# HG changeset patch
# User iuc
# Date 1508485956 14400
# Node ID d398b2e6b2ff9cdaffbb7edb6ded2a02424342c4

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e

diff -r 000000000000 -r d398b2e6b2ff macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Oct 20 03:52:36 2017 -0400
@@ -0,0 +1,17 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">snap</requirement>
+            <yield />
+        </requirements>
+    </xml>
+
+    <token name="@VERSION@">2013_11_29</token>
+
+    <xml name="citations">
+        <citations>
+        </citations>
+    </xml>
+
+</macros>
diff -r 000000000000 -r d398b2e6b2ff snap.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snap.xml	Fri Oct 20 03:52:36 2017 -0400
@@ -0,0 +1,61 @@
+<tool id="snap" name="SNAP" profile="16.04" version="@VERSION@">
+    <description>gene prediction</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+        snap
+            -gff
+            $lcmask
+            #if $strand == 'forward'
+                -plus
+            #else if $strand == 'backward'
+                -minus
+            #end if
+            -aa '${output_aa}'
+            -tx '${output_tx}'
+            '${model}'
+            '${input_genome}'
+        > '${output_gff}'
+]]>
+    </command>
+    <inputs>
+        <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>
+
+        <param name="model" type="data" format="snaphmm" label="Prediction model" help="File created with 'Train SNAP' tool"/>
+
+        <param argument="-lcmask" type="boolean"
+            label="Treat lowercase as N"
+            truevalue="-lcmask" falsevalue="" checked="false" />
+
+        <param name="strand" type="select"
+            label="Predict genes on specific strands">
+            <option value="both">both</option>
+            <option value="forward">forward</option>
+            <option value="backward">backward</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="gff" name="output_gff" label="${tool.name} on ${on_string}: GFF"/>
+        <data format="fasta" name="output_aa" label="${tool.name} on ${on_string}: Protein sequence"/>
+        <data format="fasta" name="output_tx" label="${tool.name} on ${on_string}: Coding sequence"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_genome" value="human.fa" ftype="fasta" />
+            <param name="model" value="snap.hmm" />
+            <!-- FIXME ftype temporarily removed because the not yet existing snaphmm type breaks travis tests -->
+            <!--param name="model" value="snap.hmm" ftype="snaphmm" /-->
+            <output name="output_gff" file="snap_annot.gff" ftype="gff"/>
+            <output name="output_aa" file="annot_aa.fasta" ftype="fasta"/>
+            <output name="output_tx" file="annot_tx.fasta" ftype="fasta"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+    SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>
diff -r 000000000000 -r d398b2e6b2ff test-data/annot.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot.gff3	Fri Oct 20 03:52:36 2017 -0400
@@ -0,0 +1,41 @@
+##gff-version 3
+HS08198	maker	gene	352	1848	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0
+HS08198	maker	mRNA	352	1848	2869	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|0|0|7|0|192
+HS08198	maker	exon	352	397	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:9;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	421	582	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:10;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	812	894	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1053	1123	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:12;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1208	1315	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:13;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1587	1688	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:14;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1772	1848	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:15;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	five_prime_UTR	352	397	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	five_prime_UTR	421	444	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	445	582	.	+	0	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	812	894	.	+	0	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1053	1123	.	+	1	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1208	1315	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1587	1688	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1772	1848	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+###
+HS04636	maker	gene	1813	6903	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0
+HS04636	maker	mRNA	1813	6903	8728	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|0|0|9|0|572
+HS04636	maker	exon	1813	1934	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	2055	2198	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	2852	2995	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:2;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	3426	3607	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:3;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	4340	4423	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:4;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	4543	4789	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:5;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	5072	5358	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:6;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	5860	6007	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:7;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	6494	6903	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:8;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	five_prime_UTR	1813	1861	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	1862	1934	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	2055	2198	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	2852	2995	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	3426	3607	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	4340	4423	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	4543	4789	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	5072	5358	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	5860	6007	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	6494	6903	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+###
diff -r 000000000000 -r d398b2e6b2ff test-data/annot_aa.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot_aa.fasta	Fri Oct 20 03:52:36 2017 -0400
@@ -0,0 +1,19 @@
+>HS04636-snap.1
+MSYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTHFKGFWNV
+VNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRA
+LPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPDPQGSNMMFAFF
+AQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGK
+MKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMY
+ATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQH
+LSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQK
+YNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQAS
+IDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYGDIDAV
+ELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFG
+GEVGFQIINTASIQSLICNNVKGCPFTSFSVPDPELIKTVTINASSSRSG
+LDDINPTVLLKERSTEL*
+>HS08198-snap.1
+MNPSCHPAAATMLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPK
+ANFDAQQEQGHRAEATTLHVAPQGTAMAPVVPPPRPPRDGICWQVRQLYG
+DTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARS
+LPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQFHVLDGECTAG
+ASMAAW*
diff -r 000000000000 -r d398b2e6b2ff test-data/annot_tx.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot_tx.fasta	Fri Oct 20 03:52:36 2017 -0400
@@ -0,0 +1,42 @@
+>HS04636-snap.1
+atgagttataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccg
+gaatttttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacata
+cttacccacttcaagggattttggaacgttgtgaataacattcccttccttcgaaatgca
+attatgagttatgtcttgacatccagatcacatttgattgacagtccaccaacttacaat
+gctgactatggctacaaaagctgggaagccttctctaacctctcctattatactagagcc
+cttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagctt
+cctgattcaaatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccc
+cagggctcaaacatgatgtttgcattctttgcccagcacttcacgcatcagtttttcaag
+acagatcataagcgagggccagctttcaccaacgggctgggccatggggtggacttaaat
+catatttacggtgaaactctggctagacagcgtaaactgcgccttttcaaggatggaaaa
+atgaaatatcagataattgatggagagatgtatcctcccacagtcaaagatactcaggca
+gagatgatctaccctcctcaagtccctgagcatctacggtttgctgtggggcaggaggtc
+tttggtctggtgcctggtctgatgatgtatgccacaatctggctgcgggaacacaacaga
+gtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagaca
+agcaggctaatactgataggagagactattaagattgtgattgaagattatgtgcaacac
+ttgagtggctatcacttcaaactgaaatttgacccagaactacttttcaacaaacaattc
+cagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggcatccccttctg
+cctgacacctttcaaattcatgaccagaaatacaactatcaacagtttatctacaacaac
+tctatattgctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgct
+ggcagggttgctggtggtaggaatgttccacccgcagtacagaaagtatcacaggcttcc
+attgaccagagcaggcagatgaaataccagtcttttaatgagtaccgcaaacgctttatg
+ctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttg
+gaagcactctatggtgacatcgatgctgtggagctgtatcctgcccttctggtagaaaag
+cctcggccagatgccatctttggtgaaaccatggtagaagttggagcaccattctccttg
+aaaggacttatgggtaatgttatatgttctcctgcctactggaagccaagcacttttggt
+ggagaagtgggttttcaaatcatcaacactgcctcaattcagtctctcatctgcaataac
+gtgaagggctgtccctttacttcattcagtgttccagatccagagctcattaaaacagtc
+accatcaatgcaagttcttcccgctccggactagatgatatcaatcccacagtactacta
+aaagaacgttcgactgaactgtag
+>HS08198-snap.1
+atgaacccctcctgccaccctgctgccgccaccatgctgccccctgggactgcgaccctc
+ttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccacgccggccc
+gcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggc
+caccgggccgaggccaccacactgcatgtggctccccagggcacagccatggctcctgtg
+gtgcctcctccccgcccccccagggatgggatctgctggcaggtgcgccagctctatgga
+gacacaggggtcctcggccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcac
+gtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcgggcgggg
+cagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtggg
+tttgagcagcgggtccaggaggcccacctgactgaggaccagatcttctacttccccaag
+tacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggg
+gcaagcatggcggcgtggtga
diff -r 000000000000 -r d398b2e6b2ff test-data/human.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human.fa	Fri Oct 20 03:52:36 2017 -0400
@@ -0,0 +1,200 @@
+>HS04636
+gagctcacattaactatttacagggtaactgcttaggaccagtattatgaggagaattta
+cctttcccgcctctctttccaagaaacaaggagggggtgaaggtacggagaacagtattt
+cttctgttgaaagcaacttagctacaaagataaattacagctatgtacactgaaggtagc
+tatttcattccacaaaataagagttttttaaaaagctatgtatgtatgtgctgcatatag
+agcagatatacagcctattaagcgtcgtcactaaaacataaaacatgtcagcctttctta
+accttactcgccccagtctgtcccgacgtgacttcctcgaccctctaaagacgtacagac
+cagacacggcggcggcggcgggagaggggattccctgcgcccccggacctcagggccgct
+cagattcctggagaggaagccaagtgtccttctgccctcccccggtatcccatccaaggc
+gatcagtccagaactggctctcggaagcgctcgggcaaagactgcgaagaagaaaagaca
+tctggcggaaacctgtgcgcctggggcggtggaactcggggaggagagggagggatcaga
+caggagagtggggactaccccctctgctcccaaattggggcagcttcctgggtttccgat
+tttctcatttccgtgggtaaaaaaccctgcccccaccgggcttacgcaatttttttaagg
+ggagaggagggaaaaaatttgtgggggggtacgaaaaggcggaaagaaacagtcattcac
+atgggcttggttttcagtcttataaaaaggaaggttctctcggttagcgaccaattgtca
+tacgacttgcagtgagcgtcaggagcacgtccaggaactcctcagcagcgcctccttcag
+ctccacagccagacgccctcagacagcaaagcctacccccgcgccgcgccctgcccgccg
+ctcggatgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacaggtg
+agtacctggcgccgcgcaccggggactccggttccacgcacccgggcagagtttccgctc
+tgacctcctgggtctatcccagtactccgacttctctccgaatagagaagctacgtgact
+tgggaaagagcttggaccgctagagtccgaaagaactccgtggatattccagctttccca
+caagcactgatcattatgagccagttacttaaccgatctgagacactctcacctcctaaa
+tagggatagatgatactaatttgcaggttgtcattatgataagacaggatctgatcaata
+tatgtgaattgtttatatttggaacctttttattgagtggaagaagttgttttaaatatt
+ctagtcagttctttcctgctcccaggaaagcccggattatgttttaagataagcaaaatg
+tcttaaaagtaagctgttttactttgaatttttccctaaatgttgattagtgtactagat
+ccattttaatttggaaagtgaagtgctacttatttgaacttcttaaaaatgctaatttta
+acatctaaagagttaactaagaaaagcttagtaacatgatgtaccaagttgaatatgctg
+ttatccttatttagaatagaaaattggtatttctacgttttatccattctaaggcaggtt
+aaaaaattgtatttccatgactacctatatatttcttgaatttattattgtaaagttgat
+tcatagtcaaacaattaaatgtttaaattaagattaagacactagagaatgatttatttg
+ctgtcctttaattgcagcaaatccttgctgttcccacccatgtcaaaaccgaggtgtatg
+tatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggaga
+aaactgctcaacacgtaagtttgtcctttggttgcctcattaggagtggggctggataca
+gttatcattgtatagatttgtgtcttataatgagtcccattaatttctccctccctttct
+tcgtcttcttgcagcggaatttttgacaagaataaaattatttctgaaacccactccaaa
+cacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc
+cttccttcgaaatgcaattatgagttatgtcttgacatgtaagtacaagtgtctttctaa
+ggtttttagccttctcaaagaaaaatatgctttataatactgtaagcctaatctaaaaac
+atatttccaagcttatcaaaaagactttaagatagcttttaagtttgccttccatcttaa
+tcgccaaaaatattgacatttagtcccatccagtttatacagtctgctcacaactctgta
+tacctcttctaacctttactgtttggtcagtttgtggaggtagcatggtccagctgttta
+ttgaatgcccatgggccacagaattgttctgaacatgtagcacccattaaaataaatttg
+gatttggatcagcaagaaaataactttccatgattctaaagtgggtgccatactcagcca
+ttcctttcataggcctcttggatagtgagcagatggctacctgaaaaatcaatattgcca
+gattataatgtgcagagtatatgtattttattaaagatgtatttcaagtggccattagac
+tataaagtgtagttgtttaaaaatagattttttttattttggagttacattcaacctcag
+gtgccactttccacattttacaataaaaataatggttgatttacttaacaaatgagaata
+aataaaacatttttttctttgaaaatttcagccagatcacatttgattgacagtccacca
+acttacaatgctgactatggctacaaaagctgggaagccttctctaacctctcctattat
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+gaggggcaggggacacacagaccccgttcccagagccctccacgccgcctggtgccagga
+ccccaggaaccctgtctgccctgcagcccgctcgctccctgtgagcgactcggtcctgag
+tgggtttgagcagcgggtccaggaggcccacctgactgaggaccagatcttctacttccc
+caagtacggtgagtgtccccagcaggtccccagctcagccacccccactctctggctgat
+gtccagcctgacccctgccttggcgccccaggcttctgcgaggctgcagaccagttccac
+gtcctggacggtgagtgcacagcgggggcaagcatggcggcgtggtgaggggggccactc
+gcaccggctgagtctcgtctctgctgcagaagtgaggaggtgaggccggcacacagctcc
+agtgctgagaagtcagtgccccgagagacgaccccaccagtggggtgcccgctgcctgtc
+ctccgtgaaaccagcctcagatcagggccctgccacccagggcaggggatcttctgccgg
+ctgccccagaggacagtgggtggagtggtacctacttattaaatgtctcagacccctctc
+tgactcttctgtccactctggaccggcgccagtaccaccaaggccctctctgcccccacc
+ccgcctctttaaaagcccggcgctccctgttggctggagtccacgcagggtcactgggcc
+gatttcggctcttgggatttgggaggggagatcctctctggcatatgccatcttgtgccc
+tgctggacctgggggcgtccacgtcactccaaggctgctcttgcctgggccatgcctgca
+gccc
diff -r 000000000000 -r d398b2e6b2ff test-data/snap.hmm
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/snap.hmm	Fri Oct 20 03:52:36 2017 -0400
@@ -0,0 +1,1612 @@
+zoeHMM snap_training 6 8 6 7
+
+<STATES>
+
+Einit	0	0	3	-1	explicit
+Esngl	0	0	150	-1	explicit
+Eterm	0	0	3	-1	explicit
+Exon	0	0	6	-1	explicit
+Inter	0.9	0.9	0	0	geometric
+Intron	0.1	0.1	0	0	geometric
+
+<STATE_TRANSITIONS>
+
+Einit	Intron	1
+Esngl	Inter	1
+Eterm	Inter	1
+Exon	Intron	1
+Inter	Einit	1.000000
+Inter	Esngl	0.000000
+Intron	Eterm	0.153846
+Intron	Exon	0.846154
+
+<PHASE_PREFERENCES>
+
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+
+<STATE_DURATIONS>
+
+Einit 2
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+		-3.459 -3.781 -4.196 -4.781 -5.781 
+		. . . . . 
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+		. . . . . 
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+	GEOMETRIC 250 -1
+		3
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+Esngl 1
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+Eterm 2
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+	GEOMETRIC 250 -1
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+Exon 2
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+	GEOMETRIC 250 -1
+		241
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+Inter 1
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+<SEQUENCE_MODELS>
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+		0.000	0.000	0.585	-1.000	
+		-0.807	-0.807	0.778	0.193	
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+		-0.170	0.415	-1.170	0.415	
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+		0.678	-0.322	-0.322	-0.322	
+		0.585	0.000	-1.000	0.000	
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+		-0.585	0.415	0.415	-0.585	
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+		-0.322	0.678	-0.322	-0.322	
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+		-0.585	0.415	-0.585	0.415	
+		0.000	0.000	0.000	0.000	
+		0.000	0.000	0.000	0.000	
+		0.000	0.000	0.000	0.000	
+		0.000	0.000	0.000	0.000	
+		0.415	0.415	-0.585	-0.585	
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+		1.000	-0.585	-0.585	-0.585	
+		0.778	-0.807	-0.807	0.193	
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+		0.000	0.000	0.000	0.000	
+		-0.322	0.678	-0.322	-0.322	
+		-0.322	0.678	-0.322	-0.322	
+		0.000	0.000	0.000	0.000	
+		-0.322	0.678	-0.322	-0.322	
+		0.678	-0.322	-0.322	-0.322	
+		0.000	0.000	0.000	0.000	
+		0.000	0.000	0.000	0.000	
+		-0.322	-0.322	-0.322	0.678	
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+		-0.322	0.678	-0.322	-0.322	
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+		-0.322	0.678	-0.322	-0.322	
+		-0.585	-0.585	-0.585	1.000	
+		0.415	-0.585	0.415	-0.585	
+		-0.322	-0.322	-0.322	0.678	
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+		0.778	-0.807	-0.807	0.193	
+		0.585	0.000	0.000	-1.000	
+		-0.807	-0.807	0.193	0.778	
+
+Donor SDT 2 0 4 2 0.000
+	GT WMM 9 3 4 0 0.000
+		0.497	0.497	-0.503	-1.087	
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+		-2.087	-1.087	1.372	-0.503	
+		-2.087	-2.087	1.720	-2.087	
+		-2.087	-2.087	-2.087	1.720	
+		1.234	-2.087	0.234	-2.087	
+		1.372	-2.087	-1.087	-0.503	
+		-0.503	-2.087	1.497	-2.087	
+		-0.087	-0.087	-1.087	0.720	
+	NN TRM 0 0 0 0 0.000
+
+Inter LUT 5 4 4 0 0.000
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+	-0.415	0.322	-2.000	0.807	
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+	-0.202	-0.524	0.284	0.284	
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+	-0.524	-0.524	1.177	-1.524	
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+	0.000	0.585	-1.000	0.000	
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+	0.227	-1.358	-0.188	0.642	
+	-0.026	-0.663	-0.373	0.691	
+	0.491	-0.209	-2.209	0.598	
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+
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+		-0.585	-0.585	1.000	-0.585	
+		-0.585	0.415	0.415	-0.585	
+		-0.585	0.415	-0.585	0.415	
+		-0.585	-0.585	1.000	-0.585	
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+		0.415	0.415	-0.585	-0.585	
+		0.415	-0.585	-0.585	0.415	
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+		-0.585	0.415	-0.585	0.415	
+		1.000	-0.585	-0.585	-0.585	
+		-0.585	-0.585	-0.585	1.000	
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+		0.415	0.415	-0.585	-0.585	
+		-0.585	-0.585	0.415	0.415	
+		-0.585	-0.585	0.415	0.415	
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+
+Stop SDT 3 0 4 4 0.000
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+		0.000	0.000	0.000	0.000	
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+		-0.322	-0.322	0.678	-0.322	
+		0.678	-0.322	-0.322	-0.322	
+		0.678	-0.322	-0.322	-0.322	
+		-0.322	0.678	-0.322	-0.322	
+		-0.322	-0.322	-0.322	0.678	
+		-0.322	-0.322	0.678	-0.322	
+		-0.322	-0.322	-0.322	0.678	
+		0.678	-0.322	-0.322	-0.322	
+		-0.322	-0.322	0.678	-0.322	
+	TGA WMM 9 6 4 0 0.000
+		-0.322	-0.322	0.678	-0.322	
+		-0.322	0.678	-0.322	-0.322	
+		-0.322	-0.322	0.678	-0.322	
+		-0.322	-0.322	-0.322	0.678	
+		-0.322	-0.322	0.678	-0.322	
+		-0.322	-0.322	0.678	-0.322	
+		-0.322	-0.322	-0.322	0.678	
+		-0.322	-0.322	0.678	-0.322	
+		0.678	-0.322	-0.322	-0.322	
+	NNN TRM 0 0 0 0 0.000
+
diff -r 000000000000 -r d398b2e6b2ff test-data/snap_annot.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/snap_annot.gff	Fri Oct 20 03:52:36 2017 -0400
@@ -0,0 +1,17 @@
+HS04636	SNAP	Einit	1862	1867	8.523	+	.	HS04636-snap.1
+HS04636	SNAP	Exon	1883	1934	20.348	+	.	HS04636-snap.1
+HS04636	SNAP	Exon	2055	2198	69.846	+	.	HS04636-snap.1
+HS04636	SNAP	Exon	2852	2995	67.055	+	.	HS04636-snap.1
+HS04636	SNAP	Exon	3426	3607	77.942	+	.	HS04636-snap.1
+HS04636	SNAP	Exon	4340	4423	47.588	+	.	HS04636-snap.1
+HS04636	SNAP	Exon	4543	4789	112.472	+	.	HS04636-snap.1
+HS04636	SNAP	Exon	5072	5358	122.974	+	.	HS04636-snap.1
+HS04636	SNAP	Exon	5860	6007	72.046	+	.	HS04636-snap.1
+HS04636	SNAP	Eterm	6494	6903	163.122	+	.	HS04636-snap.1
+HS08198	SNAP	Einit	99	107	-2.800	+	.	HS08198-snap.1
+HS08198	SNAP	Exon	421	582	45.298	+	.	HS08198-snap.1
+HS08198	SNAP	Exon	812	874	24.711	+	.	HS08198-snap.1
+HS08198	SNAP	Exon	1024	1123	34.281	+	.	HS08198-snap.1
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+HS08198	SNAP	Exon	1587	1688	41.983	+	.	HS08198-snap.1
+HS08198	SNAP	Eterm	1772	1848	35.796	+	.	HS08198-snap.1