator.""" def caller(*params, **kparams): ==================================================================== Second Patch - In the 'display' action of the root web controller, return the file with the appropriate wrapper ==================================================================== --- ./lib/galaxy/web/controllers/root_orig.py 2008-12-26 23:56:01.000000000 -0500 +++ ./lib/galaxy/web/controllers/root.py 2008-12-27 00:35:43.000000000 -0500 @@ -153,7 +153,7 @@ class RootController( BaseController ): m1 = trans.app.memory_usage.memory( m0, pretty=True ) log.info( "End of root/display, memory used increased by %s" % m1 ) try: - return open( data.file_name ) + return util.open_file_wrapper( data.file_name ) except: return "This dataset contains no content" else: ==================================================================== Third patch - In the BaseController object, allow streaming on compressed files (not just types.FileTypes): ==================================================================== --- ./lib/galaxy/web/framework/base_orig.py 2008-12-27 00:41:38.000000000 -0500 +++ ./lib/galaxy/web/framework/base.py 2008-12-27 00:41:37.000000000 -0500 @@ -25,6 +25,11 @@ from paste.response import HeaderDict # For FieldStorage import cgi +# For auto-decompressing files +import gzip +import bz2 +import zipfile + log = logging.getLogger( __name__ ) class WebApplication( object ): @@ -133,7 +138,7 @@ class WebApplication( object ): if callable( body ): # Assume the callable is another WSGI application to run return body( environ, start_response ) - elif isinstance( body, types.FileType ): + elif isinstance( body, (types.FileType, gzip.GzipFile, bz2.BZ2File, zipfile.ZipFile) ): # Stream the file back to the browser return send_file( start_response, trans, body ) else: ==================================================================== Fourth Patch - In the generic Data datatype object, replace the file object with a compressed file object in the peek function: ==================================================================== --- ./lib/galaxy/datatypes/data.py 2008-12-26 23:34:15.000000000 -0500 +++ ./lib/galaxy/datatypes/data_orig.py 2008-12-26 23:21:41.000000000 -0500 @@ -332,7 +332,7 @@ def get_file_peek( file_name, WIDTH=256, count = 0 file_type = '' data_checked = False - for line in util.open_file_wrapper( file_name ): + for line in file( file_name ): line = line[ :WIDTH ] if not data_checked and line: data_checked = True ====================================================================

1 0

Downloading entire history as tar.gz archive
by Assaf Gordon 24 Dec '08

24 Dec '08

Hello, Did you ever wish you could download all the datasets in the current history as TAR.GZ file ? I know I did... The attached file will allow you to do that (assuming you have your own local galaxy server). Installation ------------- 1. put the attached file (history_exporter.py) in the galaxy directory, in: [GALAXY]/lib/galaxy/web/controllers 2. Install GNU TAR version 1.20 Most linux distributions don't yet have tar 1.20, but it is required for this module to work... You'll probably have to install it from source: http://www.gnu.org/software/tar/ 3. Change line 82 (tar_exe variable) in 'history_exporter.py' to point to the path of the new tar. Usage ------ Reload galaxy and switch to a history with some datasets, then browse to: http://YOUR-GALAXY-URL/history_exporter/export This will start a download of a tar.gz file containing all the datasets in the current history (properly renamed, not as 'dataset_XXXX'). Additionally, a README.txt file is added to the tarball, describing each dataset. To see how the tar file is created, go to: http://YOUR-GALAXY-URL/history_exporter/debug Comments are welcome, Happy Holidays, Gordon.

1 0

[hg] galaxy 1686: Since tempfiles seem to occasionally be left b...
by Nate Coraor 23 Dec '08

23 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/696fc4c02a0c changeset: 1686:696fc4c02a0c user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Dec 23 13:28:27 2008 -0500 description: Since tempfiles seem to occasionally be left behind, allow logging of open tempfiles, including a traceback (to determine callers) if LOG_TEMPFILES is set in the environment when Galaxy starts. This should be considered temporary and will be removed when it's determined where/how this happens. 2 file(s) affected in this change: lib/log_tempfile.py scripts/paster.py diffs (46 lines): diff -r 82886ba9323b -r 696fc4c02a0c lib/log_tempfile.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/log_tempfile.py Tue Dec 23 13:28:27 2008 -0500 @@ -0,0 +1,27 @@ +# override tempfile methods for debugging + +import tempfile, traceback + +import logging +log = logging.getLogger( __name__ ) + +class TempFile( object ): + def __init__( self ): + tempfile._NamedTemporaryFile = tempfile.NamedTemporaryFile + tempfile._mkstemp = tempfile.mkstemp + tempfile.NamedTemporaryFile = self.NamedTemporaryFile + tempfile.mkstemp = self.mkstemp + def NamedTemporaryFile( self, *args, **kwargs ): + f = tempfile._NamedTemporaryFile( *args, **kwargs ) + try: + log.debug( ( "Opened tempfile %s with NamedTemporaryFile:\n" % f.name ) + "".join( traceback.format_stack() ) ) + except AttributeError: + pass + return f + def mkstemp( self, *args, **kwargs ): + f = tempfile._mkstemp( *args, **kwargs ) + try: + log.debug( ( "Opened tempfile %s with mkstemp:\n" % f[1] ) + "".join( traceback.format_stack() ) ) + except TypeError: + pass + return f diff -r 82886ba9323b -r 696fc4c02a0c scripts/paster.py --- a/scripts/paster.py Mon Dec 22 13:35:01 2008 -0500 +++ b/scripts/paster.py Tue Dec 23 13:28:27 2008 -0500 @@ -16,6 +16,11 @@ from galaxy import eggs import pkg_resources +if 'LOG_TEMPFILES' in os.environ: + from log_tempfile import TempFile + _log_tempfile = TempFile() + import tempfile + pkg_resources.require( "PasteScript" ) from paste.script import command

1 0

[hg] galaxy 1685: Script to enumerate GOPS JOIN jobs that could ...
by Nate Coraor 23 Dec '08

23 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/82886ba9323b changeset: 1685:82886ba9323b user: guru date: Mon Dec 22 13:35:01 2008 -0500 description: Script to enumerate GOPS JOIN jobs that could have returned an incorrect result before the issue with minimum overlap was fixed last week. 3 file(s) affected in this change: scripts/others/incorrect_gops_jobs.py scripts/others/incorrect_gops_join_jobs.py scripts/others/incorrect_gops_join_jobs.sh diffs (126 lines): diff -r c1d3004f0613 -r 82886ba9323b scripts/others/incorrect_gops_jobs.py --- a/scripts/others/incorrect_gops_jobs.py Mon Dec 22 12:15:02 2008 -0500 +++ b/scripts/others/incorrect_gops_jobs.py Mon Dec 22 13:35:01 2008 -0500 @@ -76,7 +76,10 @@ else: new_cmd_line = " ".join(map(str,cmd_line.split()[:3])) + " " + new_output.name + " " + " ".join(map(str,cmd_line.split()[4:])) job_output = cmd_line.split()[3] - os.system(new_cmd_line) + try: + os.system(new_cmd_line) + except: + pass diff_status = os.system('diff %s %s >> /dev/null' %(new_output.name, job_output)) if diff_status == 0: continue diff -r c1d3004f0613 -r 82886ba9323b scripts/others/incorrect_gops_join_jobs.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/others/incorrect_gops_join_jobs.py Mon Dec 22 13:35:01 2008 -0500 @@ -0,0 +1,99 @@ +#!/usr/bin/env python +""" +Fetch gops_join wherein the use specified minimum coverage is not 1. +""" + +from galaxy import eggs +import sys, os, ConfigParser, tempfile +import galaxy.app +import galaxy.model.mapping +import pkg_resources + +pkg_resources.require( "SQLAlchemy >= 0.4" ) +import sqlalchemy as sa + +assert sys.version_info[:2] >= ( 2, 4 ) + +class TestApplication( object ): + """Encapsulates the state of a Universe application""" + def __init__( self, database_connection=None, file_path=None ): + print >> sys.stderr, "python path is: " + ", ".join( sys.path ) + if database_connection is None: + raise Exception( "CleanupDatasetsApplication requires a database_connection value" ) + if file_path is None: + raise Exception( "CleanupDatasetsApplication requires a file_path value" ) + self.database_connection = database_connection + self.file_path = file_path + # Setup the database engine and ORM + self.model = galaxy.model.mapping.init( self.file_path, self.database_connection, engine_options={}, create_tables=False ) + +def main(): + ini_file = sys.argv[1] + conf_parser = ConfigParser.ConfigParser( {'here':os.getcwd()} ) + conf_parser.read( ini_file ) + configuration = {} + for key, value in conf_parser.items( "app:main" ): + configuration[key] = value + database_connection = configuration['database_connection'] + file_path = configuration['file_path'] + app = TestApplication( database_connection=database_connection, file_path=file_path ) + jobs = {} + try: + for job in app.model.Job.filter( sa.and_( app.model.Job.table.c.create_time < '2008-12-16', + app.model.Job.table.c.state == 'ok', + app.model.Job.table.c.tool_id == 'gops_join_1', + sa.not_( app.model.Job.table.c.command_line.like( '%-m 1 %' ) ) + ) + ).all(): + print "# processing job id %s" % str( job.id ) + for jtoda in job.output_datasets: + print "# --> processing JobToOutputDatasetAssociation id %s" % str( jtoda.id ) + hda = app.model.HistoryDatasetAssociation.get( jtoda.dataset_id ) + print "# ----> processing HistoryDatasetAssociation id %s" % str( hda.id ) + if not hda.deleted: + # Probably don't need this check, since the job state should suffice, but... + if hda.dataset.state == 'ok': + history = app.model.History.get( hda.history_id ) + print "# ------> processing history id %s" % str( history.id ) + if history.user_id: + cmd_line = str( job.command_line ) + new_output = tempfile.NamedTemporaryFile('w') + new_cmd_line = " ".join(map(str,cmd_line.split()[:4])) + " " + new_output.name + " " + " ".join(map(str,cmd_line.split()[5:])) + job_output = cmd_line.split()[4] + try: + os.system(new_cmd_line) + except: + pass + diff_status = os.system('diff %s %s >> /dev/null' %(new_output.name, job_output)) + if diff_status == 0: + continue + print "# --------> Outputs differ" + user = app.model.User.get( history.user_id ) + jobs[ job.id ] = {} + jobs[ job.id ][ 'hda_id' ] = hda.id + jobs[ job.id ][ 'hda_name' ] = hda.name + jobs[ job.id ][ 'hda_info' ] = hda.info + jobs[ job.id ][ 'history_id' ] = history.id + jobs[ job.id ][ 'history_name' ] = history.name + jobs[ job.id ][ 'history_update_time' ] = history.update_time + jobs[ job.id ][ 'user_email' ] = user.email + except Exception, e: + print "# caught exception: %s" % str( e ) + + print "\n\n# Number of incorrect Jobs: %d\n\n" % ( len( jobs ) ) + print "#job_id\thda_id\thda_name\thda_info\thistory_id\thistory_name\thistory_update_time\tuser_email" + for jid in jobs: + print '%s\t%s\t"%s"\t"%s"\t%s\t"%s"\t"%s"\t%s' % \ + ( str( jid ), + str( jobs[ jid ][ 'hda_id' ] ), + jobs[ jid ][ 'hda_name' ], + jobs[ jid ][ 'hda_info' ], + str( jobs[ jid ][ 'history_id' ] ), + jobs[ jid ][ 'history_name' ], + jobs[ jid ][ 'history_update_time' ], + jobs[ jid ][ 'user_email' ] + ) + sys.exit(0) + +if __name__ == "__main__": + main() diff -r c1d3004f0613 -r 82886ba9323b scripts/others/incorrect_gops_join_jobs.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/others/incorrect_gops_join_jobs.sh Mon Dec 22 13:35:01 2008 -0500 @@ -0,0 +1,4 @@ +#!/bin/sh + +cd `dirname $0`/../.. +python ./scripts/others/incorrect_gops_join_jobs.py ./universe_wsgi.ini >> ./scripts/others/incorrect_gops_join_jobs.log

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