Migrate fastx toolkit from tools-devteam, condafy.

tool_collections/fastx_toolkit/fasta_clipping_histogram/.shed.yml

@@ -0,0 +1,13 @@
+categories:
+- Fasta Manipulation
+- Graphics
+- Statistics
+description: Length Distribution chart
+long_description: |
+  This tool creates a histogram image of sequence lengths distribution
+  in a given fasta dataset file.
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+name: fasta_clipping_histogram
+owner: devteam
+remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram
+type: unrestricted

tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml

@@ -0,0 +1,110 @@
+<tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="@WRAPPER_VERSION@">
+    <description>chart</description>
+    <expand macro="requirements" />
+    <macros>
+        <import>fastx_macros.xml</import>
+    </macros>
+    <command><![CDATA[
+        command -v perl5.22.0 &&
+        perl5.22.0 `command -v fasta_clipping_histogram.pl` '$input' '$outfile' ||
+        fasta_clipping_histogram.pl '$input' '$outfile'
+    ]]></command>
+    <inputs>
+        <param format="fasta" name="input" type="data" label="Library to analyze" />
+    </inputs>
+    <outputs>
+        <data format="png" name="outfile" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="input.fasta" ftype="fasta"/>
+            <output name="outfile" file="histogram.pdf" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+This tool creates a histogram image of sequence lengths distribution in a given fasta dataset file.
+
+**TIP:** Use this tool after clipping your library (with **FASTX Clipper tool**), to visualize the clipping results.
+
+-----
+
+**Output Examples**
+
+In the following library, most sequences are 24-mers to 27-mers.
+This could indicate an abundance of endo-siRNAs (depending of course of what you've tried to sequence in the first place).
+
+.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_1.png
+
+In the following library, most sequences are 19,22 or 23-mers.
+This could indicate an abundance of miRNAs (depending of course of what you've tried to sequence in the first place).
+
+.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_2.png
+
+-----
+
+**Input Formats**
+
+This tool accepts short-reads FASTA files. The reads don't have to be short, but they do have to be on a single line, like so::
+
+   >sequence1
+   AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG
+   >sequence2
+   GTGTGTGTGGGAAGTTGACACAGTA
+   >sequence3
+   CCTTGAGATTAACGCTAATCAAGTAAAC
+
+If the sequences span over multiple lines::
+
+   >sequence1
+   CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
+   TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
+   aactggtctttacctTTAAGTTG
+
+Use the **FASTA Width Formatter** tool to re-format the FASTA into a single-lined sequences::
+
+   >sequence1
+   CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
+
+-----
+
+**Multiplicity counts (a.k.a reads-count)**
+
+If the sequence identifier (the text after the '>') contains a dash and a number, it is treated as a multiplicity count value (i.e. how many times that individual sequence repeated in the original FASTA file, before collapsing).
+
+Example 1 - The following FASTA file *does not* have multiplicity counts::
+
+    >seq1
+    GGATCC
+    >seq2
+    GGTCATGGGTTTAAA
+    >seq3
+    GGGATATATCCCCACACACACACAC
+
+Each sequence is counts as one, to produce the following chart:
+
+.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_3.png
+
+Example 2 - The following FASTA file have multiplicity counts::
+
+    >seq1-2
+    GGATCC
+    >seq2-10
+    GGTCATGGGTTTAAA
+    >seq3-3
+    GGGATATATCCCCACACACACACAC
+
+The first sequence counts as 2, the second as 10, the third as 3, to produce the following chart:
+
+.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_4.png
+
+Use the **FASTA Collapser** tool to create FASTA files with multiplicity counts.
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    </help>
+</tool>

tool_collections/fastx_toolkit/fasta_clipping_histogram/fastx_macros.xml

@@ -0,0 +1 @@
+../fastx_macros.xml

tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/input.fasta

@@ -0,0 +1,6 @@
+>sequence1
+AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG
+>sequence2
+GTGTGTGTGGGAAGTTGACACAGTA
+>sequence3
+CCTTGAGATTAACGCTAATCAAGTAAAC

tool_collections/fastx_toolkit/fasta_formatter/.shed.yml

@@ -0,0 +1,10 @@
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+categories:
+- Fasta Manipulation
+description: FASTA Width formatter
+long_description: |
+  This tool re-formats a FASTA file, changing the width of the nucleotides lines.
+name: fasta_formatter
+owner: devteam
+remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fasta_formatter
+type: unrestricted

tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml

@@ -0,0 +1,90 @@
+<tool id="cshl_fasta_formatter" version="@WRAPPER_VERSION@" name="FASTA Width">
+    <description>formatter</description>
+    <expand macro="requirements" />
+    <macros>
+        <import>fastx_macros.xml</import>
+    </macros>
+    <!--
+        Note:
+            fasta_formatter also has a tabular output mode (-t),
+            but Galaxy already contains such a tool, so no need
+            to offer the user a duplicated tool.
+
+            So this XML tool only changes the width (line-wrapping) of a
+            FASTA file.
+    -->
+    <command>
+    <![CDATA[
+    zcat -f < '$input' | fasta_formatter -w $width -o '$output'
+    ]]>
+    </command>
+    <inputs>
+        <param format="fasta" name="input" type="data" label="Library to re-format" />
+
+        <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." />
+    </inputs>
+    <outputs>
+        <data format="fasta" name="output" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <!-- Re-format a FASTA file into a single line -->
+            <param name="input" value="fasta_formatter1.fasta" />
+            <param name="width" value="0" />
+            <output name="output" file="fasta_formatter1.out" />
+        </test>
+        <test>
+            <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes -->
+            <param name="input" value="fasta_formatter1.fasta" />
+            <param name="width" value="60" />
+            <output name="output" file="fasta_formatter2.out" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+This tool re-formats a FASTA file, changing the width of the nucleotides lines.
+
+**TIP:** Outputting a single line (with **width = 0**) can be useful for scripting (with **grep**, **awk**, and **perl**). Every odd line is a sequence identifier, and every even line is a nucleotides line.
+
+--------
+
+**Example**
+
+Input FASTA file (each nucleotides line is 50 characters long)::
+
+    >Scaffold3648
+    AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC
+    CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG
+    TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA
+    ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
+    >Scaffold9299
+    CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
+    TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
+    aactggtctttacctTTAAGTTG
+
+
+Output FASTA file (with width=80)::
+
+    >Scaffold3648
+    AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTT
+    ATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCA
+    ATTTTAATGAACATGTAGTAAAAACT
+    >Scaffold9299
+    CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTAC
+    GTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
+
+Output FASTA file (with width=0 => single line)::
+
+    >Scaffold3648
+    AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
+    >Scaffold9299
+    CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    </help>
+</tool>

tool_collections/fastx_toolkit/fasta_formatter/fastx_macros.xml

@@ -0,0 +1 @@
+../fastx_macros.xml

tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.fasta

@@ -0,0 +1,100 @@
+>Scaffold3648
+AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC
+CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG
+TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA
+GTATAACTTTTCAAATACTTTTGTTTTACAACTTTTCTCTCTGGACTTAT
+ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATACATGTACATC
+TACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACAT
+TATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGC
+AAAAAAAGAAAAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTT
+GATCTGAATGCTTTAACATTCTATATGTACAATAAATTTTTGTATCTATA
+GCCTATTATTATATATGTTGCTATGTCAGGCACATTGACAACATTCTCAG
+AAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGCCTTGTGAACT
+AAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCT
+TCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAA
+AGTGGGGTGCATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAG
+AGTCCCTAATCTGCAGTGTAAACAAACTTTGCCAGGACATCACCAGCCCA
+ACCTTGATAAGTACTGCTTGGAACTCCTCCATGATGTTCTAGTCTTATTC
+GCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGCTACCAGTATA
+CATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTT
+ATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATA
+ATTGTCTAGTTCGATATAGTACATGGACACAATTAAATATGATATTGTCT
+>Scaffold9299
+CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
+TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
+GAAAAGCATCCTTGTTTGTTTCACTATGCTTTTTAATGGTTGACGTTAAa
+ggtaaagaccagtattggaaacgccccaatttcaaaaaatgaaatggaag
+ctctcattaccaatcatgtgaaagaatatgttttgactaatacatgatga
+taaaaaaattgccgggaaaccgcctactaattcatatatttagtaaattt
+gtttctctcatggtctgtgagagatatagggtagtcccatatacatcttt
+ctgtgtatagtgcttgtaactttacgaagaatgggccaaatttcttatca
+ttttgatgattccagaaccttgcagatgcgagatggtagatgatcaacct
+tttctgatcgattccataacgtttctttcacaatgcaatcgcatgaccat
+aactggtctttacctTTAAGTTGTAGGTCTTAATTGATAACACTATATAG
+TTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATT
+GTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGC
+CAAGGCAAAGAAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAA
+AAAAATAGTTGATCACATTGAAAAAGATGACTTAATGTTGAATATCAAGA
+AGTGTAAGATCATGTTATTTGGGACAAGAAAACGAATCAAAAATCAAAGT
+GTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAAATGAATTTAA
+ATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATAT
+CGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATT
+AAATATTATTTGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGAT
+ATTGTCACATATTGACTACGGTATTGTTTTGTGGGGATGTTCAGCAAAGT
+GTCATTTGGAAAAGTTACAAAAGTTACAAAATCGTTATGCCCGTTTAATA
+CTAAACGTAGATATTTTGACACCTCGTATTATATTATTATCCTCTCTAAG
+ATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA
+>Scaffold9309
+GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTA
+TGAAAACATAAACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAAT
+TTCAATCATATAACATGTCATTCACTTCTCTTCTCTGACTGTCAAGTATT
+AGGTATTCCTTTTTATTTCCTCTTAAAATGATCATAGTTTCCTATTTCTT
+TTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATTGTAATAAAAC
+GAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCT
+ATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATC
+GAATATAATGATTCGACCTAGTATGATATATTTTATGCACGTGATGCAAT
+ACGAGTTGTTTTGATCTTTGGTCGACTTCAAGAAAACCAGCTTTAGAAAG
+TTCGCTGTAGCCAACATGAGTTCTTGCCTTGGACTAGAACAGTTGATAAA
+TCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCTGCAATCTAAA
+TGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAttttttt
+gataatttttttttctttgataatttttttctttttctttaataaatttt
+ttggataatttttttttggataaatagttcttttttgataattctaataa
+tttttttatttattttttttttttctataattttttttaaaaaatttatt
+aatttttaattaaaaaaaaaataaGAGTTAACAGATTAAGGGAAACTGAC
+AATTCAAAAAAAAAAAAAA
+>Scaffold9310
+GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATAC
+GCTTTCTTAAGACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACT
+TTTTATTTTTAATTAAAACATTATCGAAATGAAGATACAGAGAAAAACGA
+TGAGATGTAAGAAGTGCGCGTATTTAtgtgtgtgggtgcgtgtgtgtgtg
+tgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgtACTAATTTTG
+ATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATA
+ACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgt
+gcgtgcgtgtgagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATT
+GCAATCATCTGTATCTTCATGAAAATGATAACCAGAAGAACAAAAAAAAA
+AAACATTGAGAGAACATGTTTTTTTGATGGAAGACAAGAAGTTCTCGTAA
+CGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGAGAGCAGTGAG
+AGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAA
+AAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAA
+GTGAACGGGCAGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtact
+atgtcccatttgcaggtcaaaaaaaatgaaaaagttaaattccaactgca
+tttgaaagataatactaatttacaacttccctaaaaaaggtggggcttga
+aaatgtcttcaagtgcggaaaataacgactattagttgtcaaatcgactt
+tagggCTATAGAGCCCAAAAGTAATAGTCTTGA
+>Scaffold11911
+TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAA
+GTTTAAACTTTGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGT
+ACATGTTTCTCTTAATATCTGTCGTATAGatttttaatatttttatttat
+atCTACGTCAATCTGGCTGttctttttcttgtcttctttttttttctctc
+tcttttttttcctcgtattttGTATTGATCCTTACCCTAGTTTTTGAACT
+TGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTAT
+TTGtctctgttcccctctccccccctctctctctctctctctctctctct
+ctctctctctttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTG
+TTTTCAGATTGATCTTTCTTGCTTTCCCCACCCTCCCCCTTTATGCAGTT
+AATTTTCAGTCTATTTGTGTTTTCTGTGGTTGATTCTAATCATATTCTAA
+CTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATTATATTTGTTA
+CTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAA
+GATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTT
+CTCTCTCTTTAACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTG
+GACTTCACTGGATATTTTGCTTTGATGCCAATCCAACAATTTTGCATATA
+TTA

tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.out

@@ -0,0 +1,10 @@
+>Scaffold3648
+AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAGTATAACTTTTCAAATACTTTTGTTTTACAACTTTTCTCTCTGGACTTATATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATACATGTACATCTACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACATTATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGCAAAAAAAGAAAAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTTGATCTGAATGCTTTAACATTCTATATGTACAATAAATTTTTGTATCTATAGCCTATTATTATATATGTTGCTATGTCAGGCACATTGACAACATTCTCAGAAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGCCTTGTGAACTAAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCTTCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAAAGTGGGGTGCATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAGAGTCCCTAATCTGCAGTGTAAACAAACTTTGCCAGGACATCACCAGCCCAACCTTGATAAGTACTGCTTGGAACTCCTCCATGATGTTCTAGTCTTATTCGCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGCTACCAGTATACATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTTATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATAATTGTCTAGTTCGATATAGTACATGGACACAATTAAATATGATATTGTCT
+>Scaffold9299
+CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGGAAAAGCATCCTTGTTTGTTTCACTATGCTTTTTAATGGTTGACGTTAAaggtaaagaccagtattggaaacgccccaatttcaaaaaatgaaatggaagctctcattaccaatcatgtgaaagaatatgttttgactaatacatgatgataaaaaaattgccgggaaaccgcctactaattcatatatttagtaaatttgtttctctcatggtctgtgagagatatagggtagtcccatatacatctttctgtgtatagtgcttgtaactttacgaagaatgggccaaatttcttatcattttgatgattccagaaccttgcagatgcgagatggtagatgatcaaccttttctgatcgattccataacgtttctttcacaatgcaatcgcatgaccataactggtctttacctTTAAGTTGTAGGTCTTAATTGATAACACTATATAGTTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATTGTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGCCAAGGCAAAGAAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAAAAAAATAGTTGATCACATTGAAAAAGATGACTTAATGTTGAATATCAAGAAGTGTAAGATCATGTTATTTGGGACAAGAAAACGAATCAAAAATCAAAGTGTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAAATGAATTTAAATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATATCGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATTAAATATTATTTGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGATATTGTCACATATTGACTACGGTATTGTTTTGTGGGGATGTTCAGCAAAGTGTCATTTGGAAAAGTTACAAAAGTTACAAAATCGTTATGCCCGTTTAATACTAAACGTAGATATTTTGACACCTCGTATTATATTATTATCCTCTCTAAGATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA
+>Scaffold9309
+GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTATGAAAACATAAACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAATTTCAATCATATAACATGTCATTCACTTCTCTTCTCTGACTGTCAAGTATTAGGTATTCCTTTTTATTTCCTCTTAAAATGATCATAGTTTCCTATTTCTTTTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATTGTAATAAAACGAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCTATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATCGAATATAATGATTCGACCTAGTATGATATATTTTATGCACGTGATGCAATACGAGTTGTTTTGATCTTTGGTCGACTTCAAGAAAACCAGCTTTAGAAAGTTCGCTGTAGCCAACATGAGTTCTTGCCTTGGACTAGAACAGTTGATAAATCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCTGCAATCTAAATGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAtttttttgataatttttttttctttgataatttttttctttttctttaataaattttttggataatttttttttggataaatagttcttttttgataattctaataatttttttatttattttttttttttctataattttttttaaaaaatttattaatttttaattaaaaaaaaaataaGAGTTAACAGATTAAGGGAAACTGACAATTCAAAAAAAAAAAAAA
+>Scaffold9310
+GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATACGCTTTCTTAAGACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACTTTTTATTTTTAATTAAAACATTATCGAAATGAAGATACAGAGAAAAACGATGAGATGTAAGAAGTGCGCGTATTTAtgtgtgtgggtgcgtgtgtgtgtgtgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgtACTAATTTTGATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATAACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgtgcgtgcgtgtgagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATTGCAATCATCTGTATCTTCATGAAAATGATAACCAGAAGAACAAAAAAAAAAAACATTGAGAGAACATGTTTTTTTGATGGAAGACAAGAAGTTCTCGTAACGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGAGAGCAGTGAGAGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAAAAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAAGTGAACGGGCAGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtactatgtcccatttgcaggtcaaaaaaaatgaaaaagttaaattccaactgcatttgaaagataatactaatttacaacttccctaaaaaaggtggggcttgaaaatgtcttcaagtgcggaaaataacgactattagttgtcaaatcgactttagggCTATAGAGCCCAAAAGTAATAGTCTTGA
+>Scaffold11911
+TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAAGTTTAAACTTTGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGTACATGTTTCTCTTAATATCTGTCGTATAGatttttaatatttttatttatatCTACGTCAATCTGGCTGttctttttcttgtcttctttttttttctctctcttttttttcctcgtattttGTATTGATCCTTACCCTAGTTTTTGAACTTGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTATTTGtctctgttcccctctccccccctctctctctctctctctctctctctctctctctctttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTGTTTTCAGATTGATCTTTCTTGCTTTCCCCACCCTCCCCCTTTATGCAGTTAATTTTCAGTCTATTTGTGTTTTCTGTGGTTGATTCTAATCATATTCTAACTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATTATATTTGTTACTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAAGATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTTCTCTCTCTTTAACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTGGACTTCACTGGATATTTTGCTTTGATGCCAATCCAACAATTTTGCATATATTA