- galaxy-dev - lists.galaxyproject.org

[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> + <Hsp_hit-from>2032108</Hsp_hit-from> + <Hsp_hit-to>2032137</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>CGCGGGCGCACCACGTCGCTGCTGCTGTTC</Hsp_qseq> + <Hsp_hseq>CGCGGGCGCACCACGTCGCTGCTGCTGTTC</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>26</Iteration_iter-num> + <Iteration_query-ID>lcl|26_0</Iteration_query-ID> + <Iteration_query-def>25_0.266667</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>1343811</Hsp_hit-from> + <Hsp_hit-to>1343840</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>TTTTGGGAAAACTAAATACGCATCAAAAAT</Hsp_qseq> + <Hsp_hseq>TTTTGGGAAAACTAAATACGCATCAAAAAT</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>27</Iteration_iter-num> + <Iteration_query-ID>lcl|27_0</Iteration_query-ID> + <Iteration_query-def>26_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>3112551</Hsp_hit-from> + <Hsp_hit-to>3112580</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>CAACGAGGCGCTACCGAGTTGTTCAATGCG</Hsp_qseq> + <Hsp_hseq>CAACGAGGCGCTACCGAGTTGTTCAATGCG</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>29</Iteration_iter-num> + <Iteration_query-ID>lcl|29_0</Iteration_query-ID> + <Iteration_query-def>28_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>4405442</Hsp_hit-from> + <Hsp_hit-to>4405471</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>CGCTCAATCTGCTCGCGCCTGGCTGGCGTT</Hsp_qseq> + <Hsp_hseq>CGCTCAATCTGCTCGCGCCTGGCTGGCGTT</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>30</Iteration_iter-num> + <Iteration_query-ID>lcl|30_0</Iteration_query-ID> + <Iteration_query-def>29_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>3600547</Hsp_hit-from> + <Hsp_hit-to>3600576</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>CTCGTCCGGCGGGCGGTTTTGCCGACAAGG</Hsp_qseq> + <Hsp_hseq>CTCGTCCGGCGGGCGGTTTTGCCGACAAGG</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>33</Iteration_iter-num> + <Iteration_query-ID>lcl|33_0</Iteration_query-ID> + <Iteration_query-def>32_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>1435670</Hsp_hit-from> + <Hsp_hit-to>1435699</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>TGAGGATGGTCCTCTGACTCTGCAGGCGCA</Hsp_qseq> + <Hsp_hseq>TGAGGATGGTCCTCTGACTCTGCAGGCGCA</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>34</Iteration_iter-num> + <Iteration_query-ID>lcl|34_0</Iteration_query-ID> + <Iteration_query-def>33_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>3788178</Hsp_hit-from> + <Hsp_hit-to>3788207</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>TAGTAACCCTTTAATAAGATTGTCGATTAG</Hsp_qseq> + <Hsp_hseq>TAGTAACCCTTTAATAAGATTGTCGATTAG</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>35</Iteration_iter-num> + <Iteration_query-ID>lcl|35_0</Iteration_query-ID> + <Iteration_query-def>34_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>484499</Hsp_hit-from> + <Hsp_hit-to>484528</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>TGATGTTAAATGCATGGCACCTGCCGGTGC</Hsp_qseq> + <Hsp_hseq>TGATGTTAAATGCATGGCACCTGCCGGTGC</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>36</Iteration_iter-num> + <Iteration_query-ID>lcl|36_0</Iteration_query-ID> + <Iteration_query-def>35_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>2250064</Hsp_hit-from> + <Hsp_hit-to>2250093</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>ACTGCTTTGCCGAGATATTCGAGGTTAACC</Hsp_qseq> + <Hsp_hseq>ACTGCTTTGCCGAGATATTCGAGGTTAACC</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>37</Iteration_iter-num> + <Iteration_query-ID>lcl|37_0</Iteration_query-ID> + <Iteration_query-def>36_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>3698178</Hsp_hit-from> + <Hsp_hit-to>3698207</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>TGTTGGCAACATGGCGAGCGTAATCAATTA</Hsp_qseq> + <Hsp_hseq>TGTTGGCAACATGGCGAGCGTAATCAATTA</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>39</Iteration_iter-num> + <Iteration_query-ID>lcl|39_0</Iteration_query-ID> + <Iteration_query-def>38_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>4242501</Hsp_hit-from> + <Hsp_hit-to>4242530</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>GCAGCAGGATCGGATCGAACTCTGGTTTCT</Hsp_qseq> + <Hsp_hseq>GCAGCAGGATCGGATCGAACTCTGGTTTCT</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>40</Iteration_iter-num> + <Iteration_query-ID>lcl|40_0</Iteration_query-ID> + <Iteration_query-def>39_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>3683151</Hsp_hit-from> + <Hsp_hit-to>3683180</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>TAATGCGGCATTCTCCTGATTTATTGTCAC</Hsp_qseq> + <Hsp_hseq>TAATGCGGCATTCTCCTGATTTATTGTCAC</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>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> + <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>789086</Hsp_hit-from> + <Hsp_hit-to>789115</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>AGCTGACGGTCAGCAGGGATACTTCCTGCA</Hsp_qseq> + <Hsp_hseq>AGCTGACGGTCAGCAGGGATACTTCCTGCA</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>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> + <Hsp_qseq>GCAGTGACTACATCCGCGAGGTGAATGTGG</Hsp_qseq> + <Hsp_hseq>GCAGTGACTACATCCGCGAGGTGAATGTGG</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>44</Iteration_iter-num> + <Iteration_query-ID>lcl|44_0</Iteration_query-ID> + <Iteration_query-def>43_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>4272582</Hsp_hit-from> + <Hsp_hit-to>4272611</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>GCTTTTTCCAGCATCAACGCCACTGAACAA</Hsp_qseq> + <Hsp_hseq>GCTTTTTCCAGCATCAACGCCACTGAACAA</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>45</Iteration_iter-num> + <Iteration_query-ID>lcl|45_0</Iteration_query-ID> + <Iteration_query-def>44_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>5481023</Hsp_hit-from> + <Hsp_hit-to>5481052</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>AAAGTGGTAGATAACGTGGTGCAGACTATG</Hsp_qseq> + <Hsp_hseq>AAAGTGGTAGATAACGTGGTGCAGACTATG</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>46</Iteration_iter-num> + <Iteration_query-ID>lcl|46_0</Iteration_query-ID> + <Iteration_query-def>45_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>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>1271829</Hsp_hit-from> + <Hsp_hit-to>1271858</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>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

1 0

[hg] galaxy 1684: Modified sort options in grouping tool to work...
by Nate Coraor 23 Dec '08

23 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/c1d3004f0613 changeset: 1684:c1d3004f0613 user: guru date: Mon Dec 22 12:15:02 2008 -0500 description: Modified sort options in grouping tool to work correctly on older and newer versions of unix sort. Also included functional tests. 4 file(s) affected in this change: test-data/groupby_out1.dat test-data/groupby_out2.dat tools/stats/grouping.py tools/stats/grouping.xml diffs (126 lines): diff -r 96f2c4630e62 -r c1d3004f0613 test-data/groupby_out1.dat --- a/test-data/groupby_out1.dat Fri Dec 19 14:25:43 2008 -0500 +++ b/test-data/groupby_out1.dat Mon Dec 22 12:15:02 2008 -0500 @@ -1,21 +1,20 @@ -chr10 55251623.000000 -chr11 87588756.250000 -chr1 148052568.250000 -chr12 38440094.000000 -chr13 112381694.000000 -chr14 98710240.000000 -chr15 41666442.500000 -chr16 206638.000000 -chr18 50562378.250000 -chr19 59226196.750000 -chr20 33504194.750000 -chr2 118341365.500000 -chr21 33160676.750000 -chr2 220209905.500000 -chr22 30471242.250000 -chr5 131612441.500000 -chr6 108564320.750000 -chr7 115958079.000000 -chr8 118881131.000000 -chr9 128842832.750000 -chrX 145194871.500000 +chr1 1.48053e+08 +chr10 5.52516e+07 +chr11 8.75888e+07 +chr12 3.84401e+07 +chr13 1.12382e+08 +chr14 9.87102e+07 +chr15 4.16664e+07 +chr16 206638 +chr18 5.05624e+07 +chr19 5.92262e+07 +chr2 1.69276e+08 +chr20 3.35042e+07 +chr21 3.31607e+07 +chr22 3.04712e+07 +chr5 1.31612e+08 +chr6 1.08564e+08 +chr7 1.15958e+08 +chr8 1.18881e+08 +chr9 1.28843e+08 +chrX 1.45195e+08 diff -r 96f2c4630e62 -r c1d3004f0613 test-data/groupby_out2.dat --- a/test-data/groupby_out2.dat Fri Dec 19 14:25:43 2008 -0500 +++ b/test-data/groupby_out2.dat Mon Dec 22 12:15:02 2008 -0500 @@ -1,2 +1,2 @@ -chr10 1700.00 ['NM_11', 'NM_10', 'test'] -chr22 1533.33 ['NM_17', 'NM_19', 'NM_18'] \ No newline at end of file +chr10 1700 +chr22 1533.33 \ No newline at end of file diff -r 96f2c4630e62 -r c1d3004f0613 tools/stats/grouping.py --- a/tools/stats/grouping.py Fri Dec 19 14:25:43 2008 -0500 +++ b/tools/stats/grouping.py Mon Dec 22 12:15:02 2008 -0500 @@ -69,8 +69,9 @@ start a key at POS1, end it at POS2 (origin 1) In other words, column positions start at 1 rather than 0, so we need to add 1 to group_col. + if POS2 is not specified, the newer versions of sort will consider the entire line for sorting. To prevent this, we set POS2=POS1. """ - command_line = "sort -f -k " + str(group_col+1) + " -o " + tmpfile.name + " " + inputfile + command_line = "sort -f -k " + str(group_col+1) +"," + str(group_col+1) + " -o " + tmpfile.name + " " + inputfile except Exception, exc: stop_err( 'Initialization error -> %s' %str(exc) ) diff -r 96f2c4630e62 -r c1d3004f0613 tools/stats/grouping.xml --- a/tools/stats/grouping.xml Fri Dec 19 14:25:43 2008 -0500 +++ b/tools/stats/grouping.xml Mon Dec 22 12:15:02 2008 -0500 @@ -1,4 +1,4 @@ -<tool id="Grouping1" name="Group" version="1.3.0"> +<tool id="Grouping1" name="Group" version="1.4.0"> <description>data by a column and perform aggregate operation on other columns.</description> <command interpreter="python"> grouping.py @@ -38,28 +38,26 @@ <requirements> <requirement type="python-module">rpy</requirement> </requirements> - <tests> -  -  + <test> + <param name="input1" value="1.bed"/> + <param name="groupcol" value="1"/> + <param name="optype" value="mean"/> + <param name="opcol" value="2"/> + <param name="opround" value="no"/> + <output name="out_file1" file="groupby_out1.dat"/> + </test> + +  + <test> + <param name="input1" value="1.tabular"/> + <param name="groupcol" value="1"/> + <param name="optype" value="mean"/> + <param name="opcol" value="2"/> + <param name="opround" value="no"/> + <output name="out_file1" file="groupby_out2.dat"/> </test> - --> -  -  </tests> <help>

1 0