Mercurial > repos > devteam > fasta_compute_length

changeset 2:d75972d4bd2a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 6e148b31fed1b322ce720804d8525088ec6d43f9
author devteam
date Thu, 29 Oct 2015 22:14:42 -0400
parents 2811169ce62b
children 19caae8fd9d4
files fasta_compute_length.py fasta_compute_length.xml test-data/454.fasta test-data/extract_genomic_dna_out1.fasta test-data/fasta_tool_compute_length_1.out test-data/fasta_tool_compute_length_2.out test-data/fasta_tool_compute_length_3.out
diffstat 7 files changed, 674 insertions(+), 38 deletions(-) [+]
line wrap: on
line diff
--- a/fasta_compute_length.py	Tue Oct 13 12:19:36 2015 -0400
+++ b/fasta_compute_length.py	Thu Oct 29 22:14:42 2015 -0400
@@ -6,4 +6,4 @@
 import sys
 from utils.fasta_to_len import compute_fasta_length
 
-compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], False )
\ No newline at end of file
+compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], sys.argv[4] == 'id_only' )
--- a/fasta_compute_length.xml	Tue Oct 13 12:19:36 2015 -0400
+++ b/fasta_compute_length.xml	Thu Oct 29 22:14:42 2015 -0400
@@ -1,51 +1,78 @@
-<tool id="fasta_compute_length" name="Compute sequence length" version="1.0.0">
-	<description></description>
-	<command interpreter="python">fasta_compute_length.py $input $output $keep_first</command>
-	<inputs>
-		<param name="input" type="data" format="fasta" label="Compute length for these sequences"/>
-		<param name="keep_first" type="integer" value="0" label="How many title characters to keep?" help="'0' = keep the whole thing"/>
-	</inputs>
-	<outputs>
-		<data name="output" format="tabular"/>
-	</outputs>
-	<tests>
-		<test>
-			<param name="input" value="454.fasta" />
-			<param name="keep_first" value="0"/>
-			<output name="output" file="fasta_tool_compute_length_1.out" />
-		</test>
-		
-		<test>
-			<param name="input" value="extract_genomic_dna_out1.fasta" />
-			<param name="keep_first" value="0"/>
-			<output name="output" file="fasta_tool_compute_length_2.out" />
-		</test>
-		
-		<test>
-			<param name="input" value="454.fasta" />
-			<param name="keep_first" value="14"/>
-			<output name="output" file="fasta_tool_compute_length_3.out" />
-		</test>
-	</tests>
-	<help>
+<tool id="fasta_compute_length" name="Compute sequence length" version="1.0.1">
+    <description></description>
+    <command interpreter="python">fasta_compute_length.py $input $output $keep_first $keep_first_word</command>
+    <inputs>
+        <param name="input" type="data" format="fasta" label="Compute length for these sequences"/>
+        <param name="keep_first" type="integer" value="0" label="How many title characters to keep?" help="'0' = keep the whole thing"/>
+        <param name="keep_first_word" type="boolean" truevalue="id_only" falsevalue="id_and_desc"
+            selected="false" label="Strip fasta description from header?"
+            help="Stripping the description will truncate the fasta header to just the sequence ID. Otherwise the header description will be kept. This step is done before the 'How many characters to keep' option."/>
+
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="454.fasta" />
+            <param name="keep_first" value="0"/>
+            <param name="keep_first_word" value="id_and_desc" />
+            <output name="output" file="fasta_tool_compute_length_1.out" />
+        </test>
+
+        <test>
+            <param name="input" value="extract_genomic_dna_out1.fasta" />
+            <param name="keep_first" value="0"/>
+            <param name="keep_first_word" value="id_and_desc" />
+            <output name="output" file="fasta_tool_compute_length_2.out" />
+        </test>
+
+        <test>
+            <param name="input" value="454.fasta" />
+            <param name="keep_first" value="14"/>
+            <param name="keep_first_word" value="id_and_desc" />
+            <output name="output" file="fasta_tool_compute_length_3.out" />
+        </test>
+    </tests>
+    <help>
 
 **What it does**
 
-This tool counts the length of each fasta sequence in the file. The output file has two columns per line (separated by tab): fasta titles and lengths of the sequences. The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry. 
+This tool counts the length of each fasta sequence in the file. The output file has two columns per line (separated by tab): fasta titles and lengths of the sequences. The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry.
 
------	
+-----
 
 **Example**
 
 Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run::
 
-    &gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
    TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
    TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
    &gt;EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
    AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
+    &gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
+    TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
+    TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
+    &gt;EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
+    AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
 
 Running this tool while setting **How many characters to keep?** to **14** will produce this::
-	
-	EYKX4VC02EQLO5  108
-	EYKX4VC02D4GS2	 60
+
+    EYKX4VC02EQLO5  108
+    EYKX4VC02D4GS2   60
+
+However, if your IDs are not all the same length, you may wish to just keep the fasta ID, and not the description::
+
+    &gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
+    TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
+    TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
+    &gt;EYKX4VC length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
+    AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
+
+Running this tool with **Strip fasta description from header** set to **True** and **How many characters to keep?** set to **0** will produce::
+
+    EYKX4VC02EQLO5  108
+    EYKX4VC     60
 
 
-	</help>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btq281</citation>
+    </citations>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/454.fasta	Thu Oct 29 22:14:42 2015 -0400
@@ -0,0 +1,52 @@
+>EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_
+CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA
+>EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_
+CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGG
+GGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGC
+CACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCC
+ATTGGTC
+>EYKX4VC01CD9FT length=115 xy=0865_1719 region=1 run=R_2007_11_07_16_15_57_
+GGGGGCTTTGGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGATC
+ATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACCCGCACCCAACGCG
+>EYKX4VC01B8FW0 length=95 xy=0799_0514 region=1 run=R_2007_11_07_16_15_57_
+TAAATTTCAAGGAATGCAAATCAGGGTCGTGTGTTTAGACTTCGGCTTTAGAGACCTGAA
+TACGTCAAAAACATAACTTCATGATATCTTGCAGT
+>EYKX4VC01BCGYW length=115 xy=0434_3926 region=1 run=R_2007_11_07_16_15_57_
+GGCCAGCCGGGACAGCGTTGTTGGGCTGCATGGCGACGAGCTAAAAGTCGCCATCACCGC
+CCCGCCGGTTGATGGGCAGGCTAATGCCCATCTGGTAAAAACTTTCTCGCCAAAC
+>EYKX4VC01AZXC6 length=116 xy=0292_0280 region=1 run=R_2007_11_07_16_15_57_
+GGGGGCGTTTGGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGAT
+CATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACCCGCACCCAACGCG
+>EYKX4VC01CATH5 length=82 xy=0826_0843 region=1 run=R_2007_11_07_16_15_57_
+CGAAATTGCACATTCTCGGCCATATCTCTGGACCTACATGACCGATTTGATCATCTTCGA
+ACTTAGCCTTCCTTTNTTAACG
+>EYKX4VC01BCEIV length=47 xy=0434_0757 region=1 run=R_2007_11_07_16_15_57_
+TGACGTCGTGCCGAGCTACGACAATGCCGACATGGTGATCGTTAACA
+>EYKX4VC01BWERM length=83 xy=0662_0304 region=1 run=R_2007_11_07_16_15_57_
+CGGTCGGCCTCACCATGGAGAAGATCCCGCCCCGGCCGAGGTCATGGTGGATCTCGGCCA
+GGGCGTGCTGATGAAGTTCAAAT
+>EYKX4VC01BT2O7 length=69 xy=0635_1945 region=1 run=R_2007_11_07_16_15_57_
+AGCGTTTCTCCAGCCGGTCGGCTACGCCGTTTGCCCCTGAAAGACGCTGTTCAGACCGAA
+CGCGGTAAA
+>EYKX4VC01BO0UO length=222 xy=0577_3838 region=1 run=R_2007_11_07_16_15_57_
+AGACCTGGGACAGCGGCGGGCTGCTGAAGCCGCAGGCGATAGAGGACAAACTGCAGTACC
+GCTTCTGGCTGCACTATGCCGAAGGCTCGCTGATGCCGCTGCTGTTAATGAAGCTGGTGT
+TCGCCAGCCTGGGTAAACCCCCTGTGCCCTTTGGCGTCCGCTCGCTGGGCGCCCTGCTGG
+GCAAGGGCATTCAGAAAGCGTGGCTGGATCCCCAGCTGGCCA
+>EYKX4VC01CBCPK length=83 xy=0832_1158 region=1 run=R_2007_11_07_16_15_57_
+CGGTCGGCCTCACCATGGAGAAGATCCCGCCCCGGCCGAGGTCATGGTGGATCTCGGCCA
+GGGCGTGCTGATGAAGTTCAAAT
+>EYKX4VC01B474S length=54 xy=0762_2010 region=1 run=R_2007_11_07_16_15_57_
+AGCAGTTTTCCAGCGCTTTCGAAGAGCGCTGGCGCGCGCGGGCTTCCAGCATAT
+>EYKX4VC01BB4QL length=57 xy=0431_0363 region=1 run=R_2007_11_07_16_15_57_
+GGGGAGGAGCTAATAATATGCTCTTGGGGAGGAGCTAATTATATGCTCTTGGGGAGG
+>EYKX4VC01BJ37M length=64 xy=0522_0192 region=1 run=R_2007_11_07_16_15_57_
+TCGAGTATGTATCAAGGACTACATACAAATTTGCCAAAAGAGATTATGCACTATCCCGAC
+TTCC
+>EYKX4VC01BV9R8 length=54 xy=0660_2038 region=1 run=R_2007_11_07_16_15_57_
+AAAACTCGGAGAAACTATTCAGCAGCACTGCGTTTCGCTGAATTTTAGACCGTT
+>EYKX4VC01CEPP8 length=60 xy=0870_2350 region=1 run=R_2007_11_07_16_15_57_
+CTGGGTGGGTGCACTACAGGAACGTCATTTGTTCAATCCTCACGTTGTTGTTAGTGTCAG
+>EYKX4VC01BTLME length=78 xy=0630_0292 region=1 run=R_2007_11_07_16_15_57_
+TTATCCACACGCTGTCCGGATCCAGCGCCAGGCGCCGACGCTGGACTTCCGCCGCCTGCG
+CCCAGTTGCCCTGACTTC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_genomic_dna_out1.fasta	Thu Oct 29 22:14:42 2015 -0400
@@ -0,0 +1,456 @@
+>hg17_chr1_147962192_147962580_-
+ACTTGATCCTGCTCCCTCGGTGTCTGCATTGACTCCTCATGCTGGGACTG
+GACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGT
+GATGATGCAACTTTCGAGGAATGGTTCCCCCAAGGGCGGCCCCCAAAAGT
+CCCTGTTCGTGAGGTCTGTCCAGTGACCCATCGTCCAGCCCTATACCGGG
+ACCCTGTTACAGACATACCCTATGCCACTGCTCGAGCCTTCAAGATCATT
+CGTGAGGCTTACAAGAAGTACATTACTGCCCATGGACTGCCGCCCACTGC
+CTCAGCCCTGGGCCCCGGCCCGCCACCTCCTGAGCCCCTCCCTGGCTCTG
+GGCCCCGAGCCTTGCGCCAGAAAATTGTCATTAAATGA
+>hg17_chr1_147984545_147984630_+
+ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTT
+TGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+>hg17_chr1_148078400_148078582_-
+GTTCTCAGCTTCCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAA
+GAGAGGTTCCACATGAGCATGACTGAGGAGCAGCTGCAGCTGCTGGTGGA
+GCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACG
+GCTTCCAGTACCTCACCAACGGCATCATGTGA
+>hg17_chr1_148185136_148185276_+
+ATGGAAGCGTTTTTGGGGTCGCGGTCCGGACTTTGGGCGGGGGGTCCGGC
+CCCAGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATC
+CGGCGTCTGCACTTTACAGAGGTCCAATCACGCGGACCCA
+>hg17_chr10_55251623_55253124_-
+TCTTTTCCTTCTCTACCATTTTCAACAAAGCAGGGGAAATAACTCAGTCT
+CAGAAGACAGGAAACATCAACAAGTTGTGATGCCCTTTTCTTCCAATACT
+ATTGAGGCTCACAAGTCAGCTCATGTAGACGGATCACTTAAGAGCAACAA
+ACTGAAGTCTGCAAGAAAATTCACATTTCTATCTGATGAGGATGACTTAA
+GTGCCCATAATCCCCTTTATAAGGAAAACATAAGTCAAGTATCAACAAAT
+TCAGACATTTCACAGAGAACAGATTTTGTAGACCCATTTTCACCCAAAAT
+ACAAGCCAAGAGTAAGTCTCTGAGGGGCCCAAGAGAAAAGATTCAGAGGC
+TGTGGAGTCAGTCAGTCAGCTTACCCAGGAGGCTGATGAGGAAAGTTCCA
+AATAGACCAGAGATCATAGATCTGCAGCAGTGGCAAGGCACCAGGCAGAA
+AGCTGAAAATGAAAACACTGGAATCTGTACAAACAAAAGAGGTAGCAGCA
+ATCCATTGCTTACAACTGAAGAGGCAAATTTGACAGAGAAAGAGGAAATA
+AGGCAAGGTGAAACACTGATGATAGAAGGAACAGAACAGTTGAAATCTCT
+CTCTTCAGACTCTTCATTTTGCTTTCCCAGGCCTCACTTCTCATTCTCCA
+CTTTGCCAACTGTTTCAAGAACTGTGGAACTCAAATCAGAACCTAATGTC
+ATCAGTTCTCCTGCTGAGTGTTCCTTGGAACTTTCTCCTTCAAGGCCTTG
+TGTTTTACATTCTTCACTCTCTAGGAGAGAGACACCTATTTGTATGTTAC
+CTATTGAAACCGAAAGAAATATTTTTGAAAATTTTGCCCATCCACCAAAC
+ATCTCTCCTTCTGCCTGtccccttccccctcctcctcctatttctcctcc
+ttctcctcctcctgctcctgctcctcttgctcctcctcctgacatttctc
+ctttttctcttttttgtcctcctccctctcctccttctatccctcttcct
+cttcctcctcctACATTTTTTCCACTTTCCGTTTCAACGTCTGGTCCCCC
+AACAccacctcttctacctccatttccaactcctcttcctccaccacctc
+cttctattccttgccctccacctccttcAGCTTCATTTCTGTCCACAGAG
+TGTGTCTGTATAACAGGTGTTAAATGCACGACCAACTTGATGCCTGCCGA
+GAAAATTAAGTCCTCTATGACACAGCTATCAACAACGACAGTGTGTAAAA
+CAGACCCTCAGAGAGAACCAAAAGGCATCCTCAGACACGTTAAAAACTTA
+GCAGAACTTGAAAAATCAGTAGCTAACATGTACAGTCAAATAGAAAAAAA
+CTATCTACGCACAAATGTTTCAGAACTTCAAACTATGTGCCCTTCAGAAG
+TAACAAATATGGAAATCACATCTGAACAAAACAAGGGGAGTTTGAACAAT
+ATTGTCGAGGGAACTGAAAAACAATCTCACAGTCAATCTACTTCACTGTA
+A
+>hg17_chr11_116124407_116124501_-
+ATCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGG
+CAGTGGAGGAACTTGCCTACAAATGGAGTGTTGAGGATATGTAA
+>hg17_chr11_116206508_116206563_+
+ATGCAGCCCCGGGTACTCCTTGTTGTTGCCCTCCTGGCGCTCCTGGCCTC
+TGCCC
+>hg17_chr11_116211733_116212337_-
+CCTAAAGCTCCTTGACAACTGGGACAGCGTGACCTCCACCTTCAGCAAGC
+TGCGCGAACAGCTCGGCCCTGTGACCCAGGAGTTCTGGGATAACCTGGAA
+AAGGAGACAGAGGGCCTGAGGCAGGAGATGAGCAAGGATCTGGAGGAGGT
+GAAGGCCAAGGTGCAGCCCTACCTGGACGACTTCCAGAAGAAGTGGCAGG
+AGGAGATGGAGCTCTACCGCCAGAAGGTGGAGCCGCTGCGCGCAGAGCTC
+CAAGAGGGCGCGCGCCAGAAGCTGCACGAGCTGCAAGAGAAGCTGAGCCC
+ACTGGGCGAGGAGATGCGCGACCGCGCGCGCGCCCATGTGGACGCGCTGC
+GCACGCATCTGGCCCCCTACAGCGACGAGCTGCGCCAGCGCTTGGCCGCG
+CGCCTTGAGGCTCTCAAGGAGAACGGCGGCGCCAGACTGGCCGAGTACCA
+CGCCAAGGCCACCGAGCATCTGAGCACGCTCAGCGAGAAGGCCAAGCCCG
+CGCTCGAGGACCTCCGCCAAGGCCTGCTGCCCGTGCTGGAGAGCTTCAAG
+GTCAGCTTCCTGAGCGCTCTCGAGGAGTACACTAAGAAGCTCAACACCCA
+GTGA
+>hg17_chr11_1812377_1812407_+
+ATGCTCCACCTGCATGGCTGGCAAACCATG
+>hg17_chr12_38440094_38440321_-
+GAGCTTTCTTCCTCTATGCTGGATTTGCTGCTGTGGGACTCCTTTTCATC
+TATGGCTGTCTTCCTGAGACCAAAGGCAAAAAATTAGAGGAAATTGAATC
+ACTCTTTGACAACAGGCTATGTACATGTGGCACTTCAGATTCTGATGAAG
+GGAGATATATTGAATATATTCGGGTAAAGGGAAGTAACTATCATCTTTCT
+GACAATGATGCTTCTGATGTGGAATAA
+>hg17_chr13_112381694_112381953_+
+ATGAACTCACCAGAGGCGAGGCTCTGCGTTGCTCAATGCAGAGACTCTTA
+CCCAGGGTGTCAGCCTCTGAAAGATACACGTGCCTGGGCCTCTTCCCTGA
+AGATGGACCCGGCAGGTCTGGAGGGAGGCCCCCGTGATGAATCCCGTGAT
+GAGCCGCCGATCCGAGCTCAGGCTGCGTCATGGGACCAGCCACAAGGTTG
+CCTGACCTATAAAGGTCGCAGGAGTGCCTCAGGGACACAGAAGCAGTTAC
+AGCTGCCAG
+>hg17_chr14_98710240_98712285_-
+GTAAAGATGAGCCTTCCAGCTACATTTGCACAACATGCAAGCAGCCCTTC
+AACAGCGCGTGGTTCCTGCTGCAGCACGCGCAGAACACGCACGGCTTCCG
+CATCTACCTGGAGCCCGGGCCGGCCAGCAGCTCGCTCACGCCGCGGCTCA
+CCATCCCGCCGCCGCTCGGGCCGGAGGCCGTGGCGCAGTCCCCGCTCATG
+AATTTCCTGGGCGACAGCAACCCCTTCAACCTGCTGCGCATGACGGGCCC
+CATCCTGCGGGACCACCCGGGCTTCGGCGAGGGCCGCCTGCCGGGCACGC
+CGCCTCTCTTCAGTCCCCCGCCGCGCCACCACCTGGACCCGCACCGCCTC
+AGTGCCGAGGAGATGGGGCTCGTCGCCCAGCACCCCAGTGCCTTCGACCG
+AGTCATGCGCCTGAACCCCATGGCCATCGACTCGCCCGCCATGGACTTCT
+CGCGGCGGCTCCGCGAGCTGGCGGGCAACAGCTCCACGCCGCCGCCCGTG
+TCCCCGGGCCGCGGCAACCCTATGCACCGGCTCCTGAACCCCTTCCAGCC
+CAGCCCCAAGTCCCCGTTCCTGAGCACGCCGCCGCTGCCGCCCATGCCCC
+CTGGCGGCACGCCGCCCCCGCAGCCGCCAGCCAAGAGCAAGTCGTGCGAG
+TTCTGCGGCAAGACCTTCAAGTTCCAGAGCAATCTCATCGTGCACCGGCG
+CAGTCACACGGGCGAGAAGCCCTACAAGTGCCAGCTGTGCGACCACGCGT
+GCTCGCAGGCCAGCAAGCTCAAGCGCCACATGAAGACGCACATGCACAAG
+GCCGGCTCGCTGGCCGGCCGCTCCGACGACGGGCTCTCGGCCGCCAGCTC
+CCCCGAGCCCGGCACCAGCGAGCTGGCGGGCGAGGGCCTCAAGGCGGCCG
+ACGGTGACTTCCGCCACCACGAGAGCGACCCGTCGCTGGGCCACGAGCCg
+gaggaggaggacgaggaggaggaggaggaggaggaggagCTGCTACTGGA
+GAACGAGAGCCGGCCCGAGTCGAGCTTCAGCATGGACTCGGAGCTGAGCC
+GCAACCGCGAGAACGGCGGTGGTGGGGTgcccggggtcccgggcgcgggg
+ggcggcgcggccAAGGCGCTGGCTGACGAGAAGGCGCTGGTGCTGGGCAA
+GGTCATGGAGAACGTGGGCCTAGGCGCACTGCCGCAGTACGGCGAGCTCC
+TGGCCGACAAGCAGAAGCGCGGCGCCTTCCTGAAGCGTGCggcgggcggc
+ggggacgcgggcgacgacgacgacgcgggcggctgcggggacgcgggcgc
+gggcggcgcggtcaacgggcgcgggggcggCTTCGCGCCAGGCACCGAGC
+CCTTCCCCGGGCTCTTCCCGCGCAAGCCCGCGCCGCTGCCCAGCCCCGGG
+CTCAACAGCGCCGCCAAGCGCATCAAGGTGGAGAAGGACCTGGAGCTGCC
+GCCCGCCGCGCTCATCCCGTCCGAGAACGTGTACTCGCAGTGGCTGGTGG
+GCTACGCGGCGTCGCGGCACTTCATGAAGGACCCCTTCCTGGGCTTCACG
+GACGCACGACAGTCGCCCTTCGCCACGTCGTCCGAGCACTCGTCCGAGAA
+CGGCAGCCTGCGCTTCTCCACGCCGCCCGGGGACCTGCTGGACGGCGGCC
+TCTCGGGCCGCAGCGGCACGGCCAGCGGAGGCAGCACCCCGCACCTgggc
+ggcccgggccccgggcggcccAGCTCCAAGGAGGGCCGCCGCAGCGACAC
+GTGCGAGTACTGCGGCAAGGTGTTCAAGAACTGCAGCAACTTGACGGTGC
+ACCGGCGGAGCCACACCGGCGAGCGGCCTTACAAGTGCGAGCTGTGCAAC
+TACGCGTGCGCGCAGAGCAGCAAGCTCACGCGCCACATGAAGACGCACGG
+GCAGATCGGCAAGGAGGTGTACCGCTGCGACATCTGCCAGATGCCCTTCA
+GCGTCTACAGCACCCTGGAGAAACACATGAAAAAGTGGCACGGCGAGCAC
+TTGCTGACTAACGACGTCAAAATCGAGCAGGCCGAGAGGAGCTAA
+>hg17_chr15_41486872_41487060_-
+ATATTGCTTTAGGGGTATTTGATGTGGTGGTGACGGACCCCTCATGCCCA
+GCCTCGGTGCTGAAGTGTGCTGAAGCATTGCAGCTGCCTGTGGTGTCACA
+AGAGTGGGTGATCCAGTGCCTCATTGTTGGGGAGAGAATTGGATTCAAGC
+AGCATCCAAAATATAAACACGATTATGTTTCTCACTAA
+>hg17_chr15_41673708_41673857_+
+ATGGCTGGTCCCTTCTCCCGTCTGCTGTCCGCCCGCCCGGGACTCAGGCT
+CCTGGCTTTGGCCGGAGCGGGGTCTCTAGCCGCTGGGTTTCTGCTCCGAC
+CGGAACCTGTACGAGCTGCCAGTGAACGACGGAGGCTGTATCCCCCGAG
+>hg17_chr15_41679161_41679250_-
+GTCGAAGTACAGCCTGGGGCCTCCAGGACTGGTCACGACCTTCCTGGTCC
+CTGGTATTGACTATCAGCTTCCTTGGCCACCTGCTATGA
+>hg17_chr15_41826029_41826196_+
+ATGCGCCTCCGCCGCCTAGCGCTGTTCCCGGGTGTGGCGCTGCTTCTTGC
+CGCGGCCCGCCTCGCCGCTGCCTCCGACGTGCTAGAACTCACGGACGACA
+ACTTCGAGAGTCGCATCTCCGACACGGGCTCTGCGGGCCTCATGCTCGTC
+GAGTTCTTCGCCCCCTG
+>hg17_chr16_142908_143003_+
+ATGTCTCTGACCAAGACTGAGAGGACCATCATTGTGTCCATGTGGGCCAA
+GATCTCCACGCAGGCCGACACCATCGGCACCGAGACTCTGGAGAG
+>hg17_chr16_179963_180135_-
+GTCACGCTCCCGGGATCGGCGTCGGAGGCGGTCAAGATCTACCTCCCGAG
+AGCGACGGAAATTGTCCCGGTCCCGGTCCCGAGATAGACATCGGCGCCAC
+CGCAGCCGTTCCCGGAGCCACAGCCGGGGACATCGTCGGGCTTCCCGGGA
+CCGAAGTGCGAAATACAAGTAA
+>hg17_chr16_244413_244681_+
+ATGTTGGACCACAAGGACTTAGAGGCCGAAATCCACCCCTTGAAAAATGA
+AGAAAGAAAATCGCAGGAAAATCTGGGAAATCCATCAAAAAATGAGGATA
+ACGTGAAAAGCGCGCCTCCACAGTCCCGGCTCTCCCGGTGCCGAGCGGCG
+GCGTTTTTTCTTTCATTGTTTCTCTGCCTTTTTGTGGTGTTCGTCGTCTC
+ATTCGTCATCCCGTGTCCAGACCGGCCGGCGTCACAGCGAATGTGGAGGA
+TAGACTACAGTGCCGCTG
+>hg17_chr16_259268_259383_-
+CGTGTTCCCGTTTACGTGGAGGCCACGGCACTCGAGCCCCAGCCCTGCAC
+TCCTTCCCACCCCTGTGGAGCCCACAGCGGCTTGTGGCCCTGGGGGTGGA
+GATGGGGTGGCCTAG
+>hg17_chr18_23786114_23786321_-
+GGCCTTAAAGCGGCTGACAATGACCCCACAGCTCCACCATATGACTCCCT
+GTTAGTGTTTGACTATGAAGGCAGTGGCTCCACTGCTGGGTCCTTGAGCT
+CCCTTAATTCCTCAAGTAGTGGTGGTGAGCAGGACTATGATTACCTGAAC
+GACTGGGGGCCACGGTTCAAGAAACTTGCTGACATGTATGGTGGAGGTGA
+TGACTGA
+>hg17_chr18_59406881_59407046_+
+ATGGATTCACTTGGCGCCGTCAGCACTCGACTTGGGTTTGATCTTTTCAA
+AGAGCTGAAGAAAACAAATGATGGCAACATCTTCTTTTCCCCTGTGGGCA
+TCTTGACTGCAATTGGCATGGTCCTCCTGGGGACCCGAGGAGCCACCGCT
+TCCCAGTTGGAGGAG
+>hg17_chr18_59455932_59456337_-
+CTTGAAGAGAAACTCACTGCTGAGAAATTGATGGAATGGACAAGTTTGCA
+GAATATGAGAGAGACATGTGTCGATTTACACTTACCTCGGTTCAAAATGG
+AAGAGAGCTATGACCTCAAGGACACGTTGAGAACCATGGGAATGGTGAAT
+ATCTTCAATGGGGATGCAGACCTCTCAGGCATGACCTGGAGCCACGGTCT
+CTCAGTATCTAAAGTCCTACACAAGGCCTTTGTGGAGGTCACTGAGGAGG
+GAGTGGAAGCTGCAGCTGCCACCGCTGTAGTAGTAGTCGAATTATCATCT
+CCTTCAACTAATGAAGAGTTCTGTTGTAATCACCCTTTCCTATTCTTCAT
+AAGGCAAAATAAGACCAACAGCATCCTCTTCTATGGCAGATTCTCATCCC
+CATAG
+>hg17_chr18_59600586_59600754_+
+ATGGCCTCCCTTGCTGCAGCAAATGCAGAGTTTTGCTTCAACCTGTTCAG
+AGAGATGGATGACAATCAAGGAAATGGAAATGTGTTCTTTTCCTCTCTGA
+GCCTCTTCGCTGCCCTGGCCCTGGTCCGCTTGGGCGCTCAAGATGACTCC
+CTCTCTCAGATTGATAAG
+>hg17_chr19_59068595_59069564_+
+ATGCCAGTGACGGTAACCCGCACCACCATCACAACCACCACGACGTCATC
+TTCGGGCCTGGGGTCCCCCATGATCGTGGGGTCCCCTCGGGCCCTGACAC
+AGCCCCTGGGTCTCCTTCGCCTGCTGCAGCTGGTGTCTACCTGCGTGGCC
+TTCTCGCTGGTGGCTAGCGTGGGCGCCTGGACGGGGTCCATGGGCAACTG
+GTCCATGTTCACCTGGTGCTTCTGCTTCTCCGTGACCCTGATCATCCTCA
+TCGTGGAGCTGTGCGGGCTCCAGGCCCGCTTCCCCCTGTCTTGGCGCAAC
+TTCCCCATCACCTTCGCCTGCTATGCGGCCCTCTTCTGCCTCTCGGCCTC
+CATCATCTACCCCACCACCTATGTCCAGTTCCTGTCCCACGGCCGTTCGC
+GGGACCACGCCATCGCCGCCACCTTCTTCTCCTGCATCGCGTGTGTGGCT
+TACGCCACCGAAGTGGCCTGGACCCGGGCCCGGCCCGGCGAGATCACTGG
+CTATATGGCCACCGTACCCGGGCTGCTGAAGGTGCTGGAGACCTTCGTTG
+CCTGCATCATCTTCGCGTTCATCAGCGACCCCAACCTGTACCAGCACCAG
+CCGGCCCTGGAGTGGTGCGTGGCGGTGTACGCCATCTGCTTCATCCTAGC
+GGCCATCGCCATCCTGCTGAACCTGGGGGAGTGCACCAACGTGCTACCCA
+TCCCCTTCCCCAGCTTCCTGTCGGGGCTGGCCTTGCTGTCTGTCCTCCTC
+TATGCCACCGCCCTTGTTCTCTGGCCCCTCTACCAGTTCGATGAGAAGTA
+TGGCGGCCAGCCTCGGCGCTCGAGAGATGTAAGCTGCAGCCGCAGCCATG
+CCTACTACGTGTGTGCCTGGGACCGCCGACTGGCTGTGGCCATCCTGACG
+GCCATCAACCTACTGGCGTATGTGGCTGACCTGGTGCACTCTGCCCACCT
+GGTTTTTGTCAAGGTCTAA
+>hg17_chr19_59236026_59236146_-
+ACGGCAGACCCCCAAGGAGTGACCTATGCTGAGCTAAGCACCAGCGCCCT
+GTCTGAGGCAGCTTCAGACACCACCCAGGAGCCCCCAGGATCTCATGAAT
+ATGCGGCACTGAAAGTGTAG
+>hg17_chr19_59297998_59298008_+
+ATGGCTGCGA
+>hg17_chr19_59302168_59302288_-
+ATTAAGGTTGAGGAAGACTTTGGCTTTGAAGCAGATGAGGCCCTGGATTC
+CAGTTGGGTTTCTCGGGGTCCAGACAAACTGCTGCCCTACCCGACCCTGG
+CCAGCCCAGCCTCTGACTGA
+>hg17_chr2_118288583_118288668_+
+ATGTCACACCTGCCGATGAAACTCCTGCGTAAGAAGATCGAGAAGCGGAA
+CCTCAAATTGCGGCAGCGGAACCTAAAGTTTCAGG
+>hg17_chr2_118394148_118394202_-
+GAGGGCCGCAAGAACGAGATGCTGCTGTCCAAGGTGAAAGCGAAGGCCTC
+CTGA
+>hg17_chr2_220190202_220190242_+
+ATGCTCAAAGCGGTGATCCTGATTGGAGGCCCTCAAAAGG
+>hg17_chr2_220229609_220230869_-
+TGGGAGATCCAGAATACCAGCCATCTGGCCGTTGATGGGGACCAGGCAGC
+TGCTTGGCCCGTGGGTATTCCAGCACCATCCCGCCCGGCCTCCCGCTTTG
+AGGTGCTGCGCTGGGACTACTTCACGGAGCAGCACGCTTTCTCCTGCGCC
+GATGGCTCACCCCGCTGCCCACTGCGTGGGGCTGACCGGGCTGATGTGGC
+CGATGTTCTGGGGACAGCTCTAGAGGAGCTGAACCGCCGCTACCACCCGG
+CCTTGCGGCTCCAGAAGCAGCAGCTGGTGAATGGCTACCGACGCTTTGAT
+CCGGCCCGGGGTATGGAATACACGCTGGACTTGCAGCTGGAGGCACTGAC
+CCCCCAGGGAGGCCGCCGGCCCCTCACTCGCCGAGTGCAGCTGCTCCGGC
+CGCTGAGCCGCGTGGAGATCTTGCCTGTGCCCTATGTCACTGAGGCCTCA
+CGTCTCACTGTGCTGCTGCCTCTAGCTGCGGCTGAGCGTGACCTGGCCCC
+TGGCTTCTTGGAGGCCTTTGCCACTGCAGCACTGGAGCCTGGTGATGCTG
+CGGCAGCCCTGACCCTGCTGCTACTGTATGAGCCGCGCCAGGCCCAGCGC
+GTGGCCCATGCAGATGTCTTCGCACCTGTCAAGGCCCACGTGGCAGAGCT
+GGAGCGGCGTTTCCCCGGTGCCCGGGTGCCATGGCTCAGTGTGCAGACAG
+CCGCACCCTCACCACTGCGCCTCATGGATCTACTCTCCAAGAAGCACCCG
+CTGGACACACTGTTCCTGCTGGCCGGGCCAGACACGGTGCTCACGCCTGA
+CTTCCTGAACCGCTGCCGCATGCATGCCATCTCCGGCTGGCAGGCCTTCT
+TTCCCATGCATTTCCAAGCCTTCCACCCAGCTGTGGCCCCACCACAAGGG
+CCTGGGCCCCCAGAGCTGGGCCGTGACACTGGCCGCTTTGATCGCCAGGC
+AGCCAGCGAGGCCTGCTTCTACAACTCCGACTATGTGGCAGCCCGTGGGC
+GCCTGGCGGCAGCCTCAGAACAAGAAGAGGAGCTGCTGGAGAGCCTGGAT
+GTGTACGAGCTGTTCCTCCACTTCTCCAGTCTGCATGTGCTGCGGGCGGT
+GGAGCCGGCGCTGCTGCAGCGCTACCGGGCCCAGACGTGCAGCGCGAGGC
+TCAGTGAGGACCTGTACCACCGCTGCCTCCAGAGCGTGCTTGAGGGCCTC
+GGCTCCCGAACCCAGCTGGCCATGCTACTCTTTGAACAGGAGCAGGGCAA
+CAGCACCTGA
+>hg17_chr20_33330413_33330423_-
+CCTCACCTGA
+>hg17_chr20_33513606_33513792_+
+ATGGAGACAAGAAGCCCTGGGTTGAACAACATGAAGCCCCAGTCACTGCA
+GCTGGTACTGGAAGAGCAGGTGCTGGCACTACAGCAGCAGATGGCAGAGA
+ATCAGGCAGCCTCCTGGCGGAAGCTGAAGAACTCCCAGGAGGCCCAGCAG
+AGACAAGCAACCCTTGTGAGGAAGCTGCAGGCCAAG
+>hg17_chr20_33579500_33579527_-
+ATTTTGGAAGATGGTCTGGTTCCCTAG
+>hg17_chr20_33593260_33593348_+
+ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTACCCCAAGACTTT
+GGAGGACTTCCGGGTCAAGACCTGCGGGGGCGCCACCG
+>hg17_chr21_32707032_32707192_+
+ATGCTTCTGCCGGGACGCGCACGCCAACCGCCGACGCCCCAGCCCGTGCA
+GCATCCCGGCCTCCGCCGGCAGGTAGAGCCGCCGGGGCAGCTCCTGCGCC
+TCTTCTACTGCACTGTCCTGGTCTGCTCCAAAGAGATCTCAGCGCTCACC
+GACTTCTCTG
+>hg17_chr21_32869641_32870022_-
+ATGGAGCGCCCTCTCATCTGGCACCTTCCTGGCCTCTTTCCCAGGCCCCA
+GTTCTGTCCATGCAGCTGTGGGTGCTTCCTGCATTGCGGGTCTCACGGGG
+AGGAGACGAGAGTGCCCCTGGTTGAGTCAGGAAAGAATTCTATCTTCACG
+TCGCTGCCAGCAAATGACCACAGCAGCTTCACGACCTCTGCAGGAACCTA
+TCTTGGTAAAGAAACGGGGCCTATGTGGTGGCCGAGCCTCAGGTGTGGCC
+GAGCTTCAGGTGTGGCCCTTATGCACAGCACAGCCCAAGCCTGTGGGCAC
+CACTCGCCCTGGGCTGCCTGGCACCTGGACTCCTTCCCATCCTTGGCCGA
+GGTCTGCGTGGCCCTTCAGGGCCGAATCTGA
+>hg17_chr21_33321040_33322012_+
+ATGGACTCGGACGCCAGCCTGGTGTCCAGCCGCCCGTCGTCGCCAGAGCC
+CGATGACCTTTTTCTGCCGGCCCGGAGTAAGGGCAGCAGCGGCAGCGCCT
+TCACTGGGGGCACCGTGTCCTCGTCCACCCCGAGTGACTGCCCGCCGGAG
+CTGAGCGCCGAGCTGCGCGGCGCTATGGGCTCTGCGGGCGCGCATCCTGG
+GGACAAGCTAGGAGGCAGTGGCTTCAAGTCATCCTCGTCCAGCACCTCGT
+CGTCTACGTCGTCGGCGGCTGCGTCGTCCACCAAGAAGGACAAGAAGCAA
+ATGACAGAGCCGGAGCTGCAGCAGCTGCGTCTCAAGATCAACAGCCGCGA
+GCGCAAGCGCATGCACGACCTCAACATCGCCATGGATGGCCTCCGCGAGG
+TCATGCCGTACGCACACGGCCCTTCGGTGCGCAAGCTTTCCAAGATCGCC
+ACGCTGCTGCTGGCGCGCAACTACATCCTCATGCTCACCAACTCGCTGGA
+GGAGATGAAGCGACTGGTGAGCGAGATCTACGGGGGCCACCACGCTGGCT
+TCCACCCGTCGGCCTGCGGCGGCCTGGCGCACTCCGCGCCCCTGCCCGCC
+GCCACCGCGCACCCGGCAGCAGCAGCGCACGCCGCACATCACCCCGCGGT
+GCACCACCCCATCctgccgcccgccgccgcagcggctgctgccgccgctg
+cagccgcggctgTGTCCAGCGCCTCTCTGCCCGGATCCGGGCTGCCGTCG
+GTCGGCTCCATCCGTCCACCGCACGGCCTACTCAAGTCTCCGTCTGCTgc
+cgcggccgccccgctggggggcgggggcggcggcAGTGGGGCGAGCGGGG
+GCTTCCAGCACTGGGGCGGCATGCCCTGCCCCTGCAGCATGTGCCAGGTG
+CCGCCGCCGCACCACCACGTGTCGGCTATGGGCGCCGGCAGCCTGCCGCG
+CCTCACCTCCGACGCCAAGTGA
+>hg17_chr21_33744994_33745040_-
+CACTCTGATCTACAAATTTGGAAGAACCGAAGAGCTATGGACCTGA
+>hg17_chr22_30120223_30120265_+
+ATGAGCAGCACCTTAGCTAAGATCGCGGAGATAGAAGCAGAG
+>hg17_chr22_30160419_30160661_-
+TTCTGCATCCTCCAGGCTCTGGTTCCCATGCAGCAGCTGTCAGCGTTCAG
+ACAACCCCTCAGAACGTGCCCAGCCGGTCAGGCCTGCCCCACATGCACTC
+CCAGCTGGAGCATCGCCCCAGCCAGAGGAGCAGCTCCCCTGTGGGCCTTG
+CCAAATGGTTTGGCTCAGATGTGCTACAGCAACCCCTGCCCTCCATGCCC
+GCCAAAGTTATCAGTGTAGATGAATTGGAATACCGACAGTGA
+>hg17_chr22_30665273_30665360_+
+ATGGGGGACCGGGAGCAGCTGCTGCAGCGGGCGCGGCTGGCCGAGCAGGC
+GGAGCGCTACGACGACATGGCCTCCGCTATGAAGGCG
+>hg17_chr22_30939054_30939266_-
+ATTATCCTGAGAAATCACGTGGATGCCTCAAGAAAGCTTATGACTTGTTC
+TGCGGTTTGCAGAAGGGACCCAAGCTAACCAAGGAGGAGGAGGAAGCCTT
+GAGCAAGAAGCTCACAGACACGTCTGAGAGGCCCTCGTGGAGGACAATAG
+TGAACATCAACGCCATCCTCCTCCTGGCTGTGGTGGTCTTTATTCACGGC
+TACTATGCCTGA
+>hg17_chr5_131424298_131424460_+
+ATGAGCCGCCTGCCCGTCCTGCTCCTGCTCCAACTCCTGGTCCGCCCCGG
+ACTCCAAGCTCCCATGACCCAGACAACGCCCTTGAAGACAAGCTGGGTTA
+ACTGCTCTAACATGATCGATGAAATTATAACACACTTAAAGCAGCCACCT
+TTGCCTTTGCTG
+>hg17_chr5_131556601_131556672_-
+TCTCCAATAAGTGGTTCCATGAACGAGGACAGGAGTTCTTGAGACCTTGT
+GGATCAACAGAAGTTGACTGA
+>hg17_chr5_131621326_131621419_+
+ATGCCCCATTCCGTGACCCTGCGCGGGCCTTCGCCCTGGGGCTTCCGCCT
+GGTGGGCGGCCGGGACTTCAGCGCGCCCCTCACCATCTCACGG
+>hg17_chr5_131847541_131847666_-
+GGGATATTGGGCTGAGTCTACAGCGTGTCTTCACAGATCTGAAGAACATG
+GATGCCACCTGGCTGGACAGCCTGCTGACCCCAGTCCGGTTGCCCTCCAT
+CCAGGCCATTCCCTGTGCACCGTAG
+>hg17_chr6_108299600_108299744_-
+TTGGAAGTTCATGAGGCTAAGCCTGTGCCAGAAAATCACCCACAGTGGGA
+TACAGCAATAGAGGGGGATGAAGACCAGGAGGACAGTGAGGGCTTTGAAG
+ATAGCTTTGAGGAAGAAGAGGAGGAAGAAGAAGATGATGACTAA
+>hg17_chr6_108594662_108594687_+
+ATGAGCAAGCCAGCCGGATCAACAA
+>hg17_chr6_108640045_108640151_-
+GGTCGCTGGTCATCCTCTGGCACAGAACGAACGTTGTCTTCACATGTTTT
+TACAAGATGAAATAATAGATAAAAGCTATACTCCATCTAAAATAAGACAT
+GCCTGA
+>hg17_chr6_108722976_108723115_+
+ATGGCGGCCTCCTGGTCGCTCTTGGTTACCCTGCGCCCCTTAGCACAGAG
+CCCGCTGAGAGGGAGATGTGTTGGGTGCGGGGCCTGGGCCGCCGCTCTCG
+CTCCTCTGGCCACCGCCCCTGGGAAGCCCTTTTGGAAAG
+>hg17_chr7_113660517_113660685_+
+ATGATGCAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCA
+AAATGGAATGAGCACTCTAAGCAGCCAATTAGATGCTGGCAGCAGAGATG
+GAAGATCAAGTGGTGACACCAGCTCTGAAGTAAGCACAGTAGAACTGCTG
+CATCTGCAACAACAGCAG
+>hg17_chr7_116512159_116512389_-
+GCTCCCTGGGTACAGCAGGCCGTGTGTGCAACCTGACTTCCCGGGGCATG
+GACAGCTGTGAAGTCATGTGCTGTGGGAGAGGCTACGACACCTCCCATGT
+CACCCGGATGACCAAGTGTGGGTGTAAGTTCCACTGGTGCTGCGCCGTGC
+GCTGTCAGGACTGCCTGGAAGCTCTGGATGTGCACACATGCAAGGCCCCC
+AAGAACGCTGACTGGACAACCGCTACATGA
+>hg17_chr7_116714099_116714152_+
+ATGCAGAGGTCGCCTCTGGAAAAGGCCAGCGTTGTCTCCAAACTTTTTTT
+CAG
+>hg17_chr7_116945541_116945787_-
+GAGGTCAGTCCTCTCAGCAGCCATCAAACTACTGAATGCAGCAACAGTAA
+ATCAAAGACTGAGTTGGGTGTTTCAAGAGTTAAATCTTTTCTTCCTGTTC
+CTAGAAGTAAAGTCACCCAGTGTTCCCAGAACACCAAAAGAAGCAGCAGC
+AGCAGTAATACAAGGCAAATAGAAATCAACAACAACTCAAAAGAAGTGAA
+TTGGAACTTACACAAAAATGAACACCTAGAAAAACCTAACAAATAG
+>hg17_chr8_118881131_118881317_-
+ACTTCTCGGGCTTCCCGTTGGGCTGACCCTGACCACTTTGCCCAGCGACA
+GAGCTGCATGAATACGTTTGCCAGCTGGTTTGGCTACATGCCGCTGATCC
+ACTCTCAGATGAGGCTCGACCCCGTCCTCTTTAAAGACCAGGTCTCTATT
+TTGAGGAAGAAATACCGAGACATTGAGCGACTTTGA
+>hg17_chr9_128764156_128764189_+
+ATGGCCTGCCTGAGCCCCTCGCAGCTCCAGAAG
+>hg17_chr9_128787519_128789136_-
+ATGACCCGAGAGTGCCCATCTCCGGCCCCGGGGCCTGGGGCTCCGCTGAG
+TGGATCGGTGCTGGCAGAGGCGGCAGTAGTGTTTGCAGTGGTGCTGAGCA
+TCCACGCAACCGTATGGGACCGATACTCGTGGTGCGCCGTGGCCCTCGCA
+GTGCAGGCCTTCTACGTCCAATACAAGTGGGACCGGCTGCTACAGCAGGG
+AAGCGCCGTCTTCCAGTTCCGAATGTCCGCAAACAGTGGCCTATTGCCCG
+CCTCCATGGTCATGCCTTTGCTTGGACTAGTCATGAAGGAGCGGTGCCAG
+ACTGCTGGGAACCCGTTCTTTGAGCGTTTTGGCATTGTGGTGGCAGCCAC
+TGGCATGGCAGTGGCCCTCTTCTCATCAGTGTTGGCGCTCGGCATCACTC
+GCCCAGTGCCAACCAACACTTGTGTCATCTTGGGCTTGGCTGGAGGTGTT
+ATCATTTATATCATGAAGCACTCGTTGAGCGTGGGGGAGGTGATCGAAGT
+CCTGGAAGTCCTTCTGATCTTCGTTTATCTCAACATGATCCTGCTGTACC
+TGCTGCCCCGCTGCTTCACCCCTGGTGAGGCACTGCTGGTATTGGGTGGC
+ATTAGCTTTGTCCTCAACCAGCTCATCAAGCGCTCTCTGACACTGGTGGA
+AAGTCAGGGGGACCCAGTGGACTTCTTCCTGCTGGTGGTGGTAGTAGGGA
+TGGTACTCATGGGCATTTTCTTCAGCACTCTGTTTGTCTTCATGGACTCA
+GGCACCTGGGCCTCCTCCATCTTCTTCCACCTCATGACCTGTGTGCTGAG
+CCTTGGTGTGGTCCTACCCTGGCTGCACCGGCTCATCCGCAGGAATCCCC
+TGCTCTGGCTTCTTCAGTTTCTCTTCCAGACAGACACCCGCATCTACCTC
+CTAGCCTATTGGTCTCTGCTGGCCACCTTGGCCTGCCTGGTGGTGCTGTA
+CCAGAATGCCAAGCGGTCATCTTCCGAGTCCAAGAAGCACCAGGCCCCCA
+CCATCGCCCGAAAGTATTTCCACCTCATTGTGGTAGCCACCTACATCCCA
+GGTATCATCTTTGACCGGCCACTGCTCTATGTAGCCGCCACTGTATGCCT
+GGCGGTCTTCATCTTCCTGGAGTATGTGCGCTACTTCCGCATCAAGCCTT
+TGGGTCACACTCTACGGAGCTTCCTGTCCCTTTTTCTGGATGAACGAGAC
+AGTGGACCACTCATTCTGACACACATCTACCTGCTCCTGGGCATGTCTCT
+TCCCATCTGGCTGATCCCCAGACCCTGCACACAGAAGGGTAGCCTGGGAG
+GAGCCAGGGCCCTCGTCCCCTATGCCGGTGTCCTGGCTGTGGGTGTGGGT
+GATACTGTGGCCTCCATCTTCGGTAGCACCATGGGGGAGATCCGCTGGCC
+TGGAACCAAAAAGACTTTTGAGGGGACCATGACATCTATATTTGCGCAGA
+TCATTTCTGTAGCTCTGATCTTAATCTTTGACAGTGGAGTGGACCTAAAC
+TACAGTTATGCTTGGATTTTGGGGTCCATCAGCACTGTGTCCCTCCTGGA
+AGCATACACTACACAGATAGACAATCTCCTTCTGCCTCTCTACCTCCTGA
+TATTGCTGATGGCCTAG
+>hg17_chr9_128882427_128882523_+
+ATGGCGTTCCGGAGGGCCGAGGGCACGTCTATGATCCAGGCCCTGGCCAT
+GACGGTGGCCGAGATCCCCGTGTTCCTGTACACGACGTTTGGGCAG
+>hg17_chr9_128937229_128937445_-
+GTCCCTGCCAAGACAGACTGTGTCATGTTCTTCGGGCCCGTGGTCCCCGA
+CGGCTACGGTGTCTGCTATAACCCCATGGAGGCCCACATCAACTTCTCCC
+TGTCGGCCTACAACAGCTGCGCGGAGACCAACGCCGCCCGCCTGGCGCAT
+TACCTGGAGAAGGCGCTCCTGGACATGCGTGCCCTGCTGCAGAGCCACCC
+CCGGGCCAAGCTCTGA
+>hg17_chrX_122745047_122745924_+
+ATGACTTTTAACAGTTTTGAAGGATCTAAAACTTGTGTACCTGCAGACAT
+CAATAAGGAAGAAGAATTTGTAGAAGAGTTTAATAGATTAAAAACTTTTG
+CTAATTTTCCAAGTGGTAGTCCTGTTTCAGCATCAACACTGGCACGAGCA
+GGGTTTCTTTATACTGGTGAAGGAGATACCGTGCGGTGCTTTAGTTGTCA
+TGCAGCTGTAGATAGATGGCAATATGGAGACTCAGCAGTTGGAAGACACA
+GGAAAGTATCCCCAAATTGCAGATTTATCAACGGCTTTTATCTTGAAAAT
+AGTGCCACGCAGTCTACAAATTCTGGTATCCAGAATGGTCAGTACAAAGT
+TGAAAACTATCTGGGAAGCAGAGATCATTTTGCCTTAGACAGGCCATCTG
+AGACACATGCAGACTATCTTTTGAGAACTGGGCAGGTTGTAGATATATCA
+GACACCATATACCCGAGGAACCCTGCCATGTATAGTGAAGAAGCTAGATT
+AAAGTCCTTTCAGAACTGGCCAGACTATGCTCACCTAACCCCAAGAGAGT
+TAGCAAGTGCTGGACTCTACTACACAGGTATTGGTGACCAAGTGCAGTGC
+TTTTGTTGTGGTGGAAAACTGAAAAATTGGGAACCTTGTGATCGTGCCTG
+GTCAGAACACAGGCGACACTTTCCTAATTGCTTCTTTGTTTTGGGCCGGA
+ATCTTAATATTCGAAGTGAATCTGATGCTGTGAGTTCTGATAGGAATTTC
+CCAAATTCAACAAATCTTCCAAGAAATCCATCCATGGCAGATTATGAAGC
+ACGGATCTTTACTTTTGGGACATGGATATACTCAGTTAACAAGGAGCAGC
+TTGCAAGAGCTGGATTTTATGCTTTAG
+>hg17_chrX_152648964_152649196_-
+TGACAACGAGGAGAAGGCCTTTGGCAGCAGCCAGCCATCGCTCAACGGGG
+ACATCAAGCCCCTGGGCAGTGACGACAGCCTGGCCGATTATGGGGGCAGC
+GTGGATGTTCAGTTCAACGAGGATGGTTCGTTCATTGGCCAGTACAGTGG
+CAAGAAGGAGAAGGAGGCGGCAGGGGGCAATGACAGCTCAGGGGCCACTT
+CCCCCATCAACCCTGCCGTGGCCCTAGAATAG
+>hg17_chrX_152691446_152691471_+
+ATGCTCATGGCGTCCACCACTTCCG
+>hg17_chrX_152694029_152694263_-
+GCTGTGGCACAGAACATGGACTCTGTGTTTAAGGAGCTCTTGGGAAAGAC
+CTCTGTCCGCCAGGGCCTTGGGCCAGCATCTACCACCTCTCCCAGTCCTG
+GGCCCCGAAGCCCAAAGGCCCCGCCCAGCAGCCGCCTGGGCAGGAACAAA
+GGCTTCTCCCGGGGCCCTGGGGCCCCAGCCTCACCCTCAGCTTCCCACCC
+CCAGGGCCTAGACACGACCCCCAAGCCACACTGA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_tool_compute_length_1.out	Thu Oct 29 22:14:42 2015 -0400
@@ -0,0 +1,18 @@
+EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_	54
+EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_	187
+EYKX4VC01CD9FT length=115 xy=0865_1719 region=1 run=R_2007_11_07_16_15_57_	115
+EYKX4VC01B8FW0 length=95 xy=0799_0514 region=1 run=R_2007_11_07_16_15_57_	95
+EYKX4VC01BCGYW length=115 xy=0434_3926 region=1 run=R_2007_11_07_16_15_57_	115
+EYKX4VC01AZXC6 length=116 xy=0292_0280 region=1 run=R_2007_11_07_16_15_57_	116
+EYKX4VC01CATH5 length=82 xy=0826_0843 region=1 run=R_2007_11_07_16_15_57_	82
+EYKX4VC01BCEIV length=47 xy=0434_0757 region=1 run=R_2007_11_07_16_15_57_	47
+EYKX4VC01BWERM length=83 xy=0662_0304 region=1 run=R_2007_11_07_16_15_57_	83
+EYKX4VC01BT2O7 length=69 xy=0635_1945 region=1 run=R_2007_11_07_16_15_57_	69
+EYKX4VC01BO0UO length=222 xy=0577_3838 region=1 run=R_2007_11_07_16_15_57_	222
+EYKX4VC01CBCPK length=83 xy=0832_1158 region=1 run=R_2007_11_07_16_15_57_	83
+EYKX4VC01B474S length=54 xy=0762_2010 region=1 run=R_2007_11_07_16_15_57_	54
+EYKX4VC01BB4QL length=57 xy=0431_0363 region=1 run=R_2007_11_07_16_15_57_	57
+EYKX4VC01BJ37M length=64 xy=0522_0192 region=1 run=R_2007_11_07_16_15_57_	64
+EYKX4VC01BV9R8 length=54 xy=0660_2038 region=1 run=R_2007_11_07_16_15_57_	54
+EYKX4VC01CEPP8 length=60 xy=0870_2350 region=1 run=R_2007_11_07_16_15_57_	60
+EYKX4VC01BTLME length=78 xy=0630_0292 region=1 run=R_2007_11_07_16_15_57_	78
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_tool_compute_length_2.out	Thu Oct 29 22:14:42 2015 -0400
@@ -0,0 +1,65 @@
+hg17_chr1_147962192_147962580_-	388
+hg17_chr1_147984545_147984630_+	85
+hg17_chr1_148078400_148078582_-	182
+hg17_chr1_148185136_148185276_+	140
+hg17_chr10_55251623_55253124_-	1501
+hg17_chr11_116124407_116124501_-	94
+hg17_chr11_116206508_116206563_+	55
+hg17_chr11_116211733_116212337_-	604
+hg17_chr11_1812377_1812407_+	30
+hg17_chr12_38440094_38440321_-	227
+hg17_chr13_112381694_112381953_+	259
+hg17_chr14_98710240_98712285_-	2045
+hg17_chr15_41486872_41487060_-	188
+hg17_chr15_41673708_41673857_+	149
+hg17_chr15_41679161_41679250_-	89
+hg17_chr15_41826029_41826196_+	167
+hg17_chr16_142908_143003_+	95
+hg17_chr16_179963_180135_-	172
+hg17_chr16_244413_244681_+	268
+hg17_chr16_259268_259383_-	115
+hg17_chr18_23786114_23786321_-	207
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_tool_compute_length_3.out	Thu Oct 29 22:14:42 2015 -0400
@@ -0,0 +1,18 @@
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