# HG changeset patch
# User devteam
# Date 1400517199 14400
# Node ID 03ca082aeb2e12d414b5ea0904128dc1a9ac3c27

Imported from capsule None

diff -r 000000000000 -r 03ca082aeb2e megablast_xml_parser.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/megablast_xml_parser.py	Mon May 19 12:33:19 2014 -0400
@@ -0,0 +1,78 @@
+#!/usr/bin/env python
+    
+import sys, os, re
+
+if sys.version_info[:2] >= ( 2, 5 ):
+    import xml.etree.cElementTree as ElementTree
+else:
+    from galaxy import eggs
+    import pkg_resources; pkg_resources.require( "elementtree" )
+    from elementtree import ElementTree
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+
+def __main__():
+    source  = sys.argv[1]
+    hspTags = [
+           "Hsp_bit-score",
+           "Hsp_evalue",
+           "Hsp_query-from",
+           "Hsp_query-to",
+           "Hsp_hit-from",
+           "Hsp_hit-to",
+           "Hsp_query-frame",
+           "Hsp_hit-frame",
+           "Hsp_identity",
+           "Hsp_align-len",
+           "Hsp_qseq",
+           "Hsp_hseq",
+           "Hsp_midline"
+          ]
+    hspData = []
+
+    # get an iterable
+    try: 
+        context = ElementTree.iterparse( source, events=( "start", "end" ) )
+    except:
+        stop_err( "Invalid data format." )
+    # turn it into an iterator
+    context = iter( context )
+    # get the root element
+    try:
+        event, root = context.next()
+    except:
+        stop_err( "Invalid data format." )
+
+    outfile = open( sys.argv[2], 'w' )
+    try:
+        for event, elem in context:
+           # for every <Iteration> tag
+           if event == "end" and elem.tag == "Iteration":
+               query = elem.findtext( "Iteration_query-def" )
+               qLen = elem.findtext( "Iteration_query-len" )
+               # 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" ):
+                        outfile.write( "%s\t%s\t%s\t%s" % ( query, qLen, subject, sLen ) )
+                        for tag in hspTags:
+                            outfile.write("\t%s" %(hsp.findtext( tag )))
+                            #hspData.append( hsp.findtext( tag ) )
+                        #hspData = []
+                        outfile.write('\n')
+               # prevents ElementTree from growing large datastructure
+               root.clear()
+               elem.clear()
+    except:
+        outfile.close()
+        stop_err( "The input data is malformed, or there is more than one dataset in the input file. Error: %s" % sys.exc_info()[1] )
+
+    outfile.close()
+
+if __name__ == "__main__": __main__()
diff -r 000000000000 -r 03ca082aeb2e megablast_xml_parser.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/megablast_xml_parser.xml	Mon May 19 12:33:19 2014 -0400
@@ -0,0 +1,60 @@
+<tool id="megablast_xml_parser" name="Parse blast XML output" version="1.0.0">
+<description></description>
+<command interpreter="python">megablast_xml_parser.py $input1 $output1</command>
+<inputs>
+  <param name="input1" type="data" format="blastxml" label="Megablast XML output" />
+</inputs>
+<outputs>
+  <data name="output1" format="tabular"/>
+</outputs>
+<tests>
+  <test>
+    <param name="input1" value="megablast_xml_parser_test1.gz" ftype="blastxml" />
+    <output name="output1" file="megablast_xml_parser_test1_out.tabular" ftype="tabular" />
+  </test>
+</tests>
+<help>
+
+**What it does**
+
+This tool processes the XML output of any NCBI blast tool (if you run your own blast jobs, the XML output can be generated with **-m 7** option).
+
+-----
+
+**Output fields**
+
+This tools returns tab-delimited output with the following fields::
+
+    Description                               Example
+    ----------------------------------------- ----------------- 
+
+    1. Name of the query sequence             Seq1
+    2. Length of the query sequence           30
+    3. Name of target sequence                gnl|BL_ORD_ID|0
+    4. Length of target sequence              5528445
+    5. Alignment bit score                    59.96
+    6. E-value                                8.38112e-11
+    7. Start of alignment within query        1
+    8. End of alignment within query          30
+    9. Start of alignment within target       5436010
+   10. End of alignment within target         5436039
+   11. Query frame                            1
+   12. Target frame                           1
+   13. Number of identical bases within       29 
+       the alignment
+   14. Alignment length                       30 
+   15. Aligned portion (sequence) of query    CGGACAGCGCCGCCACCAACAAAGCCACCA
+   16. Aligned portion (sequence) of target   CGGACAGCGCCGCCACCAACAAAGCCATCA
+   17. Midline indicating positions of        ||||||||||||||||||||||||||| || 
+       matches within the alignment
+
+------
+       
+.. class:: infomark
+
+Note that this form of output does not contain alignment identify value. However, it can be computed by dividing the number of identical bases within the alignment (Field 13) by the alignment length (Field 14) using *Text Manipulation->Compute* tool 
+
+
+
+</help>
+</tool>
diff -r 000000000000 -r 03ca082aeb2e repository_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Mon May 19 12:33:19 2014 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories>
+  <repository changeset_revision="de11e1a921c4" name="blast_datatypes" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+</repositories>
diff -r 000000000000 -r 03ca082aeb2e test-data/megablast_xml_parser_test1.gz
Binary file test-data/megablast_xml_parser_test1.gz has changed
diff -r 000000000000 -r 03ca082aeb2e test-data/megablast_xml_parser_test1_out.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/megablast_xml_parser_test1_out.tabular	Mon May 19 12:33:19 2014 -0400
@@ -0,0 +1,103 @@
+0_0.666667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	5436010	5436039	1	1	30	30	CGGACAGCGCCGCCACCAACAAAGCCACCA	CGGACAGCGCCGCCACCAACAAAGCCACCA	||||||||||||||||||||||||||||||
+1_0.600000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	696993	697022	1	1	30	30	AAAACACCGGATGCTCCGGCGCTGGCAGAT	AAAACACCGGATGCTCCGGCGCTGGCAGAT	||||||||||||||||||||||||||||||
+2_0.400000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	4100018	4100047	1	1	30	30	TTTGCTTTTAGTACACCGGATTCAGAACCA	TTTGCTTTTAGTACACCGGATTCAGAACCA	||||||||||||||||||||||||||||||
+3_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	30	1	2305844	2305873	1	-1	30	30	CCGTCCAGAAAGGTGTATTCATGGGGACGG	CCGTCCAGAAAGGTGTATTCATGGGGACGG	||||||||||||||||||||||||||||||
+4_0.766667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	3457901	3457930	1	1	30	30	CACGCTACGTGCGCCCCCGCCCAGAAGGCG	CACGCTACGTGCGCCCCCGCCCAGAAGGCG	||||||||||||||||||||||||||||||
+5_0.533333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	30	1	1264131	1264160	1	-1	30	30	GCACTTAACCCGCTTCGGCGGGTTTTGTTT	GCACTTAACCCGCTTCGGCGGGTTTTGTTT	||||||||||||||||||||||||||||||
+5_0.533333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	30	1	1636485	1636514	1	-1	30	30	GCACTTAACCCGCTTCGGCGGGTTTTGTTT	GCACTTAACCCGCTTCGGCGGGTTTTGTTT	||||||||||||||||||||||||||||||
+5_0.533333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	2318694	2318723	1	1	30	30	AAACAAAACCCGCCGAAGCGGGTTAAGTGC	AAACAAAACCCGCCGAAGCGGGTTAAGTGC	||||||||||||||||||||||||||||||
+5_0.533333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	2777043	2777072	1	1	30	30	AAACAAAACCCGCCGAAGCGGGTTAAGTGC	AAACAAAACCCGCCGAAGCGGGTTAAGTGC	||||||||||||||||||||||||||||||
+6_0.533333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	1185124	1185153	1	1	30	30	TAAGCCGTTACTGGCAGCAAGTGCAGGCAA	TAAGCCGTTACTGGCAGCAAGTGCAGGCAA	||||||||||||||||||||||||||||||
+7_0.400000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	2458203	2458232	1	1	30	30	TGAATTTACCGTTATCTATCTTGCCTGCCT	TGAATTTACCGTTATCTATCTTGCCTGCCT	||||||||||||||||||||||||||||||
+9_0.400000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	5286666	5286695	1	1	30	30	GCGTTTTGCTAAACTTCTGCCGGAATATAA	GCGTTTTGCTAAACTTCTGCCGGAATATAA	||||||||||||||||||||||||||||||
+10_0.500000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	2787672	2787701	1	1	30	30	AAAGAGGCGAGCAGAGTAAAACGCAGGCAA	AAAGAGGCGAGCAGAGTAAAACGCAGGCAA	||||||||||||||||||||||||||||||
+12_0.700000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	4116145	4116174	1	1	30	30	GCGGACGATCTTCACGGTCGCCACGCGGAC	GCGGACGATCTTCACGGTCGCCACGCGGAC	||||||||||||||||||||||||||||||
+13_0.533333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	5442351	5442380	1	1	30	30	TTCTTGTTGGATGGCATACTCCGGCAGCCA	TTCTTGTTGGATGGCATACTCCGGCAGCCA	||||||||||||||||||||||||||||||
+14_0.666667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	4626492	4626521	1	1	30	30	ACCCCGATATCGTCGCAGGCGTTGCCGCAC	ACCCCGATATCGTCGCAGGCGTTGCCGCAC	||||||||||||||||||||||||||||||
+15_0.666667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	346897	346926	1	1	30	30	GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC	GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC	||||||||||||||||||||||||||||||
+15_0.666667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	30	1	1466536	1466565	1	-1	30	30	GAAGCGCCTCTTCCAGCGGAGACAGCAGCC	GAAGCGCCTCTTCCAGCGGAGACAGCAGCC	||||||||||||||||||||||||||||||
+15_0.666667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	1750132	1750161	1	1	30	30	GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC	GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC	||||||||||||||||||||||||||||||
+15_0.666667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	1908046	1908075	1	1	30	30	GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC	GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC	||||||||||||||||||||||||||||||
+15_0.666667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	2279107	2279136	1	1	30	30	GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC	GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC	||||||||||||||||||||||||||||||
+15_0.666667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	2813407	2813436	1	1	30	30	GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC	GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC	||||||||||||||||||||||||||||||
+15_0.666667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	3939162	3939191	1	1	30	30	GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC	GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC	||||||||||||||||||||||||||||||
+15_0.666667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	4656510	4656539	1	1	30	30	GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC	GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC	||||||||||||||||||||||||||||||
+16_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	2595157	2595186	1	1	30	30	ATGTCCTGATCGAGCGGCGTTTTACCGACC	ATGTCCTGATCGAGCGGCGTTTTACCGACC	||||||||||||||||||||||||||||||
+17_0.533333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	717743	717772	1	1	30	30	GGTGTTGAGTGTCCAGGTAATACGCTCTCG	GGTGTTGAGTGTCCAGGTAATACGCTCTCG	||||||||||||||||||||||||||||||
+19_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	1237938	1237967	1	1	30	30	GTTGTAAGCGTCAGAACCGATGCGGTCGGT	GTTGTAAGCGTCAGAACCGATGCGGTCGGT	||||||||||||||||||||||||||||||
+20_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	4792054	4792083	1	1	30	30	CGACATCCTGTAGGCTGGCTTCAATGCGAC	CGACATCCTGTAGGCTGGCTTCAATGCGAC	||||||||||||||||||||||||||||||
+21_0.733333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	269757	269786	1	1	30	30	GGGAAGGCTGACGGGCGTCCACACCACGGC	GGGAAGGCTGACGGGCGTCCACACCACGGC	||||||||||||||||||||||||||||||
+21_0.733333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	274007	274036	1	1	30	30	GGGAAGGCTGACGGGCGTCCACACCACGGC	GGGAAGGCTGACGGGCGTCCACACCACGGC	||||||||||||||||||||||||||||||
+22_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	2706426	2706455	1	1	30	30	CGGTATTCCTCAGTTCTCGCTGCATGCCTG	CGGTATTCCTCAGTTCTCGCTGCATGCCTG	||||||||||||||||||||||||||||||
+23_0.600000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	1512107	1512136	1	1	30	30	TTGCCGTTACGCACCACGCCTTCAGTAGCG	TTGCCGTTACGCACCACGCCTTCAGTAGCG	||||||||||||||||||||||||||||||
+24_0.733333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	2032108	2032137	1	1	30	30	CGCGGGCGCACCACGTCGCTGCTGCTGTTC	CGCGGGCGCACCACGTCGCTGCTGCTGTTC	||||||||||||||||||||||||||||||
+25_0.266667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	1343811	1343840	1	1	30	30	TTTTGGGAAAACTAAATACGCATCAAAAAT	TTTTGGGAAAACTAAATACGCATCAAAAAT	||||||||||||||||||||||||||||||
+26_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	3112551	3112580	1	1	30	30	CAACGAGGCGCTACCGAGTTGTTCAATGCG	CAACGAGGCGCTACCGAGTTGTTCAATGCG	||||||||||||||||||||||||||||||
+28_0.666667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	4405442	4405471	1	1	30	30	CGCTCAATCTGCTCGCGCCTGGCTGGCGTT	CGCTCAATCTGCTCGCGCCTGGCTGGCGTT	||||||||||||||||||||||||||||||
+29_0.700000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	3600547	3600576	1	1	30	30	CTCGTCCGGCGGGCGGTTTTGCCGACAAGG	CTCGTCCGGCGGGCGGTTTTGCCGACAAGG	||||||||||||||||||||||||||||||
+32_0.600000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	1435670	1435699	1	1	30	30	TGAGGATGGTCCTCTGACTCTGCAGGCGCA	TGAGGATGGTCCTCTGACTCTGCAGGCGCA	||||||||||||||||||||||||||||||
+33_0.300000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	3788178	3788207	1	1	30	30	TAGTAACCCTTTAATAAGATTGTCGATTAG	TAGTAACCCTTTAATAAGATTGTCGATTAG	||||||||||||||||||||||||||||||
+34_0.533333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	484499	484528	1	1	30	30	TGATGTTAAATGCATGGCACCTGCCGGTGC	TGATGTTAAATGCATGGCACCTGCCGGTGC	||||||||||||||||||||||||||||||
+35_0.466667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	2250064	2250093	1	1	30	30	ACTGCTTTGCCGAGATATTCGAGGTTAACC	ACTGCTTTGCCGAGATATTCGAGGTTAACC	||||||||||||||||||||||||||||||
+36_0.433333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	3698178	3698207	1	1	30	30	TGTTGGCAACATGGCGAGCGTAATCAATTA	TGTTGGCAACATGGCGAGCGTAATCAATTA	||||||||||||||||||||||||||||||
+38_0.533333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	4242501	4242530	1	1	30	30	GCAGCAGGATCGGATCGAACTCTGGTTTCT	GCAGCAGGATCGGATCGAACTCTGGTTTCT	||||||||||||||||||||||||||||||
+39_0.400000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	3683151	3683180	1	1	30	30	TAATGCGGCATTCTCCTGATTTATTGTCAC	TAATGCGGCATTCTCCTGATTTATTGTCAC	||||||||||||||||||||||||||||||
+41_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	789086	789115	1	1	30	30	AGCTGACGGTCAGCAGGGATACTTCCTGCA	AGCTGACGGTCAGCAGGGATACTTCCTGCA	||||||||||||||||||||||||||||||
+42_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	1714771	1714800	1	1	30	30	GCAGTGACTACATCCGCGAGGTGAATGTGG	GCAGTGACTACATCCGCGAGGTGAATGTGG	||||||||||||||||||||||||||||||
+43_0.466667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	4272582	4272611	1	1	30	30	GCTTTTTCCAGCATCAACGCCACTGAACAA	GCTTTTTCCAGCATCAACGCCACTGAACAA	||||||||||||||||||||||||||||||
+44_0.433333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	5481023	5481052	1	1	30	30	AAAGTGGTAGATAACGTGGTGCAGACTATG	AAAGTGGTAGATAACGTGGTGCAGACTATG	||||||||||||||||||||||||||||||
+45_0.500000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	30	1	1271829	1271858	1	-1	30	30	ATCCGCGATAAGGTCATCCGGTATCAGGAA	ATCCGCGATAAGGTCATCCGGTATCAGGAA	||||||||||||||||||||||||||||||
+45_0.500000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	30	1	1357952	1357981	1	-1	30	30	ATCCGCGATAAGGTCATCCGGTATCAGGAA	ATCCGCGATAAGGTCATCCGGTATCAGGAA	||||||||||||||||||||||||||||||
+45_0.500000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	2310674	2310703	1	1	30	30	TTCCTGATACCGGATGACCTTATCGCGGAT	TTCCTGATACCGGATGACCTTATCGCGGAT	||||||||||||||||||||||||||||||
+45_0.500000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	2769319	2769348	1	1	30	30	TTCCTGATACCGGATGACCTTATCGCGGAT	TTCCTGATACCGGATGACCTTATCGCGGAT	||||||||||||||||||||||||||||||
+45_0.500000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	2991293	2991322	1	1	30	30	TTCCTGATACCGGATGACCTTATCGCGGAT	TTCCTGATACCGGATGACCTTATCGCGGAT	||||||||||||||||||||||||||||||
+46_0.466667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	1080570	1080599	1	1	30	30	ACCTGTACCCCAGGACCATGGTACATTTAT	ACCTGTACCCCAGGACCATGGTACATTTAT	||||||||||||||||||||||||||||||
+46_0.466667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	1476177	1476206	1	1	30	30	ACCTGTACCCCAGGACCATGGTACATTTAT	ACCTGTACCCCAGGACCATGGTACATTTAT	||||||||||||||||||||||||||||||
+47_0.533333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	2887871	2887900	1	1	30	30	ACAATGCAACCAGACCAGCCCGGATCGATA	ACAATGCAACCAGACCAGCCCGGATCGATA	||||||||||||||||||||||||||||||
+49_0.433333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	4152853	4152882	1	1	30	30	CGTTATACGGAACAACATTTAACTCCAGCG	CGTTATACGGAACAACATTTAACTCCAGCG	||||||||||||||||||||||||||||||
+50_0.466667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	3568677	3568706	1	1	30	30	TTGCTGTTGCCATCGCTTTTCAGGACATAC	TTGCTGTTGCCATCGCTTTTCAGGACATAC	||||||||||||||||||||||||||||||
+51_0.533333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	3739788	3739817	1	1	30	30	CGACGGTATCGGTACGCAGATTGTGATGGA	CGACGGTATCGGTACGCAGATTGTGATGGA	||||||||||||||||||||||||||||||
+52_0.366667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	3789407	3789436	1	1	30	30	ATGAGCATCAACATCGAAATCTCAAACCAA	ATGAGCATCAACATCGAAATCTCAAACCAA	||||||||||||||||||||||||||||||
+54_0.400000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	3161991	3162020	1	1	30	30	GTATTCTTCATTGATTTGTAAGCGGGTACC	GTATTCTTCATTGATTTGTAAGCGGGTACC	||||||||||||||||||||||||||||||
+55_0.466667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	4384753	4384782	1	1	30	30	AAGCGCTGTTCAACATAAATTGGCTGACGG	AAGCGCTGTTCAACATAAATTGGCTGACGG	||||||||||||||||||||||||||||||
+56_0.433333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	2915787	2915816	1	1	30	30	AACCGTCAGCTCTTTACGCAATATTTTGCC	AACCGTCAGCTCTTTACGCAATATTTTGCC	||||||||||||||||||||||||||||||
+57_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	294604	294633	1	1	30	30	CGCGAAATCCTCGACGTCCAGGCACGTATT	CGCGAAATCCTCGACGTCCAGGCACGTATT	||||||||||||||||||||||||||||||
+58_0.300000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	1553483	1553512	1	1	30	30	GTTATCCATTAAAATAGATCGGATCGATAT	GTTATCCATTAAAATAGATCGGATCGATAT	||||||||||||||||||||||||||||||
+59_0.300000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	1351506	1351535	1	1	30	30	AAAATCTGCATATCATGATAAGAGTGGTTA	AAAATCTGCATATCATGATAAGAGTGGTTA	||||||||||||||||||||||||||||||
+59_0.300000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	30	1	2997458	2997487	1	-1	30	30	TAACCACTCTTATCATGATATGCAGATTTT	TAACCACTCTTATCATGATATGCAGATTTT	||||||||||||||||||||||||||||||
+61_0.366667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	1987157	1987186	1	1	30	30	TCAGTTTGAAAGCTTTGTCAGCCGTTTTTT	TCAGTTTGAAAGCTTTGTCAGCCGTTTTTT	||||||||||||||||||||||||||||||
+62_0.366667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	1667830	1667859	1	1	30	30	AATCCTAAACCTAGGAATGCCAGAATATCT	AATCCTAAACCTAGGAATGCCAGAATATCT	||||||||||||||||||||||||||||||
+63_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	30	1	231418	231447	1	-1	30	30	TGGCATAAGCCAGCTTGACTGCGAGCGTGA	TGGCATAAGCCAGCTTGACTGCGAGCGTGA	||||||||||||||||||||||||||||||
+63_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	3516862	3516891	1	1	30	30	TCACGCTCGCAGTCAAGCTGGCTTATGCCA	TCACGCTCGCAGTCAAGCTGGCTTATGCCA	||||||||||||||||||||||||||||||
+63_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	4226650	4226679	1	1	30	30	TCACGCTCGCAGTCAAGCTGGCTTATGCCA	TCACGCTCGCAGTCAAGCTGGCTTATGCCA	||||||||||||||||||||||||||||||
+63_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	30	1	4808457	4808486	1	-1	30	30	TGGCATAAGCCAGCTTGACTGCGAGCGTGA	TGGCATAAGCCAGCTTGACTGCGAGCGTGA	||||||||||||||||||||||||||||||
+63_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	30	1	4904735	4904764	1	-1	30	30	TGGCATAAGCCAGCTTGACTGCGAGCGTGA	TGGCATAAGCCAGCTTGACTGCGAGCGTGA	||||||||||||||||||||||||||||||
+63_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	30	1	5048915	5048944	1	-1	30	30	TGGCATAAGCCAGCTTGACTGCGAGCGTGA	TGGCATAAGCCAGCTTGACTGCGAGCGTGA	||||||||||||||||||||||||||||||
+63_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	30	1	5089922	5089951	1	-1	30	30	TGGCATAAGCCAGCTTGACTGCGAGCGTGA	TGGCATAAGCCAGCTTGACTGCGAGCGTGA	||||||||||||||||||||||||||||||
+64_0.500000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	5440369	5440398	1	1	30	30	GAGATGACGGTTGCAGAGTCATGCGTTTGA	GAGATGACGGTTGCAGAGTCATGCGTTTGA	||||||||||||||||||||||||||||||
+65_0.533333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	3963858	3963887	1	1	30	30	TCTGGATCACGCGCAAACACTGGCTATCGT	TCTGGATCACGCGCAAACACTGGCTATCGT	||||||||||||||||||||||||||||||
+66_0.466667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	4142497	4142526	1	1	30	30	TCTGCTTTAGCAAACAGAGTGTGGTCACGA	TCTGCTTTAGCAAACAGAGTGTGGTCACGA	||||||||||||||||||||||||||||||
+67_0.400000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	3532236	3532265	1	1	30	30	GCCTTTTGTCTGATCATCCACAATAATGAC	GCCTTTTGTCTGATCATCCACAATAATGAC	||||||||||||||||||||||||||||||
+68_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	779994	780023	1	1	30	30	GAAGGATAGTTGGTCAGCAACACCAGCGGC	GAAGGATAGTTGGTCAGCAACACCAGCGGC	||||||||||||||||||||||||||||||
+70_0.466667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	1317239	1317268	1	1	30	30	TGGTGTTCAGCATCTCAACGGTAATTCGCT	TGGTGTTCAGCATCTCAACGGTAATTCGCT	||||||||||||||||||||||||||||||
+71_0.533333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	5080463	5080492	1	1	30	30	CAGGATGCAAACTGCCGGGAGATCCAGTTA	CAGGATGCAAACTGCCGGGAGATCCAGTTA	||||||||||||||||||||||||||||||
+72_0.533333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	3605409	3605438	1	1	30	30	AACTGGAAGGGCTTGGGATGACACAACAGC	AACTGGAAGGGCTTGGGATGACACAACAGC	||||||||||||||||||||||||||||||
+73_0.500000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	3280815	3280844	1	1	30	30	TTTAAGCGCCAACCAGGCTTCTTTGGTTGC	TTTAAGCGCCAACCAGGCTTCTTTGGTTGC	||||||||||||||||||||||||||||||
+75_0.533333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	2230266	2230295	1	1	30	30	ATAACCCTCTGCAACCGCCGCTTCAGCAAA	ATAACCCTCTGCAACCGCCGCTTCAGCAAA	||||||||||||||||||||||||||||||
+76_0.600000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	462631	462660	1	1	30	30	TGAAGCCGTACAACGGGCGCTGGAATTCGC	TGAAGCCGTACAACGGGCGCTGGAATTCGC	||||||||||||||||||||||||||||||
+77_0.700000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	2939076	2939105	1	1	30	30	GAGCTGCAACGCGGTCAGCCAGCTGGCGGT	GAGCTGCAACGCGGTCAGCCAGCTGGCGGT	||||||||||||||||||||||||||||||
+78_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	5422053	5422082	1	1	30	30	CGGAGTATCCGTTCCCCAACGACAAGCATC	CGGAGTATCCGTTCCCCAACGACAAGCATC	||||||||||||||||||||||||||||||
+79_0.500000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	4387420	4387449	1	1	30	30	AATACCGGGAAGAGACAACGGGGTCTCTTT	AATACCGGGAAGAGACAACGGGGTCTCTTT	||||||||||||||||||||||||||||||
+81_0.433333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	1037150	1037179	1	1	30	30	ATTAATGTTGCCGGCACAACATAATAGGGC	ATTAATGTTGCCGGCACAACATAATAGGGC	||||||||||||||||||||||||||||||
+82_0.500000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	1182188	1182217	1	1	30	30	ACTGGGTTGCTCTGAACAAGAAAGGCGCTA	ACTGGGTTGCTCTGAACAAGAAAGGCGCTA	||||||||||||||||||||||||||||||
+83_0.533333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	5430210	5430239	1	1	30	30	CGCCAGGGACGTATCGCGTCGATATCTATT	CGCCAGGGACGTATCGCGTCGATATCTATT	||||||||||||||||||||||||||||||
+84_0.533333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	310995	311024	1	1	30	30	TGCTCGTTCCCGTCGTGATGAAGCTCGAAA	TGCTCGTTCCCGTCGTGATGAAGCTCGAAA	||||||||||||||||||||||||||||||
+85_0.500000	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	4174173	4174202	1	1	30	30	AGGAAAGCAAACAACACGACCACCATCAGC	AGGAAAGCAAACAACACGACCACCATCAGC	||||||||||||||||||||||||||||||
+86_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	163690	163719	1	1	30	30	GGCAACGCAGGCGCATGATTCTGCTTGGAA	GGCAACGCAGGCGCATGATTCTGCTTGGAA	||||||||||||||||||||||||||||||
+88_0.533333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	3071785	3071814	1	1	30	30	CGTACCGGGCTGAAAGTAGAAGAGCGTTTC	CGTACCGGGCTGAAAGTAGAAGAGCGTTTC	||||||||||||||||||||||||||||||
+90_0.466667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	692131	692160	1	1	30	30	ATCACCGTTTCGCTAACCGGTACGTTTAAC	ATCACCGTTTCGCTAACCGGTACGTTTAAC	||||||||||||||||||||||||||||||
+91_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	3307050	3307079	1	1	30	30	TTCGCCCGGCAAGCTTACCCAACGCTTATC	TTCGCCCGGCAAGCTTACCCAACGCTTATC	||||||||||||||||||||||||||||||
+94_0.466667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	1813009	1813038	1	1	30	30	CCACGGTGATATCTGGTGCCATACTGATAA	CCACGGTGATATCTGGTGCCATACTGATAA	||||||||||||||||||||||||||||||
+96_0.533333	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	573782	573811	1	1	30	30	TTGCCGGGAAGAGAGATATCAATGGCAGGC	TTGCCGGGAAGAGAGATATCAATGGCAGGC	||||||||||||||||||||||||||||||
+97_0.566667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	3570563	3570592	1	1	30	30	TGCGCCGCCGGATTGTTGCTCAACATGCTT	TGCGCCGCCGGATTGTTGCTCAACATGCTT	||||||||||||||||||||||||||||||
+98_0.366667	30	gnl|BL_ORD_ID|0	5528445	59.96	8.38112e-11	1	30	4545136	4545165	1	1	30	30	AACGCGCTAACCGCCAATAATAACAAAATT	AACGCGCTAACCGCCAATAATAACAAAATT	||||||||||||||||||||||||||||||