changeset 0:74093fb62bdf draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
author iuc
date Wed, 17 Aug 2016 14:46:55 -0400
parents
children bca52822843e
files macros.xml progressivemauve.xml static/images/hemolysin.jpg static/images/xmfa2gff3.png test-data/1.gff3 test-data/1.mums test-data/1.nhx test-data/1.xmfa test-data/karma.fa test-data/merged.fa test-data/phagey.fa tool_dependencies.xml xmfa2gff3.py xmfa2gff3.xml
diffstat 14 files changed, 19832 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Aug 17 14:46:55 2016 -0400
@@ -0,0 +1,28 @@
+<?xml version="1.0"?>
+<macros>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="2.4.0">progressivemauve</requirement>
+      <requirement type="package" version="2.7">python</requirement>
+      <requirement type="package" version="1.65">biopython</requirement>
+      <requirement type="package" version="0.6.2">bcbiogff</requirement>
+      <yield/>
+    </requirements>
+  </xml>
+  <token name="@WRAPPER_VERSION@">2.4.0</token>
+  <xml name="stdio">
+    <stdio>
+      <!-- Anything other than zero is an error -->
+      <exit_code range="1:"/>
+      <exit_code range=":-1"/>
+      <!-- In case the return code has not been set propery check stderr too -->
+      <regex match="Error:"/>
+      <regex match="Exception:"/>
+    </stdio>
+  </xml>
+  <xml name="citation">
+      <citations>
+          <citation type="doi">10.1371/journal.pone.0011147</citation>
+      </citations>
+  </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/progressivemauve.xml	Wed Aug 17 14:46:55 2016 -0400
@@ -0,0 +1,439 @@
+<?xml version="1.0"?>
+<tool id="progressivemauve" name="progressiveMauve" version="@WRAPPER_VERSION@.0">
+  <description>constructs multiple genome alignments</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <version_command>progressiveMauve --version</version_command>
+  <command><![CDATA[
+## Symlink files in with correct extensions
+#for $file in $sequences:
+    ln -s $file `basename $file`;
+#end for
+
+progressiveMauve
+## Input Options
+
+#if $apply_backbone:
+    --apply-backbone=$apply_backbone
+#end if
+--island-gap-size=$island_gap_size
+$mums
+
+#if $seed_weight:
+    --seed-weight=$seed_weight
+#end if
+
+#if $max_gapped_aligner_length:
+    --max-gapped-aligner-length=$max_gapped_aligner_length
+#end if
+
+#if $match_input:
+    --match-input=$match_input
+#end if
+
+$collinear
+--scoring-scheme=$scoring_scheme
+$no_weight_scaling
+
+--max-breakpoint-distance-scale=$max_breakpoint_distance_scale
+--conservation-distance-scale=$conservation_distance_scale
+$skip_refinement
+$skip_gapped_alignment
+
+#if $bp_dist_estimate_min_score:
+    --bp-dist-estimate-min-score=$bp_dist_estimate_min_score
+#end if
+
+#if $gap_open:
+    --gap-open=$gap_open
+#end if
+
+#if $gap_extend:
+    --gap-extend=$gap_extend
+#end if
+
+#if $weight:
+    --weight=$weight
+#end if
+
+#if $min_scaled_penalty:
+    --min-scaled-penalty=$min_scaled_penalty
+#end if
+
+--hmm-p-go-homologous=$hmm_p_go_homologous
+--hmm-p-go-unrelated=$hmm_p_go_unrelated
+--hmm-identity=$hmm_identity
+
+$seed_family
+$solid_seeds
+$coding_seeds
+$no_recursion
+$disable_backbone
+
+## Outputs
+--output=$output
+#if $output_guide_tree:
+    --output-guide-tree=$output_guide_tree_file
+#end if
+
+#if $output_backbone:
+    --backbone-output=$output_backbone_file
+#end if
+
+## Sequences
+#for file in $sequences:
+    `basename "${file}"`
+#end for
+
+]]></command>
+  <inputs>
+      <param type="data" format="fasta" name="sequences" multiple="True"
+          label="Select sequences to align" help="in fasta format" />
+      <param type="data" format="xmfa" label="Apply Backbone" name="apply_backbone" optional="True"
+          help="Read an existing sequence alignment in XMFA format and apply backbone statistics to it (--apply-backbone)" />
+
+      <param type="integer" label="Island gap size" value="20" name="island_gap_size"
+          help="Alignment gaps above this size in nucleotides are considered to be islands (--island-gap-size)"/>
+
+      <param type="boolean" truevalue="--disable-backbone" falsevalue="" name="disable_backbone"
+          label="Disable backbone" help="Disable backbone detection (--disable-backbone)" />
+
+      <param type="boolean" truevalue="True" falsevalue="" name="output_guide_tree"
+          label="Output Guide Tree" help="Write out the guide tree used for alignment to a file (--output-guide-tree)" />
+
+      <param type="boolean" truevalue="True" falsevalue="" name="output_backbone"
+          label="Output Backbone" help="Write out the backbone to a file (--backbone-output)" />
+
+      <param type="boolean" truevalue="--mums" falsevalue="" label="MUMs" name="mums"
+          help="Find MUMs only, do not attempt to determine locally collinear blocks (LCBs) (--mums)" />
+
+      <param type="integer" label="Seed weight" name="seed_weight" value="0" optional="True"
+          help="Use the specified seed weight for calculating initial anchors (--seed-weight)" />
+
+      <param type="data" format="tabular" label="Match Input" name="match_input" optional="True"
+          help="Use specified match file instead of searching for matches (--match-input)" />
+
+    <!--<param type="file" label="input-id-matrix" help="An identity matrix describing similarity among all pairs of input sequences/alignments (- -input-id-matrix)" />-->
+    <param type="integer" label="Max gapped aligner length" value="0" optional="True" name="max_gapped_aligner_length"
+        help="Maximum number of base pairs to attempt aligning with the gapped aligner (--max-gapped-aligner-length)" />
+
+    <param type="data" format="nhx" label="input-guide-tree" optional="True" name="input_guide_tree"
+        help="A phylogenetic guide tree in Newick format that describes the order in which sequences will be aligned (--input-guide-tree)" />
+
+    <param type="boolean" truevalue="--collinear" falsevalue="" label="Collinear inputs" name="collinear"
+        help="Assume that input sequences are collinear--they have no rearrangements (--collinear)" />
+
+    <param type="select" label="Scoring scheme" name="scoring_scheme" help="Selects the anchoring score function. (--scoring-scheme)" >
+        <option value="sp" selected="True">Extant sum-of-pairs (sp)</option>
+        <option value="ancestral_sp">Sum-of-pairs + Ancestral (ancestral_sp)</option>
+        <option value="ancestral">Ancestral (ancestral)</option>
+    </param>
+
+    <param type="boolean" truevalue="--no-weight-scaling" falsevalue="" label="No weight scaling" name="no_weight_scaling"
+        help="Don't scale LCB weights by conservation distance and breakpoint distance (--no-weight-scaling)" />
+
+    <param type="float" min="0" max="1" label="max-breakpoint-distance-scale" value="0.5" name="max_breakpoint_distance_scale"
+        help="Set the maximum weight scaling by breakpoint distance. (--max-breakpoint-distance-scale)" />
+
+    <param type="float" min="0" max="1"  label="conservation-distance-scale" value="0.5" name="conservation_distance_scale"
+        help="Scale conservation distances by this amount. (--conservation-distance-scale)" />
+
+    <param type="boolean" truevalue="--skip-refinement" falsevalue="" label="Skip refinement" name="skip_refinement"
+        help="Do not perform iterative refinement (--skip-refinement)" />
+    <param type="boolean" truevalue="--skip-gapped-alignment" falsevalue="" label="Skip gapped alignment" name="skip_gapped_alignment"
+        help="Do not perform gapped alignment (--skip-gapped-alignment)" />
+    <param type="integer" label="BP dist estimate min score" name="bp_dist_estimate_min_score" value="0" optional="True"
+        help="Minimum LCB score for estimating pairwise breakpoint distance (--bp-dist-estimate-min-score)" />
+
+    <param type="integer" label="Gap open" name="gap_open" value="0" optional="True"
+        help="Gap open penalty (--gap-open)" />
+
+    <param type="select" label="Repeat penalty" name="repeat_penalty"
+        help="Sets whether the repeat scores go negative or go to zero for highly repetitive sequences. (--repeat-penalty)">
+        <option value="negative" selected="True">Negative</option>
+        <option value="zero">Zero</option>
+    </param>
+
+    <param type="integer" label="Gap extend" name="gap_extend" value="0" optional="True"
+        help="Gap extend penalty (--gap-extend)" />
+
+    <!--<param type="data" label="Substitution matrix" -->
+        <!--help="Nucleotide substitution matrix in NCBI format (- -substitution-matrix)" />-->
+
+    <param type="integer" label="Weight" name="weight" value="0" optional="True"
+        help="Minimum pairwise LCB score (--weight)" />
+    <param type="integer" label="Min scaled penalty" name="min_scaled_penalty" value="0" optional="True"
+        help="Minimum breakpoint penalty after scaling the penalty by expected divergence (--min-scaled-penalty)" />
+
+    <param type="float" label="HMM p go homologous" name="hmm_p_go_homologous" min="0" max="1" value="0.00001"
+        help="Probability of transitioning from the unrelated to the homologous state (--hmm-p-go-homologous)" />
+    <param type="float" label="HMM p go unrelated" name="hmm_p_go_unrelated" min="0" max="1" value="0.000000001"
+        help="Probability of transitioning from the homologous to the unrelated state (--hmm-p-go-unrelated)" />
+    <param type="float" label="HMM identity" name="hmm_identity" min="0" max="1" value="0.7"
+        help="Expected level of sequence identity among pairs of sequences(--hmm-identity)" />
+
+    <param type="boolean" truevalue="--seed-family" falsevalue="" label="Seed family" name="seed_family"
+        help="Use a family of spaced seeds to improve sensitivity (--seed-family)" />
+    <param type="boolean" truevalue="--solid-seeds" falsevalue="" label="Solid seeds" name="solid_seeds"
+        help="Use solid seeds. Do not permit substitutions in anchor matches. (--solid-seeds)" />
+    <param type="boolean" truevalue="--coding-seeds" falsevalue="" label="Coding seeds" name="coding_seeds"
+        help="Use coding pattern seeds. Useful to generate matches coding regions with 3rd codon position degeneracy. (--coding-seeds)" />
+    <param type="boolean" truevalue="--no-recursion" falsevalue="" label="No recursion" name="no_recursion"
+        help="Disable recursive anchor search (--no-recursion)" />
+  </inputs>
+  <outputs>
+    <data format="xmfa" name="output" label="${tool.name} alignment of ${on_string}">
+       <change_format>
+           <when input="mums" value="--mums" format="tabular" />
+       </change_format>
+    </data>
+    <data format="nhx" name="output_guide_tree_file" label="${tool.name} alignment of ${on_string}: Guide tree">
+        <when>output_guide_tree</when>
+    </data>
+    <data format="tabular" name="output_backbone_file" label="${tool.name} alignment of ${on_string}: Backbone">
+        <when>output_backbone</when>
+    </data>
+  </outputs>
+  <tests>
+      <test>
+          <param name="sequences" value="phagey.fa,karma.fa" />
+          <output name="output" file="1.xmfa" lines_diff="20"/>
+      </test>
+      <test>
+          <param name="sequences" value="merged.fa" />
+          <output name="output" file="1.xmfa" lines_diff="20"/>
+      </test>
+      <test>
+          <param name="sequences" value="merged.fa" />
+          <param name="output_guide_tree" value="True" />
+          <output name="output" file="1.xmfa" lines_diff="20"/>
+          <output name="output_guide_tree_file" file="1.nhx" />
+      </test>
+      <test>
+          <param name="sequences" value="merged.fa" />
+          <param name="mums" value="True" />
+          <output name="output" file="1.mums" compare="sim_size" delta="1000"/>
+      </test>
+      <test>
+          <param name="sequences" value="merged.fa" />
+          <param name="match_input" value="1.mums" />
+          <output name="output" file="1.xmfa" lines_diff="24"/>
+      </test>
+  </tests>
+  <help><![CDATA[
+What it does
+============
+
+Mauve is a system for efficiently constructing multiple genome alignments in
+the presence of large-scale evolutionary events such as rearrangement and
+inversion. Multiple genome alignment provides a basis for research into
+comparative genomics and the study of evolutionary dynamics. Aligning whole
+genomes is a fundamentally different problem than aligning short sequences.
+
+Mauve has been developed with the idea that a multiple genome aligner should
+require only modest computational resources. It employs algorithmic techniques
+that scale well in the amount of sequence being aligned. For example, a pair of
+Y. pestis genomes can be aligned in under a minute, while a group of 9
+divergent Enterobacterial genomes can be aligned in a few hours.
+
+progressiveMauve XMFA alignment visualized with the Mauve tool:
+
+.. image:: $PATH_TO_IMAGES/hemolysin.jpg
+
+Example Usage
+=============
+
++-----------------------------------+-------------+
+| Usage                             | Notes       |
++===================================+=============+
+| Align genomes                     |Simply       |
+|                                   |select as    |
+|                                   |many fasta   |
+|                                   |files with   |
+|                                   |one or more  |
+|                                   |sequences as |
+|                                   |necessary    |
++-----------------------------------+-------------+
+| Align genomes but also save       |Use the      |
+| the guide tree and produce a      |**Output     |
+| backbone file                     |Guide Tree** |
+|                                   |and **Output |
+|                                   |Backbone**   |
+|                                   |options      |
++-----------------------------------+-------------+
+| Align genomes, but do not         |Use the      |
+| detect forced alignment of        |**Disable    |
+| unrelated sequences               |backbone**   |
+|                                   |option       |
++-----------------------------------+-------------+
+| Detect forced alignment of        |Use the      |
+| unrelated sequence in the         |**Apply      |
+| alignment produced                |Backbone**   |
+| in previous example, use          |option and   |
+| custom Homology HMM transition    |specify the  |
+| parameters.                       |XMFA file    |
+|                                   |produced     |
+|                                   |in the       |
+|                                   |previous     |
+|                                   |example      |
++-----------------------------------+-------------+
+| Compute ungapped                  |Use the      |
+| local-multiple alignments among   |**MUMs**     |
+| the input sequences               |option       |
++-----------------------------------+-------------+
+| Compute an alignment of the       |Set the      |
+| same genomes, using previously    |**Match      |
+| computed local-multiple           |Input** to   |
+| alignments                        |the tabular  |
+|                                   |MUMs file    |
+|                                   |produced in  |
+|                                   |the previous |
+|                                   |example      |
++-----------------------------------+-------------+
+| Set a minimum scaled              |Use the      |
+| breakpoint penalty to cope with   |**Min Scaled |
+| the case where most genomes       |Penalty** and|
+| are aligned correctly, but manual |set to a     |
+| inspection reveals that           |value like   |
+| a divergent genome has too        |5000         |
+| many predicted rearrangements.    |             |
++-----------------------------------+-------------+
+| Globally align a set of           |Use the      |
+| collinear virus                   |**Colinear**,|
+| genomes, using seed families      |**Seed       |
+| to improve anchoring sensitivity  |Family**     |
+| in regions below 70% sequence     |options      |
+| identity.                         |             |
++-----------------------------------+-------------+
+
+
+The progressiveMauve algorithm: addressing limitations of the original algorithm
+================================================================================
+
+Comparative genomics has revealed that closely-related bacteria often have
+highly divergent gene content. While the original Mauve algorithm could align
+regions conserved among all organisms, the portion of the genome conserved
+among all taxa (the core genome) shrinks as more taxa are added to the
+analysis. As such, the original Mauve algorithm did not scale well to large
+numbers of taxa because it could not align regions conserved among subsets of
+the genomes under study. progressiveMauve employs a different algorithmic
+approach to scoring alignments that allows alignment of segments conserved
+among subsets of taxa. The progressiveMauve algorithm has been described in
+Aaron Darling's Ph.D. Thesis, and is also the subject of a manuscript published
+in PLoS ONE. A brief overview is given here.
+
+Finding initial local multiple alignments
+-----------------------------------------
+
+progressiveMauve elaborates on the original algorithm for finding local
+multiple alignments. Instead of using a single seed pattern for match
+filtration, progressiveMauve uses a combination of three seed patterns for
+improved sensitivity. The palindromic seed patterns have been described in
+Darling et al. 2006 "Procrastination leads to efficient filtration for local
+multiple alignment"
+
+Seed matches which represent a unique subsequence shared by two or more input
+genomes are subjected to ungapped extension until the seed pattern no longer
+matches. The result is an ungapped local multiple alignment with at most one
+component from each of the input genome sequences.
+
+Computing a pairwise genome content distance matrix and guide tree
+------------------------------------------------------------------
+
+progressiveMauve builds up genome alignments progressively according to a guide
+tree. The guide tree is computed based on an estimate of the shared gene
+content among each pair of input genomes. For a pair of input genomes, g.x and
+g.y, shared gene content is estimated by counting the number of nucleotides in
+gx and gy aligned to each other in the initial set of local multiple
+alignments. The count is normalized to a similarity value between 0 and 1 by
+dividing by the average size of gx and gy. The similarity value is subtracted
+from 1 to arrive at a distance estimate. Neighbor joining is then applied to
+the matrix of distance estimates to yield a guide tree topology. Note that the
+guide tree is not intended to be a phylogeny indicative of the genealogy of
+input genomes. It is merely a computational crutch for progressive genome
+alignment. Also note that alignments are later refined independently of a
+single guide tree toplogy to avoid biasing later phylogenetic inference.
+
+Computing a pairwise breakpoint distance matrix
+-----------------------------------------------
+
+Prior to alignment, progressiveMauve attempts to compute a conservative
+estimate of the number of rearrangement breakpoints among any pair of genomes.
+For each pair of genomes, pairwise alignments are created from the
+local-multiple alignments and the pairwise alignments are subjected to greedy
+breakpoint elimination. The breakpoint penalty used for greedy breakpoint
+elimination is set high for closely related genomes and scaled downward
+according to the estimate of genomic content distance. Because the breakpoint
+penalty is high, the resulting set of locally collinear blocks represent
+robustly supported segmental homology, and a conservative estimate of the
+breakpoint distance can be made on this basis. The conservative estimate of
+breakpoint distance is used later during progressive alignment to scale
+breakpoint penalties.
+
+Progressive genome alignment
+----------------------------
+
+A genome alignment is progressively built up according to the guide tree. At
+each step of the progressive genome alignment, alignment anchors are selected
+from the initial set of local multiple alignments. Anchors are selected so that
+they maximize a Sum-of-pairs scoring scheme which applies a penalty for
+predicting breakpoints among any pair of genomes. Because rates of genomic
+rearrangement are highly variable, especially in some bacterial pathogens, some
+genomes may be expected to exhibit greater rearrangement than others. As such,
+a single choice of scoring penalty is unlikely to yield accurate alignments for
+all genomes. To cope with this phenomenon, progressiveMauve scales the
+breakpoint penalty according to the expected level of sequence divergence and
+the number of well-supported genomic rearrangements among the pair of input
+genomes. These scaling values are taken from the distance matrices computed
+earlier in the algorithm.
+
+Anchored alignment
+------------------
+
+Once anchors have been computed at a node in the guide tree, a global alignment
+is computed on the basis of the anchors. Given a set of anchors among two
+genomes, a genome and an alignment, or a pair of alignments, a modified MUSCLE
+global alignment algorithm is applied to compute an anchored profile-profile
+alignment. MUSCLE is then used to perform tree-independent iterative refinement
+on the global genome alignment.
+
+Rejecting alignment of unrelated sequence
+-----------------------------------------
+
+Although we compute a global alignment among sequences, genomes often contain
+lineage-specific sequence and are thus not globally related. The global
+alignment will often contain forced alignment of unrelated sequence. A simple
+hidden Markov model structure is used to detect forced alignment of unrelated
+sequence, which are then removed from the alignment.
+
+Strengths of the progressiveMauve algorithm
+-------------------------------------------
+
+-  It can be applied to a much larger number of genomes than the original Mauve
+   algorithm
+-  It can align more divergent genomes than the original algorithm. Genomes
+   with as little as 50% nucleotide identity can be alignable
+-  Manual adjustment of the alignment scoring parameters is usually not
+   necessary
+-  It aligns the pan-genome, e.g. regions conserved among subsets of the input
+   genomes
+-  It is more accurate than the previous Mauve algorithm
+
+Notes on Reproducibility
+------------------------
+
+The command line programme progressiveMauve seems to behave differently when::
+
+    --max-breakpoint-distance-scale=0.5 --conservation-distance-scale=0.5
+
+are passed to the tool, compared to when those options are not passed. This
+means that if you wish to precisely replicate the results you see in Galaxy at
+the command line, you'll need to pass these flags with their "default" values.
+
+@ATTRIBUTION@
+]]></help>
+  <expand macro="citation" />
+</tool>
Binary file static/images/hemolysin.jpg has changed
Binary file static/images/xmfa2gff3.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.gff3	Wed Aug 17 14:46:55 2016 -0400
@@ -0,0 +1,25 @@
+##gff-version 3
+##sequence-region karma 1 1
+karma	progressiveMauve	match	83032	140930	.	-	.	ID=phagey;target=phagey
+karma	progressiveMauve	match_part	83032	83041	50.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83042	83051	60.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83060	83069	60.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83070	83079	40.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83080	83089	40.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83108	83117	40.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83125	83134	70.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83144	83153	60.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83154	83163	40.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83164	83173	70.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83196	83205	40.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	83206	83215	30.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140791	140800	40.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140801	140810	20.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140811	140820	60.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140821	140830	50.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140831	140840	50.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140841	140850	60.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140851	140860	20.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140861	140870	50.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140871	140880	40.0	+	.	Parent=phagey
+karma	progressiveMauve	match_part	140906	140915	80.0	+	.	Parent=phagey
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.mums	Wed Aug 17 14:46:55 2016 -0400
@@ -0,0 +1,409 @@
+FormatVersion	3
+SequenceCount	2
+Sequence0File	test-data/merged.fa
+Sequence0Length	159457
+Sequence1File	test-data/merged.fa
+Sequence1Length	221828
+MatchCount	402
+23	9997	10291	0x9c7f540	0	0
+23	118799	199132	0x9c7f588	0	0
+23	26654	-52948	0x9c7f5c8	0	0
+23	126561	47160	0x9c7f610	0	0
+23	110233	-209064	0x9c7f650	0	0
+23	134387	175263	0x9c7f690	0	0
+23	93373	-185643	0x9c7f700	0	0
+23	6917	167993	0x9c7f740	0	0
+23	47238	48379	0x9c7f780	0	0
+23	8742	-150092	0x9c7f7c0	0	0
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+23	123404	39006	0x9cbacd8	0	0
+23	122296	157926	0x9cbad18	0	0
+23	142815	-21431	0x9cbad58	0	0
+23	125617	-78534	0x9cbad98	0	0
+23	25902	-17866	0x9cbadd8	0	0
+23	152639	-90975	0x9cbae18	0	0
+23	21992	178389	0x9cbae58	0	0
+23	15947	92384	0x9cbae98	0	0
+23	101873	98312	0x9cbaed8	0	0
+23	3899	-119389	0x9cbaf18	0	0
+23	148397	185112	0x9cbaf58	0	0
+23	130431	-112825	0x9cbaf98	0	0
+23	143278	180137	0x9cbafd8	0	0
+23	66424	103325	0x9cbb018	0	0
+23	131360	-111662	0x9cbb058	0	0
+23	156677	153981	0x9cbb098	0	0
+23	143297	20818	0x9cbb0d8	0	0
+23	90241	-111775	0x9cbb118	0	0
+23	20107	18248	0x9cbb158	0	0
+23	83728	82051	0x9cbb198	0	0
+23	65721	104098	0x9cbb1d8	0	0
+23	70625	189133	0x9cbb218	0	0
+23	86074	-115341	0x9cbb258	0	0
+23	37121	-204123	0x9cbb298	0	0
+23	46528	165402	0x9cbb2d8	0	0
+23	106103	104995	0x9cbb318	0	0
+23	86707	-74058	0x9cbb358	0	0
+23	106556	65846	0x9cbb398	0	0
+23	131791	-108777	0x9cbb3d8	0	0
+23	66998	66464	0x9cbb418	0	0
+23	32437	-167760	0x9cbb458	0	0
+23	75950	75816	0x9cbb498	0	0
+23	69770	109722	0x9cbb4d8	0	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.nhx	Wed Aug 17 14:46:55 2016 -0400
@@ -0,0 +1,1 @@
+(seq2:0.476132,seq1:0.476132);
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.xmfa	Wed Aug 17 14:46:55 2016 -0400
@@ -0,0 +1,5967 @@
+#FormatVersion Mauve1
+#Sequence1File	test-data/phagey.fa
+#Sequence1Format	FastA
+#Sequence2File	test-data/karma.fa
+#Sequence2Format	FastA
+#BackboneFile	test-data/1.xmfa.bbcols
+> 1:83031-140929 - test-data/phagey.fa
+ttttctcctcttttttcttagt--gaccgagggctttttaccctcggatggtttactttcactgagtct--agatgttaa
+atatttatgta---gtttaccagtgaatga-ccccattatacatcaccgccttagtgtaagacaagcctt--atttactt
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+cactctgttctctaattcctcatatgttttaactatctgccctacagtcattgtacgttgcctcatattaactctcctcc
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+tgccccggccaagaagaccggctacgacgacccgccgaagaaccggcaagaaaatcggcaattttctgacacgcaatcgg
+cgcaagctgcggaaaaggctggcaaaaaagcctcttccaagaccggcaaaaagaccggcgccgacgcgccgccgtgggac
+gaggacctcgggacctacgccgacgccgtgatcaagcgtccctatgacgagggcgacccggcgctggcccaggagatcat
+cgtctccgtcggggccaacagcaagtcgatgaactggcaacccaaggccatgccgctgggcgcgttcgtcgcccagttct
+gccagcaccgcgagggcgccaaggacggcgtctccttcgtgctgggcgacatggtgccgggccagcgcaagaagacggcg
+atcaaggccctctacgccgtgggcctggacgtcgacgtgggcatgtcctcggcggcgatcgacgcggccctggccaagtt
+cgggcgcatggccgtccgctatacgacccattcccacctgaaggcggtcaccgacgtcaagaaggacgtcctgatcaagt
+ggtgcgagcaggaagccgacggcgccgactacgaggaggacgaggtcctccagcgctacttcctggccaaggaactgatg
+accccggacgtcgccaagacggtcgagttcaacgggaccgagcacaaggacggcggcatcatggtcaccgtcaagcacgc
+gccgatcgccaagcaccggatcatcgtccccctggcggcggccttcgacatctccaaggtcgcgccgacccagaaggagg
+cgatggacaagtgggccaaggtcccgaccgcgctcgcccgcgaactgggcgtgccgctggacaagtcgtgcctggacccc
+tcgcgcctgttctatctgccgcgtcacgccaagggcaagccgttcgagatcagcctgttcggcggcgacctgttcgactg
+gaagagcctgaccctcgacgatccgttcgaggccgagatcgccaagctgaccaaggggaccagcaagtccaagaccgagg
+ccggtcgcaacctgggccgctggtcgatgaaggccgcccacggcttccaggtcgtccaggtcatggaggagcactgcccc
+gacaagctgcgccaccaagtctcggccggctacgagatcgagtgcccgttcgacgagcttcactccaacgccggcgacac
+cgaggatcgcgcctgtctggcggtcaacgccggcgatggtccgagcgagtggttcaccgtccgctgccagcacgagtcct
+gccgcgagttcaccaatctcgacatgctcggcaagatggtcgaggacggctggttcgaccgcgacgtgctcgacgacgag
+acctacaacatcgtcgaggccgagaacgcccccaacccgcaggcggccaagaagatcgagaaggaggacaaggccaagga
+agcctatatgcaggcgatctttgacctccccgaatccgacttcaccgacgacgacgttgaaaaggtcctgcgcgtctgct
+gcgaggccaatctggggaccctggccgagaacaaggccaaggaagccctcaaggcgcgcctgggcgtcaccggcacggtg
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+ccgcagcatcttcgcctatgcgggcgagttcaacttcgacgaggccttcgcctgctgcttccgcgcgctggtcaacacca
+accgcgagaaggaccagccgatcttctcctgcttgcaggacaagcccgtgcgcatggcgcccgagccggatggtcgtctg
+aagttcaccgagatcggcacggccgcctccatgggggccgaactgaacgagcttgtcaccttcgtgcgcaagaacgagca
+gggccagggcgcgcgcggaagggttcccgacgacgtggcgcgccacgtgttcgagaaggcctacacccgcctgccgcgca
+cgcccgagatcatgt-acaccccgatctatacggccgagggtgacttgat-ccgcaagcccggctggtatcagaacctcg
+acatcctgatggccgacatcggcttcga
+=
+> 1:1-83030 + test-data/phagey.fa
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+cgaaagagatatattccatatggataatgagacagaatttcttttagaagaaacatttaataaggaggacaattaaatgg
+aagtaaatggggatgttatcctaggcggggttgcggcttttgtactttactcgtggttactatacaacagaggatacaga
+aaaggttcggatgacgcggccactattatactagatcgcatggaggaagtctttgagttatcagaagaagacaaggagta
+tagaagaaaaatgcagggaggtaaataatatgtatgaaaatgtgttagacgttatcaattgtagaacaaaagaggtagcg
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+gaccagacacacttcgatgttgaagactggggagtgtacgaggatgaaaagacgggtaacgtaacgatctataacgcgga
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+caagaatggcaaagttgcccgaccgatggaacgtgtctctacgtgacgatgagagccttaaatcggtaagtaagtctaga
+gctatcggactaagtgaactaacggaggagggaatgaaagatgtataacgaagaacgagacattgccattaacgatgcat
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+acgagtgtgaacgtgggttaatcaacagtgtggtctataacgcagaattagttaacaaatttcttaaacgttataaaact
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+aaaaagaaatgagaaagtcacagcgtactagaaagtttaatgaaagtatttgcttaatggctagtgaagacatggagcta
+atgagaaaaattgttgttggacagtgggccattaatgccgctctttctagtccatttgctagcagatacggattataaaa
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+gttgttggcgaaactggctaattattcctattattatattattttccctataatcgggtagttagtttgttacaggttcc
+ttttctggttctgttgcaggttgttcattagttgtcgtaacattaggtgctggcttctcgtgatcgtcacgaggttgagc
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+tctttattggccttttgtagttcagcctccaatttggctacatggttatctgcctcttgtgctttgtcatacgcttgttg
+cagcagtgattcatagttcttaattttagcgttagcatttgctaagtccttttgggctttatcatatgcggctattttct
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+=
+> 1:140930-159457 + test-data/phagey.fa
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+acaggaatggtggcataacctacctcacaacattgctcaaggctcagttgatttaatggcatggctgtatgagttatgtt
+cagacttaatattgaagacgcctttatggttattcgataatgaatggttcgaaaatactacctatatgtttagcttatta
+tctattggattagtatctgtccttactatcctggaagctatgaaacgtatgatttccggtcttcgcaagaaaggtactag
+aaatagtcaaccaatggaattacagaccattatgaaacggtggtttgtggtagctggattcacaactgttttaccgattg
+tgtttcaaaaaggttttcaattgttgaataaagtatccgatatgatctcgggtatgggtgctaagacgatgaccaatatt
+agtctcccttctactatcagtgcattcgaagtaactacccttgtcttattcgatatcgtgctcatctcaacaatcgtacc
+aatgctgtggaaaaacggtcgccggttctttgatttgttagtgctcgggctagtaagtcctctcgcctgcacctgctgga
+tatttgacagctatagaaattattttaacacatggttgggaaatgttaaacacttgtctcttgttcaagtatactattct
+atttttcttctagtgatcggttgggtattgttcggcacaccgacccctgcgagcttcactggatttatcttaaagctact
+ggtcaccattggcgggttctcaaagttaagctctcctccaaaatttgtaagtaaacacttagataatggatcagggtttg
+actcagtatatacaccagctaaagatacagtctctaaaacagttcgtaacttccgagatacagtggacattatccgtaaa
+cctactactgttgtaaagaaggtacacgagcgattacaaactcctgagcgggtaggtaagactcgtatgcaacgtttcca
+cccgccagtaccaaaaccaggtaagtctacgcctaaaccaaaaagaaaataaggagtgaataacatgagtacagtatcag
+tattaattatcattaatcttacctcgcttgttttcagcagcgggatgcagatcgcaaacagtttaatggttatgaagcat
+attaagggggagagaagatgaaaaagctttctgcaaattaccataacctagctaacttgtttatgcctgtagaagatata
+gaaggtcactttgtcgatatccttgaacagattaacgattcggtattcggagtagagacccatttaaccggtgagggggc
+taatacttttgtcattgcaccctctcatatcgaaaccggggcagaacttgttctaagacatcgagaagcgcctacagagg
+gttttaatttcttcgaggggtatttatcggaagcgttctttctccctctcagacaggataagaacggcctcttccttact
+gatttactggacttggctttacatcctgatgaagaggtacatgcgcaatggttattacgcaggcggtatggttggcaaga
+tcgcgcaattgatatgtacgatagctatattcaagggaacgaaaaaccttcttggtctagatggagtcgtaaactgcagg
+ataaagctgttcgagtgttaaacaaaatacagccagaggattacaagccttacgaaccgttagcagaagagaagataaag
+agtgagtgcttccaatttcagctcagaatagcagttaagtccgagagggtaaacgatatcatccagtatattcaatacgc
+tctagggtcttatacggctttaaacgagttgaaactggttaagtcgtcagataaacaatttattactaactatactgact
+gtgtattagcagcttacacaaaagatcaactacttagcttaaacgaagtattctccttattaggtggtacagtagagaaa
+acggaaaaagtattagaagaggtagtggagcgtaaggcgtacccatttgatctgttacctatgtataagcgagagcaagg
+tactctagatgaaggaatagttagtaagctagcggaaggtatgaagcgggtaaaattgattgatacggctaggttataca
+atgaacggattgactgtggggtgcggttaggggttgtccaggtaagtatacctaaagatgtaaccttttctaagattgaa
+aagtccattaatgacttacgagctgcaacaggtattagcgggttaggtgttgagaatggggatattgccgacacggttaa
+gtttacggttcctttagctgcttcaccggttattagtctccgtgaactggttgaaaccgaggagtttatcagtatggtag
+aagaaaaagaattaatgttcgtggctggtgtagatacactaggggagccgatctatctatctttgactgaatgtgtacat
+ttattggtggcagggacaacaggtagcggtaagtcggtcttcgtaaatgtgattattgtaagcatgatgttaatgtatcc
+acctgaaaagctacagtttattatgattgacccggctatggtagagctaagtaagtatgaggatagtccacacgtactag
+acgtagtgacagatgctaaagaagcttgccaagtattagcagggctgacaatggagatggataagcgatatgctcttatg
+aaggaaaaaggtacgaagttgttatctttgtataatgaagtagcggaggagccgttaccctatctagtgtgtattgtaga
+tgaatatgcagatttacgtgctgttgacaaaggggtagaagattatattgctcggttagggcagaaggcaaggaaaacag
+gtatacatttagtggtggctacccagtatcctagtgcagatattgtaagcgggcggattaaggccaacttacctactgcg
+attagttttagactgaacaagaataaggattacacaactatattcggagtcgggttaggtactactgtgttagatggtaa
+gggggatggggttattcggttagcgagtggaggggactttattcgtttccagagtcctatggtcagtgtggatgagaaga
+gagagcagcaggtttgtcgagatatcttcaccttctatcaagggagccgaattgtggactacaagattgctgtcgcagat
+aaaccgttagagcccgtacaagacgttttagaagaagagaaggtaaatacaccagaagagtgtaaagagacccctaagca
+agctctagaggcgttagaggctatgtttagcagtacagaggatgatcccctgtataaattaaagaaaattgttgcaaata
+caggagaaacccgatcaaatccactaagaaaagagctaggtattggtcgtgataagatgaagccccttatgacacagtta
+gttgaagaagggtggctagagaaagataatgaccctacaaaaggctataagctggttgctaccgaagatatgctcgcaga
+atggaaagattgagcctgtataggcttattttttttgtccgttaaaccgttatattactaataagcgtatcaggaaatat
+ttaacaccgtatttaagacccttgatatgactgtgttcttagctgttttatctaaataactgacacattataatcttaac
+gtccctctttatatattatttaattatttataaagatatataagagaataataaatataataatacgaggagcttaaacc
+gtataatatgtcaggaatatttttaaaagtacctctaagccagcaataccaacggattaaaatacgtcaggtacctctaa
+ctctgaaaatttatcaaaatagttgttgacttttagtagtatgtcccgtatacttttgttatgagttacagggatgaata
+catgtcctagtgtaggcgatacagtgtagaacgtttgggaggacttctaccgggtatcatccatactaacagataatcta
+ctgatcttgggagggttcaatggattaactgaactcaggaggtgtaagaatgaactacagagagttatcagatgaggaat
+tacttagccagatgtctaccgtacataatgtactagctaacgaagaatgggtttatcgttatgggatgaatttaccttac
+cgattagacaagtttaatagaattttaaactgtttatcttggcaagtagtagctgactcgacttgcgataaattaatccg
+gagacaggctaacgaggtacgaatggtaaaacagttaagcacctattaaaaaggagctgcttaacaatggcaattagaaa
+atatgaattcaaattaaaaattaaacaactattagcggagagaggaatttctcaagctgacctagctgaaatgactggat
+taaggcgtgccactatttcagagatgtctcgtaattcacggtctgttctgaataaggtacatgtagctaaagtcatggat
+gcgttagacgtaactgagttgaatgatatagtggagcttgaggtcactgaggagttctaaaggagaaaataaaatggata
+gtgtacaaaagtttatttcagaaaatagtcaccaattcggttatatcatgcaagaggctagccgtcaatgggtcgcaaaa
+gaccctatcggagccctaactgtaggtacatgtaagtcttttatagacagctatggagactatcatacgattttagacaa
+gttacaagctattgaagaggctaaagtccctaaaaaagatgtgtataaggcagttatctcgggacatattttcgaagaac
+ctgaatttgggaacagtattgaaatatttactttcgtgaataacgacgttaaaaatacagatatattcacagatgttgaa
+tatgagctgatcgaagagttaaaacataatcttaaatataaggaaagccacttctttacggctattgtgtatgctcgttg
+gtcatcttggcaaagtcaagaaggaactgagtatgatgtagagtacgacatccatgagatcaaacaaattagtgacctag
+ataaaggagcggacttttaatggatacacatttaacgttaactaaactaaaggattctttggatcataattatgtaaaga
+aggtagctagtcatcttatcctggtagttaaacgtggggataagcatgagcagatcgtgttagacaaaccttttgcagag
+aagattgaaaatatttgtaacgaccatgaagaggattgtacattaaagggtgctccccatattaaaatcatcgcagctaa
+gtatacgactacacggttattaacagaaaatctacaaagaattcacgagcatctacaaaagtaaaaacctaaccaaatag
+tgtataatataactataggataaacaattatttacgattatgtttatcctatttgtttttgtccaagatatactaaatta
+tcttaaccagtaaatcctaactaaacagtggatttttcgtgtatatttatacattttcgaaaattaggtgagagatttat
+tatattagagacagaagcttagacagcaaggattatactctgtttaacatatacactattttgagagggttgaaataact
+tatgacaaataaaaaagacctaaaaaagaaaaatattagttccagttcagtacttgtgcagctgtacaataatccaaagt
+tacgatctaaagtagagaatatgcttgacgaggggcaaacatacgactatattcaagagtatcttagttcgaagaacttt
+agtatgtcgaaagcatctcttactaactataagaagaagcgtgaggaatctatcgaaacaggccagccactcattcaatt
+actggacaagcgtgcgaaagataacgtctcttatattgcagataaggaagttaaaccatttagtacagtagaatcaacta
+gtagctcctcagctacagtgcatgatcttagtaagcgagatagtgtttatagtgacctagaactactggacgaaacaatc
+cggaaatcgatgaaaggcttaaagcagtttgatgtggttgaccttcctctaggtatgaaggccattgagctaaaggccaa
+attaactggaaattctcttaacgggctcagcctcgcaggactgagggagcttcacctaagacaggcagcaaaagaggccg
+cgttaattgaagtaatcatgaaatacgtcccagaggatttgcatatagacgtattccaagacctcgaaaattcagaaaaa
+gagttcttcgaaaacctagatttaacagaggaggaaaagagaatatctgcggcaattcgtagaagcggtctaggacttta
+aggaggggaaggtctatgaagtttgagagcaagaaaacagtcccgttggttgacaagatagctatagcagatgagcgagg
+atacacacttaatgaaacggaaaacttcacagtgaactcacaggtacatctgattgaaaattccacaggctttgagtacc
+ttgttcactggggtaactttacgaaaggtataaaacctagtaagacaacattagagagtaaaataaagtatgcagcttca
+cgaggttacactctccataggaaagataattttactacatcatccagtgtagaagttacaaacagattagatggtttaga
+gtacagggtgcaatgggatcactttgtgaaaggggcttcgccagctatcttaaccttagaaggtaagcgacagctggcgc
+gtaatcgaggctatacactcctagaggacacagacttctcaaataggagtaaggttattatccgatgtaacgaaagcgga
+gtagaatatgaagcgaactgggggagctttactaatgggaattctccccgccataccacactaaaccagaaaataaagga
+gacagcggagcgaggttataagctgctagaaacagacaacttctatacaaacagtcaggcaagaataaagtcattagcta
+ctgggagggaatacacggtctggtatgctagttttctacacaaggggtaccaagaaaacaactctaaaggtgaatcaatc
+ctctattactttttcttgtctaaccttgctagtgagtatagctttgagtaccagtatagagtagattactcggagagtaa
+gaaggggttcttcgacttctgtataaaagataaaaatggccgtactttagcttttgtagagtataatggcaaacaacact
+atgaaccttgctttggtcaaaaagctttcgagctgactttactatctgataaactaaagcaggaatacgcagcagttaaa
+aaggtacctttgattgttatcccttatacgtatagtacacaaaaagagatcgtagacttcgcttcacctatccttaaaga
+gtacttactgactgagtacgtggagttcacccctaaatggtcaagtttatcctcaagcaccttagaagacaaacaaagaa
+ttgctgaggaggcaggttacacgttacacccagatactatgtacaattttgttaataaagatagggtgacggtcataaac
+cagcagacaggggaagagtgggaagtccaatggggtcacttcctaaagtgtgtagtaccaaacaagactaaccataaacg
+agtaataaaacttagtctagaagaaaagaagcagatagctagctctatagggtatactttattagaagaagaggacttcc
+cggttattaataaggttcgtttaatgaacgccaacggtgaagagattacaagaggttggcgaactatccacaagcagtat
+aaaaagaggaaagatagaggtgacttatcgtggcgttgaatgaaacagaactactacaatatacgttagttccttttgct
+acatacgaaacgttagaatctaagttacaggccctgttagcaggtgagattttattccttaaaaagtttgaacgtaatga
+aggtgtagacgtacttgttagacttgtacaaaagaaatttacggttacacaagtctcttatgatgttacagtccgggatg
+aagatatcccacgttactggacaacgtataacatcggtctaaatgatatctcactgtttacctgctttaagtttgcagag
+gatgcatttacgaaagaaaataagtatatgattaatgaccgtgtactctatgttagtgttgacgggctaaaggatgcagc
+tattattgaagaggtgtaccaacacaatactgatcctactaagtttgcttatcgtttatctagagacggagcggtttacg
+gtgaagacgagttgtacgataactcttatatgtaagtgaagatacaagacctaaaaagtcttgtattttttttttggaaa
+agctgttgacttctggtaaatagggtgttattatgtaattacagaaggcgatacaagctctcgtttgggaggacgagaga
+ttggtagcttctgaaataagcgtaactaatgggaggagaagtaaatgaaactctacgtgttgagcgaaagagaaattatc
+gattgtgagggtgaatactcttttgtagtaggtgtttttggtagctttaaaaaagcacaagattatgcagcatcccaagg
+ctacaccgagtatatagaagaaggttactacggtgatgactccgaatttatacctacaaaggacaaaagatacacaagag
+attatgatggtaaatcgtatgtgctagatgttgcaaaactagatagacctttgtacgatgatggtataatcgacatgaaa
+gagtatgaacctaaagaagtaacatcctatttaaacggtgagaagattgcaaaagctaaaactataccaggtgacactac
+tagattcaatccagttggtacggtaacaagcggacttgattcgagtaaggaaaacaaatcagcaaaaccaaaaagcaata
+taaacttccctaaagatcaggaggaaaagtaaatggagctgtttgtaactgaaaaggtgttcaatagaaaattaaacggt
+aaagccattcgaattaaaggttatgatacagatggggagaaatgggacggtgtatatctagttaaggaaactagatttga
+ccagattgtagttactagtcgaacaggtaatgaacactttatttatatggaggagttcgaaacaggagaactactaactc
+taatagtattggagggaaattagatgactctaaagtatgattaccgtgtacaagcaaaagccaaccacgtttgtcatatg
+atttgggaagaaacaggaaaagtagatcacccgtcacctaagcttagatcagatgtagaagacaccatgatggctgcagt
+taattattataaggtagcgttagataatgaattacagaagaagaacgagtataagctaaacgaacttagaagaggtatac
+ataggttaaagcctaactcgcatgaagatattatagatttattcgctaaggttatggccggtgaaagtgtacaaacaatg
+aaaccatataaaagggagagagaattagtatgacaaaattgctaaaagaagaatggccgaagaatattgatgaacttatc
+gcttacttccaggagttaaaagagtactctagagattacaacacatctgcggaagcagtagcctatggtacagtagcggc
+atttaactatttagcagcagacgaacacggattgactggattccaggctagttggtctgctatgaaagctttgtctatta
+ttagaaatattgatggtgcgtttactattgttagtacggatgccttaaagtttaataccatcgaagatgaattagctcgt
+gtaaagaagtttttacacgacagcattaaaaagcaggaggagaataacaatgagtaacatatttgttgtccagtattcta
+atgggttagaacatgagcagttagagaccgatgtagtagcggtattcgattctgaaaaggaaatacgagcgtacgcagaa
+cgagaagggtttgttccttataatggtattcttatttgtgggttctatagagagtacaagagcggacaccgggacttact
+atttgtctcaccagtgaaaataaacgagcctattgtggcttgtttggaggagttagagtgagcaagtcagatataactcg
+taggctagaaaaggcaatttacacggcgacgattaaacaaggtgtgtttggttgttttgaggttacaatcggttggttcg
+ggaaagagcgtgtggatttcataacctacgacacaaaaaatatctggcgatgctatgagattaagtcctctgttgcggac
+tttagaagtgaggcttacaagactttctgcggtaattacaactactatgtgatgactaaggaactttatgagaaggttaa
+actagaaattcccacccatattggggtttatattgagggccgttgtgtcaagcgacctaaaaggcaagaagtaactgtgg
+aagaggaaatactaaagaattcactaatacgttcactagctagagaagccgacaaacttgctaagagcaatgatcctgat
+ttgttaaatcggctacgaagaagcttagctagagaacaagaagacaaaagaaggtacagtcgggagtacacagacttgaa
+aaataaattatataggaagtacggccgaaactgggaggaggtactagagttagaatgaattatacagatgctaagatagc
+aattcaagtattacatgcagcgggatataggaaatggataaaaggggagccgtactaccacaaacgatgggaacggggct
+cgaatgactataaccagcttatatcattcaatgaaattaaatattcgctaatggatatcccttggattatacagaagtac
+gaagaaaaagccgaaggagagttagaaaaattaaatgaaggagagtgctgttaaatgggcggttacattgcgttacaacc
+caacgggctatactgcaggtattccacagtggtagaggctttaacacatataaacatgacgagggaagattatgtatcta
+attttacaggtacagtaagaagccgagaggaagcggaagacatcttgggtaactatctacatagcttcagtaccgtagag
+aaaatggtcactcgactgaatgtagaggaagcggaatggaagagaattaagacgcatgttacactacctaaaaacagtat
+atttgtctacccgaaagttttataaaaagtattgacaggtattggttggtgtagtaaactctaactatatcaaccaatac
+aaggaaaggatgagtacaagttggcaaagaagaactttagttgggattcagaggagttactaggtatttaccctgtatca
+gataaaaagcagtttgaatataagttatgtatgctaaaggacaaggagtacgtatcagtagctgagcagcgcatgacaga
+cgaaggctggaagtactacggaaacaaaacgttagagatgagtgtatacagacagttagtagcatttatggacaaccgtt
+aatattttagtaggtggttgacttatagcatatgttagccacctatcatactaaaggaggagttagtaatgcggagaaaa
+attaagtgtgaattgtgtgatggtagcggtgcctcgccttggtctgctctaggagggccttgtatacaatgcgagggtgc
+ggggtttctatttgaacctgaagggaagcctaagtttaaggtagacttcggtgagttagacgggcttactaaaatggaag
+atactacagacttaagtgatccacatattaaaatagatatgaacggcatcagctttaaagacaaggatggtaactggact
+gatccgacaaaaccattcgctaactttgaaaatatcacaattaaccactcaaatggtaaaactataaaaggcgggaaagg
+ggttctgaaaccgatgggattattcgatgattttatggaggctattgaagcagaagagacaggaagaccaatcgtaaagc
+atttgctagtttggagtgttgatgagctactagaccttcacaacgattacaagcagctgtacgatctatttaaggacgag
+gagtacttgctatatatgaaggacgtactaaaagttataaaagcaaaaacaaattagtagtcattctttatagactgcac
+gcatagtataaactataacaagaagggaggaattacagtgaatgcggaagataaacgaattctaatgaaaatagtaggaa
+gtatagccgggatgtttataatgggatacctattcggtttcctaggggttattattagtttagtagctatttactttgtg
+tttaagaatgataatggtaagcaggtaggagaagacccggagagtgaagctaaggccgcctttatctggttctgtgtgat
+gctagtgttagggatcgtgcttgcgtatctattcggtatcattggagtaattatcggtttagggttaatcgcaggagcca
+tctataatataatgttcgggtaaataaagaattttttttaaatagttgttgactttaaagaaacatggtgctagaattag
+cttatcaaccaaaggaggtaacaaagtgagaataacacatgaacagaagatggaaattctcgaagagtggaaccttatag
+gagagaacgattgtagaacggctctacctcacttaacagagctacttactaaaatacttgatagtgtttctgatcctgaa
+aagataaactgtgggtgttatgtgtggagtgaaaaactacaagagcatgttgaacctaatccactctgtaagaaatgcgg
+cgggatgggttggtattacaagagagaaaggaagtaatcgatatgcaacagacagcagctaagaacacacaaccagaagg
+tttacatctttacatggcaattggatcgtatgagtcggccattaacaaatatgcgcacccatataatcctggttactgga
+ataagtataagaaactaaaacagaaaatccttcagtggcagcagcaaa
+=
+> 2:1-81634 + test-data/karma.fa
+gggctctgggcgaagttttgtgggactactatgacttgcattatttcaagcgcaagcggtccgagtggaagtaccaaaga
+tttgctttggtttatcaacaacttgccgacgcggcctcggacacctccatcgcgtccaagtttcagacctacgatcacct
+gccccacctggagccgaaggtgctcaaggcccggcttgacgcgggtcacgccgacgagcgcgggcggccgattccggacc
+gcaaggagcacttccggcgggtggtggtcagcgtcgactcggccaacaagcccggcgcccgcaacgactacagcgtcgcc
+caggtctggggggagacccacgcccgcaagcactacctgatctaccaggagcgcaagaaggtcgacatcaccggcctgac
+cgagatgatcgagcgggtggccaagcgctacgaggtcgacgccatcctggtcgaagacaagggcaacggcaccgcctaca
+tccaggcgcggggccagaccgacagccagcggcggctcgccccggccccgatcgaggcgatccaggtcccgagcacctat
+tccaaggagttccgcttcaacgagatcgtcccgatgatcgaggccggcgaggtcttcctgccgggcaaggccccgtggct
+cgacctgctgatccgcgaaatcggtcagttccccgaaggcgcccatgacgaccaagtcgacgccatgacgcagtacctcc
+gctgggccaagtccaagcgcacgcggttcggcgcgcgcaaggtcggctcgatgggctgacgaggcccgttaaccacgttt
+gttaacctccgccggggccttaaccctaacacggcgagggttaacaggtccagggacccttcgaaattaacctttcgggg
+accctgggaaatcgtaaggcagggaccctggccattttccggctggggaccctggcaaattcaccgccggggaccctccg
+aaattcatcctcggggaccctggcaaatcaaggagccggcgatggccgaatttctcgccctgatccccaacctcgcgccg
+ttcctggtctggggaatcctcctctggatcgccgccgaggtggtctggagcgtctgcctctgggtctatggcctgcggac
+cctgttcaagttgcaccgcgatgatctggccgaggcgatcagcttcgagcgggccttgagccccttcgactaggcgcggc
+ctgccgacctaagtcacggactgtaggtttcgtgacaaggtgagatattccacaacgatttcaaaggcttactgcgatgt
+cgatccgcacgttcttccacgatctggccgtccgtttcgtcgttttggggtggatttttgcccgaaaaccgctgaaatgg
+gctccaaaagggcataattttcagcctaaaccgccggtccaggtcggcgccctggcggccggctcgctcctcgccctcag
+tctggcgctcggcgggctctggttccgcttcacgtttccggacaaaagtcaagtggtctcgcgccggccgcaggctatgt
+catagaccgtgggcttcgtgaccagatcacgcttccgttaccgctccagcccttgtgaggcctcggatgttcgcctttct
+ccgccggctcagcctcgccgccgtccatggcgtgctctgggcgatcctcctggcgatgctcgccctgggcgggccgcgcc
+gcccgctctaaagcgtcatatctgacgcctaaggccccctaaggcctcatctgtgagacattcaacgccctcgtgttcct
+ctgaacgcgggggcgttttgacgtcggcgcatttttgacttgacgcgcgagcgttttgacgcgggcgcatttttgattcg
+acgggcgagcgttttgacgtccgagcatttttcaacttgacgtcgttccatttaccgggagcgccttagggttaacgccg
+gccgccgagccctggggcgatttaccaccgccacgttaacctaacgcctgttaacctatcggttgttaaggttaacgccc
+cgttagggttaacgccccttaaccctgcccgcgttaaggttaacgcgccccggcccaggccctacccgttaaccttaacc
+gcccgacccccgcgcccaggccatacccggtagggcctgacggccctaccgggtatgaccccgcgccccggcggaggcca
+gggaccgccccggcgctttttcgcgccccgtttaccttttgttaacgtctggcctctagggtcgcccttgtccccgccgc
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+=
+> 2:118886-221828 + test-data/karma.fa
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+gcaaatccccgcccgcgacggccgcccgcaatacgtcgccgggaccgcccatagtgaatgggacggggtgaccctctacc
+ccgccgaccgctacgacaacccgcttgacgcggcgagcgccgccgaccgtcacgccgaacgcgacgccgaagaggaacgc
+gaatatcaaaccgcgtggcaagcgggccagcgctacgccgaactcggcgccgaagccaaggaggcccgcaaggaagcgct
+ggcgatcctcgccgaacgccgcaaggtcaaggggctggaaacccccgccttgtgcggcgcgatccgggcgcaagtcgcgg
+ccctgctaggccggatcgaagaggcgcgcgcctcgcgcgccaagctcaaggaaggcgaggactcgcgcctcatgttctac
+ccctccgccgccatggtcgcggccttcaatgacggcgcggcgtcgtgaaggtcgcccgcgatagcttcgccgtgttctgg
+accctcccgcaaggcggggtccaatttcacgccgacataaaacgggcgctctatccgaccgcccgcgacgccgcccgcgc
+ttttagcgccatgttcccccgtgaccgggtccggagcgtccgcgacgcctccggccgcttcctggccttcaaggagtccg
+ccccgtgcgcctgacaagctacaacgtcaacggaaccggctttaagggcggctccgccccgcccgtccccgcccaaggcc
+tgaccggtcacgccgacggcttgaacctttgggttccctcgcgcgagcatatcgccgccatgctcccgcaacgctggcgc
+cacgccttcgcccgcgcgtcgttttggtatgacgcgcacgacaataaaaagccgtgtcgcgccgacctctacgactcgcg
+cggccggtacctgactcaggtctgggcgcacccggttttcagctaggccaggacgccccggaaaatcttccggggcgttt
+accttttgttaacctctggcctctagggtgactttcgccgccgggcaatcccgcccgccggaccctctttcaaggattgc
+tcccgtcatgacctctcattccatggtcgcgcaccgttgggcgcaggacgacgagaacggccgcaccgcgcgcggcttca
+acatgtatttcgagcgctacgggcgcggcgccgaccgcgtcaacgtgattttttcctacgggactcacttcccggccgcc
+gccttcgtgaccgacgcgcacggccgccgcgtggttctggtgacgactcgcggctacagcgtttcgaccgcgaaacacct
+ttcccacatccgccgcgccatcccgtccgggaccccctgcttttccgtgccgcacgtgtcgcggatgcacaagccgggcg
+ggtcgggcgacttccacggggacaacctgcgcgcctatgtcgagagcgccgccggcctcgccgaaaaggccaagcgcgcc
+cgcgtcaacggcccttggctgcttagccaagcccgcgaaaccctcgccgaagcgcaacgctacgccgacgccttcaagct
+gaaaaccaaggttccggccttggaagacgtcgccggccaatgggcgaagatgacggccgccaaggcgcgggccgaagcca
+aggccaagcgtgacgccgaaaaggccgccaaggcgcgccgcgaagccgaacggctcgccgacgccgaagccttcgccgct
+tggatgcgcggcgagcgccagagcgccccgtttagctaccgggtgcgcgatgacgggaccgtctatcttcgccgcttccg
+gggcgtggtccgcgacctgcgcagccaagagcgcgacggctcgcgcgtcgatgaactgcaaacctcgcaaggcgcggccg
+tgccgtgggaacacgcggtcaaggccttccggttcatcaagctttgccgcgaacgcggcgagagcttccaccgcaacggc
+cgggtgattcgcgtcggacacttccaagttgacgcgatcagcccgaacggggacatgacggccggttgtcaccggttcgc
+gtgggatgaaatcgaacgcctcgccagggccgaaggggttttcgacctccccgccgacgctggcgccgtcgaaacccggc
+aagccgaaccggcctaagcctccccgcccctctcgcgccccggctccccgccggggcgttttcgtgtacgcggtaacctt
+ttgttaacttctggcctctagggtgactttcgccgccgggcaatcccgcccgccggccaaggatcgcagactatgaatct
+tttcgttgtcgccattgaccccgccctcatcccttcggccgccggcttcgtggtcgcctccccctacgggtgcggcaagt
+ggcgcgcgtgcgtcgggagcgaggcggacatgatcgcgcttcgcgacaagatgcgccgcgcgcacccggccccggaaggc
+tacagcgtccagcccctggcgtcgttcctggcctatctggagacggtcggggatagcccttatgaccggttccgcgccca
+tgacgccgccgcccgcatccttgacaccctgacgacgcatctcgccgcctagccccgccaagcccccggccgcgcgccgg
+gggcgctttccctcgaaaggatcgccgaccatgacaacccgtcttatcgccgttcgcggcccgaccgccgccgaactcgc
+cgacccgtccagccgcgcgggcggcgccgaagtcgttttcgagcgccgcgaccgcgaaggccgcacgcgccttgtgttcg
+cctcgacctgctacggctcatatcagcaatggggcgaaacccgcgacgtgctcgccgacaacgtcgaggcggtcacgctc
+tgggccgaaggcatggcggccgttgccgccctcatcgacgagagcgacgacgacgacgagagcgacgacgccccggccga
+agatgacgacggggaggcgtgagccatgcgcacaaccaaggctcaacgcttcgccgccatcgcctttgacgccctggcca
+aggccctaagcgagccgcgccaagccgtcgcccgcgtgaccaaatgggagggcgcgggccatagcttcgccaacctgcaa
+cgcgattatgagcggtacggccccggcgcccgctcatggttcggccgggctgaaatgcgcttctttgggacgcgcctaga
+ggccgcgccgctggatttcccggcgctgggctgcaccctctttctgacctccgaaaccccgcccggcgccggccgggtct
+ggacccttcgcgcctatgtctgggcttcggccgatatcaccacgctaacccatggcgacgaaaccgacgcggcgaccgcg
+caagcggcctttgacctgctttggcgggtcctttccggacagtaaccttttgttaacttctgcccgctagggtcttcttg
+cggccgggcaatcccgcccggccgcatcttggagacagcgcccatgacccgcgctcaagccctcgccgacatgaacgccc
+ttcccggtatcatcgcctcctttgagcgcgagacgggcgaatatcgcgtgaccctgcgctttggcccgctccccatgggg
+cgcggcgcccaagagtggatgcgcgcgcgccgcgaagccgtcgccagctacagcgacgacaaggccgacgccctggccac
+cgcccgcgacatgtccgcccgctgggaggcgatgagcgccgaagagcgttcgcgcctctatcacaaccccgcctaagacc
+ccgcgcgccgccctggccttcgccggggcggctccctcaacccctcgcaaggatcgcaccccatgaccgcccgtaagccc
+ctgaccaaggaacaaaaggcccgccgccgcgcgacccgccgcgccgcccgcctcaactggtcggatgagcgccgcgctcg
+cgaattcgagcgtcaagcccgcttcttcctgatgatcgccacccgcgcccaaggcgccggccaaggccaggaagccgccc
+gcctcgccacggtcgcacaacgcaaggtgactaactggcgcatggcgcaggcctgcgcccggattaacgccctggccgcg
+catccgttcgcggccgtggtcgcctaaggaggcccgcccgatgacgcaccctcacgccctggcgctgatcgccctcgccg
+aaaaggtgttaccgcttacccggctgcacccgctcgaccaacgcgccgccgccgtcgatctaatcggcgacctctaccgc
+ctcgccgacgatatcgacgcgaccccgcaagcccccgccctgacgcaaccgaaggccgcctaagccatgaacccgaaccg
+ctaccgcctcgcgccccgcgaccgcttcagccgtgagcttgccgaaacgctctatcaggcggccgaagccgtcgcccgcg
+tgattccgctcatgccggagtccgcccccgatgagcgccgcgcgctgggcaaggtccgcgccgaccttctaacccatagc
+gccggcgcccttgttcccaagccgccggccgccgtgctcgaaaccctcgtttgggttgtcgagatggcgcaagatcgcgc
+gactaacgccgatttcaacaccgcccaagaaggactcgacgagcacgagtccctagcctttgtcgccgactggctggaag
+ccgaaggccaggacgtgacgccgattcgcaacgcgcaaccgtccgccgacgccctggccgaactcgccgcccgccgcgac
+gccgaacaagcggcgctagacgccttggaggccgaagccctggccgaagcgccgggcgacgtgatcaccgacgccttgcg
+cccctatctgggcgccgccctggccgaaaaccacgccgacgacgtgctagacgccctcacgcgcgccggcttccaaatca
+cccgcaaggaggcctaaagcccatgaccgactccgccaagatcaccggcgcgctcgcgctactcgccatcgcggccgata
+atctccgccaaggcccggccatgtccaaggccgccgacaacgtcaccaacgtctgtaactacgccctgacgcgcgcgacc
+atgctcaaggccgccgaccaaatcggcgaggcgctggaggcgctgggcgccctgcaagcgggcggctatgtgatcgcccg
+ccgccgcgacgttttcaccgatgcgggcgagaagctgggcgacctgttggcggcgctttatgacgccgtcccgaactacg
+ccgtaagatcgcagcgcctcgccgacgccctgagtcccgcgcgaaattacgtctatcagccccggttccgggtcaagctg
+gacgccgcgcccggcgcgcttttgaccgactgcgacacgggcgcaacggtctatttccagccgggcgacgacgccgacgc
+cttccgggccgaattcgccccgtgggttcacgccgccaacgtgacggccgaaggcgcggccctggcctcgatgatgaacc
+cgaccgccgaagagtatttcagccccgccacgggggtctaacgcccgtggccctgaccttcgccccgcaatcgacgcgct
+acgccgtggaagtccccgaacgcgactttctggccctgacccgcgccgaggaaattctagcccctggcccctatctggag
+ccgtcgcttagcgagcgtttggaggcgcaagccggcgtttgggatgtcgagtataacggccatttcggcgcggccgttta
+cttgacgctcgacgttgacgccgactccccggccgcccgcgacgccctggcctcgatcatcgccgaccaactggccaagg
+ccaaggcgtggaagcgccagcccgcctaagtcatcattcctatcgtctatgacttgtcaccggccgaactcttgcccggt
+gacagtctgggcaagtaaagctcactctggattttatgacttagcgcaaaggattgaaattgctcgaaaaattcctcgaa
+gctcacaaagttgttttctggctgcttttgctggcctgtttgtggcgcttttaacggtttgttaacccctggccctctag
+ggtcgaattcccggcgcggcaatcccgccgcccggccttccttcggagcttctgatcatgttcgcttccgtgacccttcc
+cgcccatgacgcccaaggcctgagcctcgaaaccgtccacatggttttcgcccgcgaactggcgcaacatttcgaccacg
+tgatttccgcccccgtggtcgaaagctggcgcgacgaggacaccggcgccgaccacgcgcaagccgccgtttgcttcacc
+gtctcggcgacccccgccgcgtgggaagccaagggcgggcgcctcgcgcgccggctggaaaacctcgccgcgcgctatgc
+cgccgactgcgacgccccggccctgactgtcacccactgcgacggccaaacggtctatgtcggcgctctggaagccctgg
+cgcgccccgccccggtgcaaggcccgacccgtgaggcggacccggctttcctcccccgccagcgtgaggacaaggccgcc
+cgcttcgatcgcctgaccgcctagcccctggcctccccctagcgcaccgcccctagaaaggcggtgcgcttttctgtgtc
+tgtttacttgttgttaaggaatagcctgctagtgtccccttgttggcggacgcatcccgcgcccgcccctttctggatcg
+ctccccatggctcgcccctctgacctgctcaacgtcaacgccgcccgcgtcctggcttgccttgagcctatcgccgccgc
+cgctaagaccgccccggccgccgaccgcgccgccctttcctacctgctcgacgctggcgagtatgtcgccgcgtggcgcc
+gcaacctcacggaaaccgaccgccgcaaggcctatggcgcggcctgcgccgccgaagccctggcgctcgctaacgcctat
+cagcccgccaccctgcaaggcggcgccgtccgccgcgctctgggcgcctatgccgccgccctaaaggtcctgctagacgg
+ggagccggtcaaggcggtgcgcgccgccgaaggcgcggcgctttcggtccgcgctcgctacgccaacacccgcctttaac
+ctcttgttaacacctcccggctatggtcgggaggtcgcaaggagacacccgacatgacccgccccggccccgcctcgctc
+ctgaccccgcaagcccgcttctcgtcgccgcgcgtcctgatccttccgggcgcggctcccatgccgattcgccagccgcg
+cggcctttgcgccgtcgagtgcgtcgcccttggcgtgacgctgggcgcggcgctctacctcgccgcccgcgtgttcggtc
+tggtctgaccagacccccgccccgcccccggtcggaccggtcgggggtgtgtcccataatgacacacccccgccacctag
+tatcttttttgattcggagggacccaaaggccccctacgttaaccatttttggcggcgccccc
+=
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/karma.fa	Wed Aug 17 14:46:55 2016 -0400
@@ -0,0 +1,3699 @@
+>karma
+gggctctgggcgaagttttgtgggactactatgacttgcattatttcaagcgcaagcggt
+ccgagtggaagtaccaaagatttgctttggtttatcaacaacttgccgacgcggcctcgg
+acacctccatcgcgtccaagtttcagacctacgatcacctgccccacctggagccgaagg
+tgctcaaggcccggcttgacgcgggtcacgccgacgagcgcgggcggccgattccggacc
+gcaaggagcacttccggcgggtggtggtcagcgtcgactcggccaacaagcccggcgccc
+gcaacgactacagcgtcgcccaggtctggggggagacccacgcccgcaagcactacctga
+tctaccaggagcgcaagaaggtcgacatcaccggcctgaccgagatgatcgagcgggtgg
+ccaagcgctacgaggtcgacgccatcctggtcgaagacaagggcaacggcaccgcctaca
+tccaggcgcggggccagaccgacagccagcggcggctcgccccggccccgatcgaggcga
+tccaggtcccgagcacctattccaaggagttccgcttcaacgagatcgtcccgatgatcg
+aggccggcgaggtcttcctgccgggcaaggccccgtggctcgacctgctgatccgcgaaa
+tcggtcagttccccgaaggcgcccatgacgaccaagtcgacgccatgacgcagtacctcc
+gctgggccaagtccaagcgcacgcggttcggcgcgcgcaaggtcggctcgatgggctgac
+gaggcccgttaaccacgtttgttaacctccgccggggccttaaccctaacacggcgaggg
+ttaacaggtccagggacccttcgaaattaacctttcggggaccctgggaaatcgtaaggc
+agggaccctggccattttccggctggggaccctggcaaattcaccgccggggaccctccg
+aaattcatcctcggggaccctggcaaatcaaggagccggcgatggccgaatttctcgccc
+tgatccccaacctcgcgccgttcctggtctggggaatcctcctctggatcgccgccgagg
+tggtctggagcgtctgcctctgggtctatggcctgcggaccctgttcaagttgcaccgcg
+atgatctggccgaggcgatcagcttcgagcgggccttgagccccttcgactaggcgcggc
+ctgccgacctaagtcacggactgtaggtttcgtgacaaggtgagatattccacaacgatt
+tcaaaggcttactgcgatgtcgatccgcacgttcttccacgatctggccgtccgtttcgt
+cgttttggggtggatttttgcccgaaaaccgctgaaatgggctccaaaagggcataattt
+tcagcctaaaccgccggtccaggtcggcgccctggcggccggctcgctcctcgccctcag
+tctggcgctcggcgggctctggttccgcttcacgtttccggacaaaagtcaagtggtctc
+gcgccggccgcaggctatgtcatagaccgtgggcttcgtgaccagatcacgcttccgtta
+ccgctccagcccttgtgaggcctcggatgttcgcctttctccgccggctcagcctcgccg
+ccgtccatggcgtgctctgggcgatcctcctggcgatgctcgccctgggcgggccgcgcc
+gcccgctctaaagcgtcatatctgacgcctaaggccccctaaggcctcatctgtgagaca
+ttcaacgccctcgtgttcctctgaacgcgggggcgttttgacgtcggcgcatttttgact
+tgacgcgcgagcgttttgacgcgggcgcatttttgattcgacgggcgagcgttttgacgt
+ccgagcatttttcaacttgacgtcgttccatttaccgggagcgccttagggttaacgccg
+gccgccgagccctggggcgatttaccaccgccacgttaacctaacgcctgttaacctatc
+ggttgttaaggttaacgccccgttagggttaacgccccttaaccctgcccgcgttaaggt
+taacgcgccccggcccaggccctacccgttaaccttaaccgcccgacccccgcgcccagg
+ccatacccggtagggcctgacggccctaccgggtatgaccccgcgccccggcggaggcca
+gggaccgccccggcgctttttcgcgccccgtttaccttttgttaacgtctggcctctagg
+gtcgcccttgtccccgccgcactcccgcgccgggcaaggagcttcccgccatggtccccg
+actcgatcatgaacccccgcgaccacttccaccgcctgcgcgaggaaaccgcccgcgctc
+tggtcgaggccttcgccgaatccgaccccggcgaggattaccgcgccgaggaaaaggccg
+gcgcgtgggttgtcgcctattacgacgcggcgggcgaattcgtcgcctatctctagccgc
+cttcgccccctggcgccgcgttaacggtttgttaacatgtcggcgccagggtcgccctag
+cccggcgcgtcgccgcgccttcggagaaaaccgccatgctctacacccccgccgcccgcc
+gccttcgcggctatcgcgaaaccgccgcgaagaacgccgaaattcacgcccgcccgcaca
+tggccggcaacgtcgccggctacaacgagtcggtgtggccgacgacggcgctaggcgtcg
+ccgccaaggccggcgccttcaagcgccccgaaaccgccggcaactggtcggaggatcgca
+aagcctattacgcccccgcgtggccggccggctggcgcgtgctgggcacggccgaagagg
+tctgccgcaaggaaggctcgcgccgggtggaacattccggatggtacacgacgcccgacg
+actacagcgccacgctttcgggctatgtgctgcaaatccccgcccgcgacggccgcccgc
+aatacgtcgccgggaccgcccatagtgaatgggacggggtgaccctctaccccgccgacc
+gctacgacaacccgcttgacgcggcgagcgccgccgaccgtcacgccgaacgcgacgccg
+aagaggaacgcgaatatcaaaccgcgtggcaagcgggccagcgctacgccgaactcggcg
+ccgaagccaaggaggcccgcaaggaagcgctggcgatcctcgccgaacgccgcaaggtca
+aggggctggaaacccccgccttgtgcggcgcgatccgggcgcaagtcgcggccctgctag
+gccggatcgaagaggcgcgcgcctcgcgcgccaagctcaaggaaggcgaggactcgcgcc
+tcatgttctacccctccgccgccatggtcgcggccttcaatgacggcgcggcgtcgtgaa
+ggtcgcccgcgatagcttcgccgtgttctggaccctcccgcaaggcggggtccaatttca
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+catgttcccccgtgaccgggtccggagcgtccgcgacgcctccggccgcttcctggcctt
+caaggagtccgccccgtgcgcctgacaagctacaacgtcaacggaaccggctttaagggc
+ggctccgccccgcccgtccccgcccaaggcctgaccggtcacgccgacggcttgaacctt
+tgggttccctcgcgcgagcatatcgccgccatgctcccgcaacgctggcgccacgccttc
+gcccgcgcgtcgttttggtatgacgcgcacgacaataaaaagccgtgtcgcgccgacctc
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+aggacgccccggaaaatcttccggggcgtttaccttttgttaacctctggcctctagggt
+gactttcgccgccgggcaatcccgcccgccggaccctctttcaaggattgctcccgtcat
+gacctctcattccatggtcgcgcaccgttgggcgcaggacgacgagaacggccgcaccgc
+gcgcggcttcaacatgtatttcgagcgctacgggcgcggcgccgaccgcgtcaacgtgat
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+ggccgaagccaaggccaagcgtgacgccgaaaaggccgccaaggcgcgccgcgaagccga
+acggctcgccgacgccgaagccttcgccgcttggatgcgcggcgagcgccagagcgcccc
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+aatcgaacgcctcgccagggccgaaggggttttcgacctccccgccgacgctggcgccgt
+cgaaacccggcaagccgaaccggcctaagcctccccgcccctctcgcgccccggctcccc
+gccggggcgttttcgtgtacgcggtaaccttttgttaacttctggcctctagggtgactt
+tcgccgccgggcaatcccgcccgccggccaaggatcgcagactatgaatcttttcgttgt
+cgccattgaccccgccctcatcccttcggccgccggcttcgtggtcgcctccccctacgg
+gtgcggcaagtggcgcgcgtgcgtcgggagcgaggcggacatgatcgcgcttcgcgacaa
+gatgcgccgcgcgcacccggccccggaaggctacagcgtccagcccctggcgtcgttcct
+ggcctatctggagacggtcggggatagcccttatgaccggttccgcgcccatgacgccgc
+cgcccgcatccttgacaccctgacgacgcatctcgccgcctagccccgccaagcccccgg
+ccgcgcgccgggggcgctttccctcgaaaggatcgccgaccatgacaacccgtcttatcg
+ccgttcgcggcccgaccgccgccgaactcgccgacccgtccagccgcgcgggcggcgccg
+aagtcgttttcgagcgccgcgaccgcgaaggccgcacgcgccttgtgttcgcctcgacct
+gctacggctcatatcagcaatggggcgaaacccgcgacgtgctcgccgacaacgtcgagg
+cggtcacgctctgggccgaaggcatggcggccgttgccgccctcatcgacgagagcgacg
+acgacgacgagagcgacgacgccccggccgaagatgacgacggggaggcgtgagccatgc
+gcacaaccaaggctcaacgcttcgccgccatcgcctttgacgccctggccaaggccctaa
+gcgagccgcgccaagccgtcgcccgcgtgaccaaatgggagggcgcgggccatagcttcg
+ccaacctgcaacgcgattatgagcggtacggccccggcgcccgctcatggttcggccggg
+ctgaaatgcgcttctttgggacgcgcctagaggccgcgccgctggatttcccggcgctgg
+gctgcaccctctttctgacctccgaaaccccgcccggcgccggccgggtctggacccttc
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+cggcgaccgcgcaagcggcctttgacctgctttggcgggtcctttccggacagtaacctt
+ttgttaacttctgcccgctagggtcttcttgcggccgggcaatcccgcccggccgcatct
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+tcatcgcctcctttgagcgcgagacgggcgaatatcgcgtgaccctgcgctttggcccgc
+tccccatggggcgcggcgcccaagagtggatgcgcgcgcgccgcgaagccgtcgccagct
+acagcgacgacaaggccgacgccctggccaccgcccgcgacatgtccgcccgctgggagg
+cgatgagcgccgaagagcgttcgcgcctctatcacaaccccgcctaagaccccgcgcgcc
+gccctggccttcgccggggcggctccctcaacccctcgcaaggatcgcaccccatgaccg
+cccgtaagcccctgaccaaggaacaaaaggcccgccgccgcgcgacccgccgcgccgccc
+gcctcaactggtcggatgagcgccgcgctcgcgaattcgagcgtcaagcccgcttcttcc
+tgatgatcgccacccgcgcccaaggcgccggccaaggccaggaagccgcccgcctcgcca
+cggtcgcacaacgcaaggtgactaactggcgcatggcgcaggcctgcgcccggattaacg
+ccctggccgcgcatccgttcgcggccgtggtcgcctaaggaggcccgcccgatgacgcac
+cctcacgccctggcgctgatcgccctcgccgaaaaggtgttaccgcttacccggctgcac
+ccgctcgaccaacgcgccgccgccgtcgatctaatcggcgacctctaccgcctcgccgac
+gatatcgacgcgaccccgcaagcccccgccctgacgcaaccgaaggccgcctaagccatg
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+tttcctacctgctcgacgctggcgagtatgtcgccgcgtggcgccgcaacctcacggaaa
+ccgaccgccgcaaggcctatggcgcggcctgcgccgccgaagccctggcgctcgctaacg
+cctatcagcccgccaccctgcaaggcggcgccgtccgccgcgctctgggcgcctatgccg
+ccgccctaaaggtcctgctagacggggagccggtcaaggcggtgcgcgccgccgaaggcg
+cggcgctttcggtccgcgctcgctacgccaacacccgcctttaacctcttgttaacacct
+cccggctatggtcgggaggtcgcaaggagacacccgacatgacccgccccggccccgcct
+cgctcctgaccccgcaagcccgcttctcgtcgccgcgcgtcctgatccttccgggcgcgg
+ctcccatgccgattcgccagccgcgcggcctttgcgccgtcgagtgcgtcgcccttggcg
+tgacgctgggcgcggcgctctacctcgccgcccgcgtgttcggtctggtctgaccagacc
+cccgccccgcccccggtcggaccggtcgggggtgtgtcccataatgacacacccccgcca
+cctagtatcttttttgattcggagggacccaaaggccccctacgttaaccatttttggcg
+gcgccccc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/merged.fa	Wed Aug 17 14:46:55 2016 -0400
@@ -0,0 +1,6360 @@
+>phagey
+tggtattacaagagagaaaggaagtaatcgatatgcaacagacagcagctaagaacacac
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+gcaccccatgaccgcccgtaagcccctgaccaaggaacaaaaggcccgccgccgcgcgac
+ccgccgcgccgcccgcctcaactggtcggatgagcgccgcgctcgcgaattcgagcgtca
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+cgcccgcctcgccacggtcgcacaacgcaaggtgactaactggcgcatggcgcaggcctg
+cgcccggattaacgccctggccgcgcatccgttcgcggccgtggtcgcctaaggaggccc
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+atcatcgccgaccaactggccaaggccaaggcgtggaagcgccagcccgcctaagtcatc
+attcctatcgtctatgacttgtcaccggccgaactcttgcccggtgacagtctgggcaag
+taaagctcactctggattttatgacttagcgcaaaggattgaaattgctcgaaaaattcc
+tcgaagctcacaaagttgttttctggctgcttttgctggcctgtttgtggcgcttttaac
+ggtttgttaacccctggccctctagggtcgaattcccggcgcggcaatcccgccgcccgg
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+cgcgcaagccgccgtttgcttcaccgtctcggcgacccccgccgcgtgggaagccaaggg
+cgggcgcctcgcgcgccggctggaaaacctcgccgcgcgctatgccgccgactgcgacgc
+cccggccctgactgtcacccactgcgacggccaaacggtctatgtcggcgctctggaagc
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+cccctagcgcaccgcccctagaaaggcggtgcgcttttctgtgtctgtttacttgttgtt
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+gatcgctccccatggctcgcccctctgacctgctcaacgtcaacgccgcccgcgtcctgg
+cttgccttgagcctatcgccgccgccgctaagaccgccccggccgccgaccgcgccgccc
+tttcctacctgctcgacgctggcgagtatgtcgccgcgtggcgccgcaacctcacggaaa
+ccgaccgccgcaaggcctatggcgcggcctgcgccgccgaagccctggcgctcgctaacg
+cctatcagcccgccaccctgcaaggcggcgccgtccgccgcgctctgggcgcctatgccg
+ccgccctaaaggtcctgctagacggggagccggtcaaggcggtgcgcgccgccgaaggcg
+cggcgctttcggtccgcgctcgctacgccaacacccgcctttaacctcttgttaacacct
+cccggctatggtcgggaggtcgcaaggagacacccgacatgacccgccccggccccgcct
+cgctcctgaccccgcaagcccgcttctcgtcgccgcgcgtcctgatccttccgggcgcgg
+ctcccatgccgattcgccagccgcgcggcctttgcgccgtcgagtgcgtcgcccttggcg
+tgacgctgggcgcggcgctctacctcgccgcccgcgtgttcggtctggtctgaccagacc
+cccgccccgcccccggtcggaccggtcgggggtgtgtcccataatgacacacccccgcca
+cctagtatcttttttgattcggagggacccaaaggccccctacgttaaccatttttggcg
+gcgccccc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phagey.fa	Wed Aug 17 14:46:55 2016 -0400
@@ -0,0 +1,2661 @@
+>phagey
+tggtattacaagagagaaaggaagtaatcgatatgcaacagacagcagctaagaacacac
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+ttagagatgagtgtatacagacagttagtagcatttatggacaaccgttaatattttagt
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+aattagtagtcattctttatagactgcacgcatagtataaactataacaagaagggagga
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+atgtttataatgggatacctattcggtttcctaggggttattattagtttagtagctatt
+tactttgtgtttaagaatgataatggtaagcaggtaggagaagacccggagagtgaagct
+aaggccgcctttatctggttctgtgtgatgctagtgttagggatcgtgcttgcgtatcta
+ttcggtatcattggagtaattatcggtttagggttaatcgcaggagccatctataatata
+atgttcgggtaaataaagaattttttttaaatagttgttgactttaaagaaacatggtgc
+tagaattagcttatcaaccaaaggaggtaacaaagtgagaataacacatgaacagaagat
+ggaaattctcgaagagtggaaccttataggagagaacgattgtagaacggctctacctca
+cttaacagagctacttactaaaatacttgatagtgtttctgatcctgaaaagataaactg
+tgggtgttatgtgtggagtgaaaaactacaagagcatgttgaacctaatccactctgtaa
+gaaatgcggcgggatgggttggtattacaagagagaaaggaagtaatcgatatgcaacag
+acagcagctaagaacacacaaccagaaggtttacatctttacatggcaattggatcgtat
+gagtcggccattaacaaatatgcgcacccatataatcctggttactggaataagtataag
+aaactaaaacagaaaatccttcagtggcagcagcaaa
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Aug 17 14:46:55 2016 -0400
@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="progressivemauve" version="2.4.0">
+    <repository changeset_revision="0aeb3a1b5106" name="package_progressivemauve_2_4_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="python" version="2.7">
+    <repository changeset_revision="8b09fe018cac" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="biopython" version="1.65">
+    <repository changeset_revision="030f1a505d40" name="package_biopython_1_65" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="bcbiogff" version="0.6.2">
+    <repository changeset_revision="8ee2210f6074" name="package_python_2_7_bcbiogff_0_6_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+</tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xmfa2gff3.py	Wed Aug 17 14:46:55 2016 -0400
@@ -0,0 +1,162 @@
+#!/usr/bin/env python
+import sys
+from Bio import SeqIO
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+from Bio.SeqFeature import SeqFeature, FeatureLocation
+import argparse
+from BCBio import GFF
+import logging
+logging.basicConfig(level=logging.INFO)
+log = logging.getLogger(__name__)
+
+
+def parse_xmfa(xmfa):
+    """Simple XMFA parser until https://github.com/biopython/biopython/pull/544
+    """
+    current_lcb = []
+    current_seq = {}
+    for line in xmfa.readlines():
+        if line.startswith('#'):
+            continue
+
+        if line.strip() == '=':
+            if 'id' in current_seq:
+                current_lcb.append(current_seq)
+                current_seq = {}
+            yield current_lcb
+            current_lcb = []
+        else:
+            line = line.strip()
+            if line.startswith('>'):
+                if 'id' in current_seq:
+                    current_lcb.append(current_seq)
+                    current_seq = {}
+                data = line.strip().split()
+                id, loc = data[1].split(':')
+                start, end = loc.split('-')
+                current_seq = {
+                    'rid': '_'.join(data[1:]),
+                    'id': id,
+                    'start': int(start),
+                    'end': int(end),
+                    'strand': 1 if data[2] == '+' else -1,
+                    'seq': ''
+                }
+            else:
+                current_seq['seq'] += line.strip()
+
+
+def _percent_identity(a, b):
+    """Calculate % identity, ignoring gaps in the host sequence
+    """
+    match = 0
+    mismatch = 0
+    for char_a, char_b in zip(list(a), list(b)):
+        if char_a == '-':
+            continue
+        if char_a == char_b:
+            match += 1
+        else:
+            mismatch += 1
+
+    if match + mismatch == 0:
+        return 0
+    return 100 * float(match) / (match + mismatch)
+
+
+def _id_tn_dict(sequences):
+    """Figure out sequence IDs
+    """
+    label_convert = {}
+    if sequences is not None:
+        if len(sequences) == 1:
+            for i, record in enumerate(SeqIO.parse(sequences[0], 'fasta')):
+                label_convert[str(i + 1)] = record.id
+        else:
+            for i, sequence in enumerate(sequences):
+                for record in SeqIO.parse(sequence, 'fasta'):
+                    label_convert[str(i + 1)] = record.id
+                    continue
+    return label_convert
+
+
+def convert_xmfa_to_gff3(xmfa_file, relative_to='1', sequences=None, window_size=1000):
+    label_convert = _id_tn_dict(sequences)
+
+    lcbs = parse_xmfa(xmfa_file)
+
+    records = [SeqRecord(Seq("A"), id=label_convert.get(relative_to, relative_to))]
+    for lcb in lcbs:
+        ids = [seq['id'] for seq in lcb]
+
+        # Doesn't match part of our sequence
+        if relative_to not in ids:
+            continue
+
+        # Skip sequences that are JUST our "relative_to" genome
+        if len(ids) == 1:
+            continue
+
+        parent = [seq for seq in lcb if seq['id'] == relative_to][0]
+        others = [seq for seq in lcb if seq['id'] != relative_to]
+
+        for other in others:
+            other['feature'] = SeqFeature(
+                FeatureLocation(parent['start'], parent['end'] + 1),
+                type="match", strand=parent['strand'],
+                qualifiers={
+                    "source": "progressiveMauve",
+                    "target": label_convert.get(other['id'], other['id']),
+                    "ID": label_convert.get(other['id'], 'xmfa_' + other['rid'])
+                }
+            )
+
+        for i in range(0, len(lcb[0]['seq']), window_size):
+            block_seq = parent['seq'][i:i + window_size]
+            real_window_size = len(block_seq)
+            real_start = abs(parent['start']) - parent['seq'][0:i].count('-') + i
+            real_end = real_start + real_window_size - block_seq.count('-')
+
+            if (real_end - real_start) < 10:
+                continue
+
+            if parent['start'] < 0:
+                strand = -1
+            else:
+                strand = 1
+
+            for other in others:
+                pid = _percent_identity(block_seq, other['seq'][i:i + real_window_size])
+                # Ignore 0% identity sequences
+                if pid == 0:
+                    continue
+                other['feature'].sub_features.append(
+                    SeqFeature(
+                        FeatureLocation(real_start, real_end),
+                        type="match_part", strand=strand,
+                        qualifiers={
+                            "source": "progressiveMauve",
+                            'score': pid
+                        }
+                    )
+                )
+
+        for other in others:
+            records[0].features.append(other['feature'])
+    return records
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Convert XMFA alignments to gff3', prog='xmfa2gff3')
+    parser.add_argument('xmfa_file', type=file, help='XMFA File')
+    parser.add_argument('--window_size', type=int, help='Window size for analysis', default=1000)
+    parser.add_argument('--relative_to', type=str, help='Index of the parent sequence in the MSA', default='1')
+    parser.add_argument('--sequences', type=file, nargs='+',
+                        help='Fasta files (in same order) passed to parent for reconstructing proper IDs')
+    parser.add_argument('--version', action='version', version='%(prog)s 1.0')
+
+    args = parser.parse_args()
+
+    result = convert_xmfa_to_gff3(**vars(args))
+    GFF.write(result, sys.stdout)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xmfa2gff3.xml	Wed Aug 17 14:46:55 2016 -0400
@@ -0,0 +1,66 @@
+<?xml version="1.0"?>
+<tool id="xmfa2gff3" name="Convert XMFA to gapped GFF3" version="@WRAPPER_VERSION@.0">
+  <description></description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <version_command>python xmfa2gff3.py --version</version_command>
+  <command interpreter="python"><![CDATA[
+xmfa2gff3.py
+$xmfa
+--window_size $window_size
+--relative_to $relative_to
+--sequences
+#for file in $sequences:
+    "${file}"
+#end for
+> $output
+
+]]></command>
+  <inputs>
+      <param type="data" format="xmfa" name="xmfa"
+          label="XMFA MSA" />
+
+      <param type="data" format="fasta" name="sequences" multiple="True"
+          label="Select sequences used in progressiveMauve alignment"
+          help="Should be provided in the same order as in original progressiveMauve run"/>
+
+      <param type="integer" label="Window Size" value="100" name="window_size"
+          help="maximum length of a match_part feature. Lower number = larger GFF output" />
+
+      <param type="integer" label="Generate relative to Nth sequence in XMFA file" value="1" name="relative_to"
+          help="progressiveMauve (un)helpfully strips original sequence IDs and replaces with integer numbers. This option lets you generate the alignment relative to e.g. the second genome if you wished to display against that base sequence" />
+  </inputs>
+  <outputs>
+    <data format="gff3" name="output">
+    </data>
+  </outputs>
+  <tests>
+      <test>
+          <param name="xmfa" value="1.xmfa"/>
+          <param name="sequences" value="karma.fa,phagey.fa" />
+          <param name="window_size" value="10" />
+          <param name="relative_to" value="1" />
+          <output name="output" file="1.gff3"/>
+      </test>
+  </tests>
+  <help><![CDATA[
+What it does
+============
+
+XMFA Alignments are great, but now you need a way to visualize this data!
+
+This tool provides a conversion step to GFF3 formatted output consiting of
+``match``es and ``match_part``s with scores indicating percent identity over
+that chunk of sequence.
+
+A rendering of the output GFF3 file in JBrowse is shown below:
+
+.. image:: $PATH_TO_IMAGES/xmfa2gff3.png
+
+]]></help>
+  <citations>
+  </citations>
+</tool>