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changeset 2:2aa02d2a6af3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c
author iuc
date Tue, 18 Jul 2017 13:56:16 -0400
parents 15197951a756
children 6e9aea89e388
files abricate.xml abricate_list.xml test-data/output_cull100.txt test-data/output_db-card.txt test-data/output_gbk.txt test-data/output_list.txt test-data/output_minid100.txt test-data/output_mrsa.txt test-data/output_noheader.txt test-data/output_noresults.txt test-data/test.gbk
diffstat 11 files changed, 173 insertions(+), 104 deletions(-) [+]
line wrap: on
line diff
--- a/abricate.xml	Fri Mar 03 14:56:09 2017 -0500
+++ b/abricate.xml	Tue Jul 18 13:56:16 2017 -0400
@@ -1,39 +1,34 @@
-<tool id="abricate" name="ABRicate" version="0.3">
+<tool id="abricate" name="ABRicate" version="0.5">
     <requirements>
-        <requirement type="package" version="0.3">abricate</requirement>
+        <requirement type="package" version="0.5">abricate</requirement>
     </requirements>
 
     <version_command>abricate --version</version_command>
 
     <command detect_errors="exit_code"><![CDATA[
-        abricate '$fasta_input'
-        #if $settings.advanced == "advanced"
-            $settings.no_header
-            #if str($settings.min_dna_id)
-                --minid=$settings.min_dna_id
-            #end if
-            #if str($settings.cull_limit)
-                --cull=$settings.cull_limit
-            #end if
+        abricate '$file_input'
+        $adv.no_header
+        #if $adv.min_dna_id
+            --minid=$adv.min_dna_id
         #end if
+        --db=$adv.db
         > '$report'
     ]]></command>
 
     <inputs>
-        <param name="fasta_input" type="data" format="fasta" label="FASTA file" help="To screen for antibiotic resistant genes" />
-        <conditional name="settings">
-            <param name="advanced" type="select" label="Specify advanced parameters">
-                <option value="simple" selected="true">No, use program defaults.</option>
-                <option value="advanced">Yes, see full parameter list.</option>
+        <param name="file_input" type="data" format="fasta,genbank,embl" label="Input file (Fasta, Genbank or EMBL file)" help="To screen for antibiotic resistant genes, can be a fasta file, a genbank file or an EMBL file." />
+        <section name="adv" title="Advanced options" expanded="False">
+            <param argument="--db" type="select" label="Database to use - default is 'resfinder'" help="Option to switch to other AMR/other database">
+                <option value="argannot">argannot</option>
+                <option value="card">card</option>
+                <option value="ncbibetalactamase">ncbi betalactamase</option>
+                <option value="resfinder" selected="true">resfinder</option>
+                <option value="plasmidfinder">plasmidfinder</option>
+                <option value="vfdb">vfdb</option>
             </param>
-            <when value="simple">
-            </when>
-            <when value="advanced">
-                <param name="no_header" argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Suppress header" help="Suppress output file's column headings" />
-                <param name="min_dna_id" argument="--minid" type="float" value="75" min="0" max="100" optional="true" label="Minimum DNA identity" />
-                <param name="cull_limit" argument="--cull" type="integer" value="1" min="0" optional="true" label="Culling limit (encompassing hits)" />
-            </when>
-        </conditional>
+            <param name="no_header" argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Suppress header" help="Suppress output file's column headings" />
+            <param name="min_dna_id" argument="--minid" type="float" value="75" min="0" max="100" optional="true" label="Minimum DNA identity" />
+        </section>
     </inputs>
 
     <outputs>
@@ -41,49 +36,51 @@
     </outputs>
 
     <tests>
-        <!-- Basic test - will produce no results. -->
+        <!-- Basic test 0 - will produce no results. -->
         <test>
-            <param name="fasta_input" value="Acetobacter.fna"/>
-            <param name="advanced" value="simple"/>
+            <param name="file_input" value="Acetobacter.fna"/>
             <output name="report" ftype="tabular" file="output_noresults.txt" />
         </test>
 
-        <!-- Basic test - will produce results. -->
+        <!-- Basic test 1 - will produce results. -->
         <test>
-            <param name="fasta_input" value="MRSA0252.fna"/>
-            <param name="advanced" value="simple"/>
+            <param name="file_input" value="MRSA0252.fna"/>
             <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
         </test>
 
-        <!-- Advanced test - No header. -->
+        <!-- Advanced test 2 - No header. -->
         <test>
-            <param name="fasta_input" value="MRSA0252.fna"/>
-            <param name="advanced" value="advanced"/>
+            <param name="file_input" value="MRSA0252.fna"/>
             <param name="no_header" value="True"/>
             <output name="report" ftype="tabular" file="output_noheader.txt" compare="contains"/>
         </test>
 
-        <!-- Advanced test - Cull limit 100 -->
+        <!-- Advanced test 3 - Changed DB to card -->
         <test>
-            <param name="fasta_input" value="MRSA0252.fna"/>
-            <param name="advanced" value="advanced"/>
-            <param name="cull_limit" value="100"/>
-            <output name="report" ftype="tabular" file="output_cull100.txt" compare="contains"/>
+            <param name="file_input" value="MRSA0252.fna"/>
+            <param name="db" value="card"/>
+            <output name="report" ftype="tabular" file="output_db-card.txt" compare="contains"/>
         </test>
 
-        <!-- Advanced test - Min DNA ID 100 -->
+        <!-- Advanced test 4 - Min DNA ID 100 -->
         <test>
-            <param name="fasta_input" value="MRSA0252.fna"/>
-            <param name="advanced" value="advanced"/>
+            <param name="file_input" value="MRSA0252.fna"/>
             <param name="min_dna_id" value="100"/>
             <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
         </test>
+
+        <!-- Filetype test 5 - input a gbk -->
+        <test>
+            <param name="file_input" value="test.gbk"/>
+            <output name="report" ftype="tabular" file="output_gbk.txt" compare="contains"/>
+        </test>
+
     </tests>
 
     <help><![CDATA[
 **What it does**
 
-Given a FASTA contig file, ABRicate will perform a mass screening of contigs and identify the presence of antibiotic resistance genes. The database of these genes is built from ResFinder.
+Given a FASTA contig file or a genbank file, ABRicate will perform a mass screening of contigs and identify the presence of antibiotic resistance genes. The user can choose which database to search from a list of available AMR databases.
 
 **Output**
 
@@ -113,18 +110,20 @@
 +---------------+------------------------------------------------+
 |  %IDENTITY    | Proportion of exact nucleotide matches         |
 +---------------+------------------------------------------------+
+|  DATABASE     | The database this sequence comes from          |
++---------------+------------------------------------------------+
+|  ACCESSION    | The genomic source of the sequence             |
++---------------+------------------------------------------------+
 
 
 **Example Output**
 
 ::
 
-	#FILE   SEQUENCE    START   END GENE    COVERAGE    COVERAGE_MAP    GAPS    %COVERAGE   %IDENTITY
-	Processing: 6008.fna
-	Found 12 ABR genes in 6008.fna
-	Klebsiella.fna  NC_021232.1 872545  872964  fosA    1-420/420   =============== 0   100.00  100.00
-	Klebsiella.fna  NC_021232.1 1381252 1382427 oqxA    1-1176/1176 =============== 0   100.00  99.32
-	Klebsiella.fna  NC_021232.1 2584899 2585759 blaSHV1 1-861/861   =============== 0   100.00  99.88
+        #FILE     SEQUENCE     START   END     GENE     COVERAGE     COVERAGE_MAP     GAPS  %COVERAGE  %IDENTITY  DATABASE   ACCESSION
+        6159.fna  NC_017338.1  39177   41186   mecA_15  1-2010/2010  ===============  0/0   100.00     100.000    resfinder  AB505628
+        6159.fna  NC_017338.1  727191  728356  norA_1   1-1166/1167  ===============  0/0   99.91      92.367     resfinder  M97169
+        6159.fna  NC_017339.1  10150   10995   blaZ_32  1-846/846    ===============  0/0   100.00     100.000    resfinder  AP004832
     ]]></help>
 
     <citations>
--- a/abricate_list.xml	Fri Mar 03 14:56:09 2017 -0500
+++ b/abricate_list.xml	Tue Jul 18 13:56:16 2017 -0400
@@ -1,6 +1,6 @@
-<tool id="abricate_list" name="ABRicate List" version="0.3">
+<tool id="abricate_list" name="ABRicate List" version="0.5">
     <requirements>
-        <requirement type="package" version="0.3">abricate</requirement>
+        <requirement type="package" version="0.5">abricate</requirement>
     </requirements>
 
     <version_command>abricate --version</version_command>
@@ -18,7 +18,7 @@
 
     <tests>
         <test>
-            <output name="report" ftype="txt" file="output_list.txt" />
+            <output name="report" ftype="txt" file="output_list.txt" compare="contains"/>
         </test>
     </tests>
 
--- a/test-data/output_cull100.txt	Fri Mar 03 14:56:09 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY
-gi|49482253|ref|NC_002952.2|	40786	41556	aadD	1-771/771	===============	0	100.00	99.74
-gi|49482253|ref|NC_002952.2|	1913827	1914672	blaZ	1-846/846	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	55890	56621	erm(A)	1-732/732	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	1796513	1797244	erm(A)	1-732/732	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	55983	56576	erm(A)	1-594/594	===============	0	100.00	85.52
-gi|49482253|ref|NC_002952.2|	1796606	1797199	erm(A)	1-594/594	===============	0	100.00	85.52
-gi|49482253|ref|NC_002952.2|	44919	46928	mecA	1-2010/2010	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	44919	46925	mecA	1-2007/2007	===============	0	100.00	99.95
-gi|49482253|ref|NC_002952.2|	782414	783580	norA	1-1167/1167	===============	0	100.00	91.69
-gi|49482253|ref|NC_002952.2|	1797370	1798152	spc	1-783/783	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	56747	57529	spc	1-783/783	===============	0	100.00	100.00
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_db-card.txt	Tue Jul 18 13:56:16 2017 -0400
@@ -0,0 +1,17 @@
+#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION
+NC_002952.2	40786	41547	ANT(4')-Ib	1-762/762	===============	0/0	100.00	100.00	card	NC_013342.1:26738-27500
+NC_002952.2	44918	46925	mecA	1-2008/2008	===============	0/0	100.00	99.90	card	KC243783:1-2008
+NC_002952.2	47025	48783	mecR1	1-1759/1759	===============	0/0	100.00	99.94	card	NC_009487:40849-42607
+NC_002952.2	48782	49154	mecI	1-373/373	===============	0/0	100.00	99.73	card	NC_002745:48894-49266
+NC_002952.2	55890	56622	ErmA	1-733/733	===============	0/0	100.00	100.00	card	NC_009632:49745-50477
+NC_002952.2	152865	154217	tet(38)	1-1353/1353	===============	0/0	100.00	98.52	card	AY825285:1-1354
+NC_002952.2	376045	376465	mepR	1-421/421	===============	0/0	100.00	99.05	card	NC_009782:379935-380355
+NC_002952.2	376571	377926	mepA	1-1356/1356	===============	0/0	100.00	98.53	card	AY661734.1:840-2196
+NC_002952.2	774312	774756	mgrA	1-445/445	===============	0/0	100.00	99.78	card	NC_013450:694853-695297
+NC_002952.2	782414	783543	norA	1-1130/1165	========/======	7/14	96.39	76.08	card	AY566250:392-1556
+NC_002952.2	1486310	1487666	arlS	1-1357/1357	===============	0/0	100.00	98.38	card	NC_007795:1360281-1361637
+NC_002952.2	1487662	1488322	arlR	1-661/661	===============	0/0	100.00	99.09	card	NC_009641:1461589-1462249
+NC_002952.2	1796513	1797245	ErmA	1-733/733	===============	0/0	100.00	100.00	card	NC_009632:49745-50477
+NC_002952.2	1913826	1914672	PC1_beta-lactamase_(blaZ)	1-847/847	===============	0/0	100.00	97.17	card	NC_010066:9683-10529
+NC_002952.2	2047036	2048773	sav1866	1-1738/1738	===============	0/0	100.00	99.19	card	NC_002951:1987720-1989457
+NC_002952.2	2488459	2488878	FosB	1-420/420	===============	0/0	100.00	79.05	card	NC_010419.1:17043-17463
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_gbk.txt	Tue Jul 18 13:56:16 2017 -0400
@@ -0,0 +1,2 @@
+#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION
+STANORAX	246	1412	norA_1	1-1167/1167	===============	0/0	100.00	100.00	resfinder	M97169
--- a/test-data/output_list.txt	Fri Mar 03 14:56:09 2017 -0500
+++ b/test-data/output_list.txt	Tue Jul 18 13:56:16 2017 -0400
@@ -1,16 +1,7 @@
-aminoglycoside	169
-beta-lactamase	1305
-colistin	1
-fosfomycin	21
-fusidicacid	2
-macrolide	131
-nitroimidazole	14
-oxazolidinone	3
-phenicol	36
-quinolone	103
-rifampicin	9
-sulphonamide	49
-tetracycline	104
-trimethoprim	53
-vancomycin	123
-TOTAL	2123
+abricate: corrupt database? - 
+argannot:  1749 sequences -  Jul 8, 2017
+card:  2124 sequences -  Jul 8, 2017
+ncbibetalactamase:  1557 sequences -  Mar 17, 2017
+plasmidfinder:  263 sequences -  Mar 19, 2017
+resfinder:  2228 sequences -  Jul 8, 2017
+vfdb:  2597 sequences -  Mar 17, 2017
--- a/test-data/output_minid100.txt	Fri Mar 03 14:56:09 2017 -0500
+++ b/test-data/output_minid100.txt	Tue Jul 18 13:56:16 2017 -0400
@@ -1,7 +1,7 @@
-#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY
-gi|49482253|ref|NC_002952.2|	1913827	1914672	blaZ	1-846/846	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	55890	56621	erm(A)	1-732/732	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	1796513	1797244	erm(A)	1-732/732	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	44919	46928	mecA	1-2010/2010	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	1797370	1798152	spc	1-783/783	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	56747	57529	spc	1-783/783	===============	0	100.00	100.00
+#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION
+NC_002952.2	44919	46928	mecA_15	1-2010/2010	===============	0/0	100.00	100.00	resfinder	AB505628
+NC_002952.2	55890	56621	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216
+NC_002952.2	56747	57529	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588
+NC_002952.2	1796513	1797244	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216
+NC_002952.2	1797370	1798152	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588
+NC_002952.2	1913827	1914672	blaZ_36	1-846/846	===============	0/0	100.00	100.00	resfinder	AJ400722
--- a/test-data/output_mrsa.txt	Fri Mar 03 14:56:09 2017 -0500
+++ b/test-data/output_mrsa.txt	Tue Jul 18 13:56:16 2017 -0400
@@ -1,9 +1,9 @@
-#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY
-gi|49482253|ref|NC_002952.2|	40786	41556	aadD	1-771/771	===============	0	100.00	99.74
-gi|49482253|ref|NC_002952.2|	1913827	1914672	blaZ	1-846/846	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	55890	56621	erm(A)	1-732/732	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	1796513	1797244	erm(A)	1-732/732	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	44919	46928	mecA	1-2010/2010	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	782414	783580	norA	1-1167/1167	===============	0	100.00	91.69
-gi|49482253|ref|NC_002952.2|	1797370	1798152	spc	1-783/783	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	56747	57529	spc	1-783/783	===============	0	100.00	100.00
+#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION
+NC_002952.2	40786	41556	aadD_1	1-771/771	===============	0/0	100.00	99.74	resfinder	AF181950
+NC_002952.2	44919	46928	mecA_15	1-2010/2010	===============	0/0	100.00	100.00	resfinder	AB505628
+NC_002952.2	55890	56621	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216
+NC_002952.2	56747	57529	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588
+NC_002952.2	782414	783580	norA_1	1-1167/1167	===============	0/0	100.00	91.69	resfinder	M97169
+NC_002952.2	1796513	1797244	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216
+NC_002952.2	1797370	1798152	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588
+NC_002952.2	1913827	1914672	blaZ_36	1-846/846	===============	0/0	100.00	100.00	resfinder	AJ400722
--- a/test-data/output_noheader.txt	Fri Mar 03 14:56:09 2017 -0500
+++ b/test-data/output_noheader.txt	Tue Jul 18 13:56:16 2017 -0400
@@ -1,8 +1,8 @@
-gi|49482253|ref|NC_002952.2|	40786	41556	aadD	1-771/771	===============	0	100.00	99.74
-gi|49482253|ref|NC_002952.2|	1913827	1914672	blaZ	1-846/846	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	55890	56621	erm(A)	1-732/732	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	1796513	1797244	erm(A)	1-732/732	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	44919	46928	mecA	1-2010/2010	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	782414	783580	norA	1-1167/1167	===============	0	100.00	91.69
-gi|49482253|ref|NC_002952.2|	1797370	1798152	spc	1-783/783	===============	0	100.00	100.00
-gi|49482253|ref|NC_002952.2|	56747	57529	spc	1-783/783	===============	0	100.00	100.00
+NC_002952.2	40786	41556	aadD_1	1-771/771	===============	0/0	100.00	99.74	resfinder	AF181950
+NC_002952.2	44919	46928	mecA_15	1-2010/2010	===============	0/0	100.00	100.00	resfinder	AB505628
+NC_002952.2	55890	56621	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216
+NC_002952.2	56747	57529	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588
+NC_002952.2	782414	783580	norA_1	1-1167/1167	===============	0/0	100.00	91.69	resfinder	M97169
+NC_002952.2	1796513	1797244	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216
+NC_002952.2	1797370	1798152	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588
+NC_002952.2	1913827	1914672	blaZ_36	1-846/846	===============	0/0	100.00	100.00	resfinder	AJ400722
--- a/test-data/output_noresults.txt	Fri Mar 03 14:56:09 2017 -0500
+++ b/test-data/output_noresults.txt	Tue Jul 18 13:56:16 2017 -0400
@@ -1,1 +1,1 @@
-#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY
+#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.gbk	Tue Jul 18 13:56:16 2017 -0400
@@ -0,0 +1,72 @@
+LOCUS       STANORAX                1601 bp    DNA     linear   BCT 27-MAY-1993
+DEFINITION  Staphylococcus aureus fluoroquinolone resistance protein (norA)
+            gene, complete cds.
+ACCESSION   M97169
+VERSION     M97169.1
+KEYWORDS    fluoroquinolone resistance protein; norA gene.
+SOURCE      Staphylococcus aureus
+  ORGANISM  Staphylococcus aureus
+            Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
+            Staphylococcus.
+REFERENCE   1  (bases 1 to 1601)
+  AUTHORS   Kaatz,G.W., Seo,S.M. and Ruble,C.A.
+  TITLE     Efflux-mediated fluoroquinolone resistance in Staphylococcus aureus
+  JOURNAL   Antimicrob. Agents Chemother. 37 (5), 1086-1094 (1993)
+   PUBMED   8517696
+FEATURES             Location/Qualifiers
+     source          1..1601
+                     /organism="Staphylococcus aureus"
+                     /mol_type="genomic DNA"
+                     /db_xref="taxon:1280"
+     gene            117..1412
+                     /gene="norA"
+     regulatory      117..122
+                     /regulatory_class="minus_35_signal"
+                     /gene="norA"
+                     /note="putative"
+     regulatory      141..146
+                     /regulatory_class="minus_10_signal"
+                     /gene="norA"
+     CDS             246..1412
+                     /gene="norA"
+                     /function="fluoroquinolone efflux"
+                     /standard_name="NORA1199 wild-type gene"
+                     /codon_start=1
+                     /transl_table=11
+                     /protein_id="AAA26658.1"
+                     /translation="MNKQILVLYFNIFLIFLGIGLVIPVLPVYLKDLGLTGSDLGLLV
+                     AAFALSQMIISPFGGTLADKLGKKLIICIGLILFSVSEFMFAIGQNFLILMLSRVIGG
+                     MSAGMVMPGVTGLIADISPSHQKAKNFGYMSAIINSGFILGPGIGGFMAEVSHRMPFY
+                     FAGALGILAFIMSIVLIHDPKKVSTNGFQKLEPQLLTKINWKVFITPVILTLVLSFGL
+                     SAFETLYSLYTADKVNYSPKDISIAITGGGIFGALFQIYFFDKFMKYFSELTFIAWSL
+                     IYSVIVLVLLVIADGYWTIMVISFVVFIGFDMIRPAITNYFSNIAGDRQGFAGGLNST
+                     FTSMGNFIGPLIAGALFDVHIEAPIYMAIGVSLAGVVIVLIEKQHRAKLKQQDL"
+ORIGIN
+        1 ctagtagtat agtatgatta cttttttgca atttcatatg atcaatcccc tttattttaa
+       61 tatgtcatta attatacaat taaatggaaa atagtgataa ttacaaagaa aaaatattgt
+      121 caaatgtagc aatattgtaa tacaatatag aaacttttta cgaatattta gcatgaattg
+      181 caatctgtcg tggaaaagaa aaataacagc ttgaagagtg acaagtagaa aaaagaggtg
+      241 agcaaatgaa taaacagatt ttggtattat attttaatat tttcttaatt tttttaggta
+      301 tcggtctagt gataccagtc ttacctgttt atttaaaaga tttggggtta actggtagtg
+      361 atttaggatt attagttgct gctttcgcct tatctcaaat gattatatcg ccattcggtg
+      421 gtacgttagc tgataaatta ggaaagaaat taattatatg tataggatta attttgtttt
+      481 cagtgtcaga atttatgttt gctatcggtc agaatttttt aattttgatg ttatcaaggg
+      541 ttatcggtgg tatgagtgct ggtatggtta tgcctggggt gacaggttta atagctgata
+      601 tttcaccaag ccatcaaaaa gcaaaaaact ttggctacat gtcagcgatt atcaattcag
+      661 gattcatttt aggaccaggg attggtggat ttatggcaga agtttcacat cgtatgccat
+      721 tttattttgc aggtgcatta ggtattctag catttataat gtcaattgta ttgattcacg
+      781 accctaaaaa agtttcgaca aatggattcc aaaagttgga gccacaattg ctaacgaaaa
+      841 ttaactggaa agtgtttatt acaccagtta ttctaacact tgtattatcg tttggtttat
+      901 ctgcatttga aacattgtat tcactataca cagctgacaa ggtaaattat tcacctaaag
+      961 atatttcgat tgcaattaca ggtggcggta tctttggtgc acttttccaa atttatttct
+     1021 ttgataaatt tatgaaatac ttctctgagt taacatttat tgcatggtca ttaatatatt
+     1081 cagttattgt attagtgcta ttagttattg ccgatggtta ctggacaatt atggtaataa
+     1141 gctttgttgt ctttatcggg ttcgatatga taagacctgc tattacaaat tatttttcaa
+     1201 atattgctgg tgatagacag ggatttgcag gtgggttaaa ctcaacattc actagcatgg
+     1261 ggaattttat aggtccttta atcgcaggtg cgttatttga tgtgcacatt gaagccccaa
+     1321 tttatatggc tataggtgtg tcattagctg gtgttgtcat tgttttaatt gaaaagcaac
+     1381 atagagctaa gttaaaacaa caagatttgt aatatcgcac atggttgtca ttcgattaat
+     1441 gtttttcgac aactaaagca tttcaaaata agcatcgatt ttcttacaat tatagtgaag
+     1501 aaaagtcgat gctttaaatt tataaagatt aaaaactttt aaatgtttta gtctttatat
+     1561 ttaaatgtta tatgtaacaa aaaatgattt tgagtaataa a
+//