Mercurial > repos > rnateam > graphprot_predict_profile

Binary file data/EWSR1_eCLIP_K562_ENCSR887LPK.tar.gz has changed
Binary file data/FMR1_eCLIP_K562_ENCSR331VNX.tar.gz has changed
Binary file data/HNRNPC_eCLIP_HepG2_ENCSR550DVK.tar.gz has changed
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Binary file data/KHDRBS1_eCLIP_K562_ENCSR628IDK_structure.tar.gz has changed
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/graphprot_predict_profile.xml	Fri May 25 12:17:44 2018 -0400
@@ -0,0 +1,227 @@
+<tool id="graphprot_predict_profile" name="GraphProt predict profile" version="1.1.7">
+    <description>- Predict RBP binding profiles</description>
+    <requirements>
+        <requirement type="package" version="1.1.7">graphprot</requirement>
+    </requirements>
+    <command><![CDATA[
+    #if $select_model.model_selector == 'select_model_from_repo':
+        mkdir -p ./model &&
+        tar -zxvf '$__tool_directory__/data/${select_model.repo_model}.tar.gz' -C ./model &&
+    #end if
+    perl '$__tool_directory__/graphprot_predict_profile_wrapper.pl'
+        -fasta '$fasta_file'
+        #if $select_model.model_selector == 'select_model_from_history':
+            -model '$select_model.model_file'
+            #if $select_model.set_params.set_params_selector == 'supply_params_file':
+                -params '$select_model.set_params.params_file'
+            #elif $select_model.set_params.set_params_selector == 'manual_params_setting':
+                #if $select_model.set_params.model_type.model_type_selector == 'sequence':
+                    -onlyseq
+                #elif $select_model.set_params.model_type.model_type_selector == 'structure':
+                    -abstraction $select_model.set_params.model_type.gp_abstraction
+                #end if
+                -R $select_model.set_params.gp_r
+                -D $select_model.set_params.gp_d
+                -bitsize $select_model.set_params.gp_bitsize
+                -lambda $select_model.set_params.gp_lambda
+                -epochs $select_model.set_params.gp_epochs
+                #if $select_model.set_params.gev_options.distr_my
+                    -distr-my $select_model.set_params.gev_options.distr_my
+                #end if
+                #if $select_model.set_params.gev_options.distr_sigma
+                    -distr-sigma $select_model.set_params.gev_options.distr_sigma
+                #end if
+                #if $select_model.set_params.gev_options.distr_xi
+                    -distr-xi $select_model.set_params.gev_options.distr_xi
+                #end if
+            #end if
+        #elif $select_model.model_selector == 'select_model_from_repo':
+            -model './model/${select_model.repo_model}.model'
+            -params './model/${select_model.repo_model}.params'
+        #end if
+        $peak_region_options.p50_output
+        #if $peak_region_options.merge_dist
+            -merge-dist $peak_region_options.merge_dist
+        #end if
+        #if $peak_region_options.p_val_thr
+            -thr-p $peak_region_options.p_val_thr
+        #end if
+        #if $peak_region_options.score_thr
+            -thr-sc $peak_region_options.score_thr
+        #end if
+    ]]></command>
+    <inputs>
+        <param name="fasta_file" type="data" format="fasta" label="Input FASTA file" argument="-fasta"
+               help="FASTA file containing sequences to predict binding profiles on"/>
+
+        <conditional name="select_model">
+            <param name="model_selector" type="select" label="Select GraphProt model"
+                   help="Select GraphProt model for binding profile prediction">
+                <option value="select_model_from_history" selected="true">Select model from history</option>
+                <option value="select_model_from_repo">Select model from repository</option>
+            </param>
+            <when value="select_model_from_history">
+                <param name="model_file" type="data" format="data" label="GraphProt model file" argument="-model"
+                       help="Predict binding profile for the given GraphProt RBP model"/>
+                <conditional name="set_params">
+                    <param name="set_params_selector" type="select" label="Set model parameters">
+                        <option value="supply_params_file" selected="true">Select parameter file from history</option>
+                        <option value="manual_params_setting">Manually set model parameters</option>
+                    </param>
+                    <when value="supply_params_file">
+                        <param name="params_file" type="data" format="txt"
+                               label="Model parameter file" argument="-params"
+                               help="Parameter file containing model parameters"/>
+                    </when>
+                    <when value="manual_params_setting">
+                        <conditional name="model_type">
+                            <param name="model_type_selector" type="select" label="Select model type">
+                                <option value="sequence" selected="true">Supplied model is a sequence model</option>
+                                <option value="structure">Supplied model is a structure model</option>
+                            </param>
+                            <when value="sequence"/>
+                            <when value="structure">
+                                <param name="gp_abstraction" type="integer" value="3" argument="-abstraction"
+                                       label="RNAshapes abstraction level for RNA structure graphs"/>
+                            </when>
+                        </conditional>
+                        <param name="gp_r" type="integer" value="1" min="0" max="4"
+                               label="GraphProt radius" argument="-R"/>
+                        <param name="gp_d" type="integer" value="4" min="0" max="6"
+                               label="GraphProt distance" argument="-D"/>
+                        <param name="gp_bitsize" type="integer" value="14"
+                               label="GraphProt bitsize used for feature encoding" argument="-bitsize"/>
+                        <param name="gp_lambda" type="float" value="10e-6"
+                               label="SGD parameter lambda for classification" argument="-lambda"/>
+                        <param name="gp_epochs" type="integer" value="10"
+                               label="SGD parameter epochs for classification" argument="-epochs"/>
+                        <section name="gev_options" title="GEV distribution parameters for signifying GraphProt scores">
+                            <param name="distr_my" type="float" optional="True"
+                                   label="GEV distribution parameter my" argument="-distr-my"/>
+                            <param name="distr_sigma" type="float" optional="True"
+                                   label="GEV distribution parameter sigma" argument="-distr-sigma"/>
+                            <param name="distr_xi" type="float" optional="True"
+                                   label="GEV distribution parameter xi" argument="-distr-xi"/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+            <when value="select_model_from_repo">
+                <param name="repo_model" type="select" label="Select model" help="Select model from a list of pre-trained GraphProt models">
+                    <option value="EWSR1_eCLIP_K562_ENCSR887LPK" selected="true">EWSR1_eCLIP_K562_ENCSR887LPK.model</option>
+                    <option value="FMR1_eCLIP_K562_ENCSR331VNX">FMR1_eCLIP_K562_ENCSR331VNX.model</option>
+                    <option value="HNRNPC_eCLIP_HepG2_ENCSR550DVK">HNRNPC_eCLIP_HepG2_ENCSR550DVK.model</option>
+                    <option value="HUR_PAR-CLIP_HEK293_Mukherjee">HUR_PAR-CLIP_HEK293_Mukherjee.model</option>
+                    <option value="IGF2BP1-3_PAR-CLIP_HEK293_Hafner">IGF2BP1-3_PAR-CLIP_HEK293_Hafner.model</option>
+                    <option value="IGF2BP1-3_PAR-CLIP_HEK293_Hafner_structure">IGF2BP1-3_PAR-CLIP_HEK293_Hafner_structure.model</option>
+                    <option value="KHDRBS1_eCLIP_K562_ENCSR628IDK">KHDRBS1_eCLIP_K562_ENCSR628IDK.model</option>
+                    <option value="KHDRBS1_eCLIP_K562_ENCSR628IDK_structure">KHDRBS1_eCLIP_K562_ENCSR628IDK_structure.model</option>
+                    <option value="PUM2_PAR-CLIP_HEK293_Hafner">PUM2_PAR-CLIP_HEK293_Hafner.model</option>
+                    <option value="PUM2_eCLIP_K562_exonized_3utr">PUM2_eCLIP_K562_exonized_3utr.model</option>
+                    <option value="QKI_PAR-CLIP_HEK293_Hafner">QKI_PAR-CLIP_HEK293_Hafner.model</option>
+                    <option value="QKI_eCLIP_HepG2_ENCSR570WLM">EWSR1_eCLIP_K562_ENCSR887LPK.model</option>
+                    <option value="QKI_eCLIP_HepG2_ENCSR570WLM_structure">QKI_eCLIP_HepG2_ENCSR570WLM_structure.model</option>
+                </param>
+            </when>
+        </conditional>
+        <section name="peak_region_options" title="Peak region options">
+            <param name="merge_dist" type="integer" optional="True"
+                   label="Maximum distance between two peak regions for merging" argument="-merge-dist"
+                   help="By default all non-overlapping regions will be reported. E.g. a distance of 1 means that two regions above the set threshold (score or p-value) will be merged if they is 1 nucleotide that separates the two regions"/>
+            <param name="p_val_thr" type="float" optional="True"
+                   label="Set p-value threshold for reporting peak regions"
+                   help="Regions with p-value lower or equal the given value are reported. If no distribution parameters are given (either manually or in .params file), no p-values will be calculated and peak regions will be filtered by their peak scores instead (default: 0.05)"/>
+            <param name="score_thr" type="float" optional="True"
+                   label="Set GraphProt peak score threshold for reporting peak regions"
+                   help="Regions with peak score higher or equal the given value are reported. If distribution parameters are given (either manually or in .params file), p-value threshold will be used instead of the peak score threshold for filtering (default: 0)"/>
+            <param name="p50_output" label="Also output p50 score filtered peak regions file" type="boolean"
+                       truevalue="-p50-out" falsevalue="" checked="False"
+                       help="Output is a peak regions BED file using the best average score found in at least 50 % of the positive training sites (p50) as threshold for defining peak regions. NOTE that if the score is not given in .params file, an empty file will be output if selected."/>
+        </section>
+    </inputs>
+    <outputs>
+        <data format="txt" name="average_profile_outfile" label="${tool.name} on ${on_string} (average profile)" from_work_dir="GraphProt.average_profile"/>
+        <data format="bed" name="peak_regions_outfile" label="${tool.name} on ${on_string} (peak regions)" from_work_dir="GraphProt.peak_regions.bed"/>
+        <data format="bed" name="peak_regions_p50_outfile" label="${tool.name} on ${on_string} (peak regions p50)" from_work_dir="GraphProt.peak_regions_p50.bed"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta_file" value="test.fa" ftype="fasta"/>
+            <param name="model_selector" value="select_model_from_history"/>
+            <param name="model_file" value="test.model"/>
+            <param name="set_params_selector" value="supply_params_file"/>
+            <param name="params_file" value="test.params"/>
+            <param name="p50_output" value="True"/>
+            <output name="average_profile_outfile" file="GraphProt_predict_profile_test_out1.average_profile"/>
+            <output name="peak_regions_outfile" file="GraphProt_predict_profile_test_out1.peak_regions.bed"/>
+            <output name="peak_regions_p50_outfile" file="GraphProt_predict_profile_test_out1.peak_regions_p50.bed"/>
+        </test>
+        <test>
+            <param name="fasta_file" value="test.fa" ftype="fasta"/>
+            <param name="model_selector" value="select_model_from_history"/>
+            <param name="model_file" value="test.model"/>
+            <param name="set_params_selector" value="manual_params_setting"/>
+            <param name="model_type_selector" value="sequence"/>
+            <param name="gp_r" value="1"/>
+            <param name="gp_d" value="4"/>
+            <param name="gp_epochs" value="20"/>
+            <param name="gp_lambda" value="0.001"/>
+            <param name="gp_bitsize" value="14"/>
+            <param name="merge_dist" value="1"/>
+            <param name="score_thr" value="1"/>
+            <output name="average_profile_outfile" file="GraphProt_predict_profile_test_out2.average_profile"/>
+            <output name="peak_regions_outfile" file="GraphProt_predict_profile_test_out2.peak_regions.bed"/>
+        </test>
+        <test>
+            <param name="fasta_file" value="test.fa" ftype="fasta"/>
+            <param name="model_selector" value="select_model_from_history"/>
+            <param name="model_file" value="structure_test.model"/>
+            <param name="set_params_selector" value="supply_params_file"/>
+            <param name="params_file" value="structure_test.params"/>
+            <param name="model_type_selector" value="structure"/>
+            <param name="gp_abstraction" value="3"/>
+            <param name="score_thr" value="2"/>
+            <output name="average_profile_outfile" file="GraphProt_predict_profile_test_out3.average_profile"/>
+            <output name="peak_regions_outfile" file="GraphProt_predict_profile_test_out3.peak_regions.bed"/>
+        </test>
+        <test>
+            <param name="fasta_file" value="test.fa" ftype="fasta"/>
+            <param name="model_selector" value="select_model_from_repo"/>
+            <param name="repo_model" value="FMR1_eCLIP_K562_ENCSR331VNX"/>
+            <param name="p50_output" value="True"/>
+            <output name="average_profile_outfile" file="GraphProt_predict_profile_test_out4.average_profile"/>
+            <output name="peak_regions_outfile" file="GraphProt_predict_profile_test_out4.peak_regions.bed"/>
+            <output name="peak_regions_p50_outfile" file="GraphProt_predict_profile_test_out4.peak_regions_p50.bed"/>
+        </test>
+
+    </tests>
+    <help>
+
+Use GraphProt (-action predict_profile) to predict binding profiles for a given RBP model (supplied as .model and .params file) on a given set of FASTA sequences. After predicting position-wise scores, the scores are averaged over small windows (11 nt with averaged score position in center) to smooth out the profiles and peak regions are extracted based on the set thresholds (p-value or score) and merge distance.
+
+**Output files**
+
+The procedure has three output files (third is optional):
+
+1) An average_profile file containing averaged position-scores over all supplied sequences
+
+2) A peak regions BED file which contains peak-scoring regions above the supplied threshold (p-value default: 0.05, score default: 0)
+
+3) A peak regions BED file using the best average score found in at least 50 % of the positive training sites (p50). NOTE that this requires the p50 score to be given in the .params file, otherwise if set an empty file will be output.
+
+**Model selection**
+
+The GraphProt model used for profile prediction can either be uploaded to history or chosen from an example collection of models (Select model from repository). For the repository models, the corresponding parameter file is selected automatically, providing all model parameters necessary for prediction and p-value calculation. If you choose to upload a model to the history, it is recommended to use the corresponding .params file for automatically setting the model parameters. Otherwise the model parameters have to be entered manually.
+
+**p-value calculation**
+
+Signifying the GraphProt scores is done by fitting a generalized extreme value (GEV) distribution on a set of scores derived from 10000 transcript sequences for each GraphProt model. The GEV distribution has three parameters: my (location), sigma (scale), and xi (shape). The fitted parameter values usually are read in from the .params file, but can also be entered manually. Parameter fitting was done in R using the minpack.lm_ package, using the probability density function (PDF) described here_. If no GEV parameter values are specified (either in .params file or manually), p-value calculation for the scores will be skipped and the peak regions will be extracted based on the set threshold score.
+
+.. _here: https://en.wikipedia.org/wiki/Generalized_extreme_value_distribution
+.. _minpack.lm: https://cran.r-project.org/web/packages/minpack.lm
+
+    </help>
+    <citations>
+        <citation type="doi">10.1186/gb-2014-15-1-r17</citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/graphprot_predict_profile_wrapper.pl	Fri May 25 12:17:44 2018 -0400
@@ -0,0 +1,764 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+use Getopt::Long;
+use Pod::Usage;
+use Cwd qw(getcwd abs_path);
+use List::Util qw(sum);
+
+=head1 NAME
+
+=head1 SYNOPSIS
+
+Galaxy wrapper script for GraphProt (-action predict_profile) to compute
+the binding profile for a given model on a given set of sequences provided
+in FASTA format. After profile prediction, average profiles get computed,
+scores signified and binding peak regions extracted. The score signification
+is done using the provided fitted GEV parameters, either from .params file
+or manually set. If score threshold is set (-thr-sc), p-value assignment
+will be skipped and set score threshold will be used to extract peak
+regions. NOTE: Additional lines .params file are used to store and get
+GEV parameters, as well as type of model (model_type: sequence|structure).
+Also, this wrapper currently works for classification mode only.
+
+PARAMETERS:
+
+    -help|h         display help page
+    -fasta          Input FASTA file (option -fasta)
+    -model          Input .model file (option -model)
+    -params         Input .params file
+                    NOTE: uses .params file with additional
+                    parameters
+                    Manually set parameters (below) will override
+                    found settings in .params file
+    -data-id        Data ID (option -prefix)
+
+GraphProt model parameters (by default get from .params file):
+
+    -onlyseq        Set if model is a sequence model
+    -R              GraphProt model R parameter
+    -D              GraphProt model D parameter
+    -epochs         GraphProt model epochs parameter
+    -lambda         GraphProt model lambda parameter
+    -bitsize        GraphProt model bitsize parameter
+    -abstraction    GraphProt model RNAshapes abstraction level
+                    parameter (set for structure models)
+
+Peak region extraction parameters:
+
+    -thr-sc         Score threshold for extracting peak regions
+                    By default p-value of 0.05 is used. If no p-value
+                    calculation possible, -thr-sc is used with default: 0
+    -thr-p          p-value threshold for extracting peak regions
+                    By default, peak regions with p = 0.05 are extracted,
+                    as well as p50 score peak regions (if info given)
+                    Default: 0.05
+    -merge-dist     Maximum merge distance for nearby peak regions
+                    Default: report all non-overlapping regions
+    -p50-out        Output p50 score filtered peak regions BED file
+                    default: false
+
+GEV distribution parameters:
+
+    -distr-my       GEV distribution my parameter for calculating p-values
+                    from scores
+    -distr-sigma    GEV distrubution sigma parameter for calculating
+                    p-values from scores
+    -distr-xi       GEV distribution xi parameter for calculating p-values
+                    from scores
+    -ap-extlr       Used average profile left right extension for
+                    averaging scores, which were used for distribution
+                    fitting. NOTE: usually a value of 5 was used for
+                    for getting GEV distribution and parameters. If you
+                    choose a different value here, calculated p-values
+                    will be wrong!
+                    default : 5
+
+
+=head1 DISCRIPTION
+
+5) Write manual
+6) add output p50 file with NOTE
+
+6) put GP into rna_tools
+
+NOTE:
+Additional lines .params file used to store and get gev parameters, as well
+as type of model (model_type: sequence|structure).
+
+Example .params content:
+epochs: 20
+lambda: 0.001
+R: 1
+D: 4
+bitsize: 14
+model_type: sequence
+#ADDITIONAL MODEL PARAMETERS
+ap_extlr: 5
+gev_my: -2.5408
+gev_sigma: 1.6444
+gev_xi: -0.1383
+p50_score: 6.51534
+p50_p_val: 0.0009059744
+
+=cut
+
+############################
+# COMMAND LINE CHECKING.
+############################
+
+# Command line argument variables.
+my ($i_help, $i_fasta, $i_model, $i_params, $i_data_id, $i_thr_sc, $i_thr_p, $i_max_merge_dist, $i_p50_out, $i_gp_r, $i_gp_d, $i_gp_epochs, $i_gp_lambda, $i_gp_bitsize, $i_gp_abstr, $i_gp_onlyseq, $i_distr_my, $i_distr_sigma, $i_distr_xi, $i_ap_extlr);
+
+# Parse the command line.
+GetOptions ( "help|h" => \$i_help,
+             "fasta:s" => \$i_fasta,
+             "model:s" => \$i_model,
+             "params:s" => \$i_params,
+             "data-id:s" => \$i_data_id,
+             "thr-sc:f" => \$i_thr_sc,
+             "thr-p:f" => \$i_thr_p,
+             "p50-out" => \$i_p50_out,
+             "merge-dist:i" => \$i_max_merge_dist,
+             "R:i" => \$i_gp_r,
+             "D:i" => \$i_gp_d,
+             "epochs:i" => \$i_gp_epochs,
+             "lambda:f" => \$i_gp_lambda,
+             "bitsize:i" => \$i_gp_bitsize,
+             "abstr:i" => \$i_gp_abstr,
+             "onlyseq" => \$i_gp_onlyseq,
+             "distr-my:f" => \$i_distr_my,
+             "distr-sigma:f" => \$i_distr_sigma,
+             "distr-xi:f" => \$i_distr_xi,
+             "ap-extlr:i" => \$i_ap_extlr ) or pod2usage(1);
+
+# Check.
+pod2usage(1) if $i_help;
+($i_fasta and $i_model) or pod2usage "ERROR: -fasta, -model are mandatory";
+if ($i_distr_my or $i_distr_sigma or $i_distr_xi) {
+    ($i_distr_my and $i_distr_sigma and $i_distr_xi) or pod2usage "ERROR: expects all three distribution parameters to be set";
+}
+
+#######################
+# SET PARAMETERS.
+#######################
+
+# Prefix.
+my $data_id = "GraphProt";
+if ($i_data_id) {
+    $data_id = $i_data_id;
+}
+my $thr_sc = 0;
+if ($i_thr_sc) {
+    $thr_sc = $i_thr_sc;
+}
+my $thr_p = 0.05;
+if ($i_thr_p) {
+    $thr_p = $i_thr_p;
+}
+my $ap_extlr = 5;
+if ($i_ap_extlr) {
+    $ap_extlr = $i_ap_extlr;
+}
+my $max_merge_dist = 0;
+if ($i_max_merge_dist) {
+    $max_merge_dist = $i_max_merge_dist;
+}
+
+# Get parameters from .params file.
+my %params;
+if ($i_params) {
+    open(IN, $i_params) or die "Cannot open $i_params: $!";
+    while(<IN>) {
+        next if ($_ =~ /^#/);
+        if ($_ =~ /(.+):\s(.+)/) {
+            $params{$1} = $2;
+        }
+    }
+    close IN;
+}
+
+# Create GP parameter string.
+my $params_string = "";
+# -onlyseq
+my $model_type = "structure";
+if (exists $params{"model_type"}) {
+    if ($params{"model_type"} eq "sequence") {
+        $params_string .= " -onlyseq";
+        $model_type = "sequence";
+    }
+} elsif ($i_gp_onlyseq) {
+    $params_string .= " -onlyseq";
+    $model_type = "sequence";
+}
+# -R
+if ($i_gp_r) {
+    $params_string .= " -R $i_gp_r";
+} elsif (exists $params{"R"}) {
+    my $v = $params{"R"};
+    $params_string .= " -R $v";
+} else {
+    die "ERROR: -R needs to be set";
+}
+# -D
+if ($i_gp_d) {
+    $params_string .= " -D $i_gp_d";
+} elsif (exists $params{"D"}) {
+    my $v = $params{"D"};
+    $params_string .= " -D $v";
+} else {
+    die "ERROR: -D needs to be set";
+}
+# -epochs
+if ($i_gp_epochs) {
+    $params_string .= " -epochs $i_gp_epochs";
+} elsif (exists $params{"epochs"}) {
+    my $v = $params{"epochs"};
+    $params_string .= " -epochs $v";
+} else {
+    die "ERROR: -epochs needs to be set";
+}
+# -lambda
+if ($i_gp_lambda) {
+    $params_string .= " -lambda $i_gp_lambda";
+} elsif (exists $params{"lambda"}) {
+    my $v = $params{"lambda"};
+    $params_string .= " -lambda $v";
+} else {
+    die "ERROR: -lambda needs to be set";
+}
+# -bitsize
+if ($i_gp_bitsize) {
+    $params_string .= " -bitsize $i_gp_bitsize";
+} elsif (exists $params{"bitsize"}) {
+    my $v = $params{"bitsize"};
+    $params_string .= " -bitsize $v";
+} else {
+    die "ERROR: -bitsize needs to be set";
+}
+# -abstraction
+if ($i_gp_abstr) {
+    $params_string .= " -bitsize $i_gp_abstr";
+    die "ERROR: -abstraction set with -onlyseq" unless ($model_type eq "structure");
+} elsif (exists $params{"abstraction"}) {
+    my $v = $params{"abstraction"};
+    $params_string .= " -abstraction $v";
+    die "ERROR: -abstraction set with -onlyseq" unless ($model_type eq "structure");
+}
+
+# Distribution parameters.
+my ($distr_my, $distr_sigma, $distr_xi);
+if ($i_distr_my) {
+    $distr_my = $i_distr_my;
+} elsif (exists $params{"gev_my"}) {
+    $distr_my = $params{"gev_my"};
+}
+if ($i_distr_sigma) {
+    $distr_sigma = $i_distr_sigma;
+} elsif (exists $params{"gev_sigma"}) {
+    $distr_sigma = $params{"gev_sigma"};
+}
+if ($i_distr_xi) {
+    $distr_xi = $i_distr_xi;
+} elsif (exists $params{"gev_xi"}) {
+    $distr_xi = $params{"gev_xi"};
+}
+# Average profile extension parameter.
+if (exists $params{"ap_extlr"}) {
+    $ap_extlr = $params{"ap_extlr"};
+}
+
+print STDOUT "model_type:     $model_type\n";
+print STDOUT "ap_extlr:       $ap_extlr\n";
+
+if ($distr_my and $distr_sigma and $distr_xi) {
+    print STDOUT "distr_my:       $distr_my\n";
+    print STDOUT "distr_sigma:    $distr_sigma\n";
+    print STDOUT "distr_xi:       $distr_xi\n";
+}
+print STDOUT "max_merge_dist: $max_merge_dist\n";
+
+# p50 filter score.
+my $p50_sc;
+if (exists $params{"p50_score"}) {
+    $p50_sc = $params{"p50_score"};
+    print STDOUT "p50_score:      $p50_sc\n";
+}
+# p50 p-value.
+my $p50_p;
+if (exists $params{"p50_p_val"}) {
+    $p50_p = $params{"p50_p_val"};
+    print STDOUT "p50_p_val:      $p50_p\n";
+}
+
+
+
+##################################
+# RUN GP PROFILE PREDICTION.
+##################################
+
+# Read in FASTA file headers.
+my @fasta_ids;
+my $headers = qx/grep ">" $i_fasta/;
+while ($headers =~ />(.+?)\n/g) {
+    push(@fasta_ids,$1);
+}
+
+# Run GP profile prediction.
+my $gp_call = "GraphProt.pl -action predict_profile -model $i_model -fasta $i_fasta -prefix $data_id $params_string";
+print STDOUT "GraphProt call: $gp_call\n";
+# &> profile_prediction.log
+qx/$gp_call/;
+
+
+####################################
+# CALCULATE AVERAGE PROFILE.
+####################################
+
+# Calculate .average_profile from GraphProt .profile file.
+# Also add p-value column if distr parameters set.
+my $add_p = 0;
+if ($distr_my and $distr_sigma and $distr_xi) {
+    $add_p = 1;
+}
+
+# Average_profile: 1-based, FASTA headers as IDs, using ap_extlr for averaging scores.
+my $profile = "$data_id.profile";
+my $average_profile = "$data_id.average_profile";
+# Calculate window size.
+my $win = $ap_extlr * 2 + 1;
+
+open (IN, $profile) or die "Cannot open $profile: $!\n";
+open (OUT, '>', $average_profile) or die "Cannot open $average_profile: $!";
+
+# Old ID.
+my $old_id = "-";
+# Current ID.
+my $cur_id = "-";
+# Start position of the window.
+my $pos_inc = 0;
+# Score array.
+my @scores;
+# Input row counter.
+my $c_in = 0;
+# Output row counter.
+my $c_out = 0;
+
+while (<IN>) {
+
+    if ($_ =~ /(.+?)\t\d+?\t(.+?)\n/) {
+
+        $cur_id = $1;
+        my $score = $2;
+        $c_in++;
+
+        # Case: New refseq ID / new paragraph.
+        if ($cur_id ne $old_id) {
+
+            # Print remaining entries at the end of former paragraph.
+            while (scalar(@scores) >= ($ap_extlr + 1)) {
+                # Calculate avg array score.
+                my $mean = array_mean(@scores);
+                $c_out++;
+                $pos_inc++;
+                if ($add_p) {
+                    my $y = exp(-1*(1 + ( ($mean-$distr_my)/$distr_sigma )*$distr_xi)**(-1/$distr_xi));
+                    my $p = sprintf("%.8f", (1-$y));
+                    print OUT "$fasta_ids[$old_id]\t$pos_inc\t$mean\t$p\n";
+                } else {
+                    print OUT "$fasta_ids[$old_id]\t$pos_inc\t$mean\n";
+                }
+                # Remove old score from beginning.
+                shift(@scores);
+            }
+
+            # Reset for new paragraph.
+            $pos_inc = 0;
+            @scores = ();
+            $old_id = $cur_id;
+            # Save first score.
+            push(@scores, $score);
+            next;
+
+        }
+
+        # Push score in array for average calculation.
+        push(@scores, $score);
+
+        # Case: array smaller $win.
+        if (scalar(@scores) < $win) {
+            # Subcase: array more than half size, start with calculation.
+            if (scalar(@scores) >= ($ap_extlr + 1)) {
+                # Calculate avg array score.
+                my $mean = array_mean(@scores);
+                $c_out++;
+                $pos_inc++;
+                if ($add_p) {
+                    my $y = exp(-1*(1 + ( ($mean-$distr_my)/$distr_sigma )*$distr_xi)**(-1/$distr_xi));
+                    my $p = sprintf("%.8f", (1-$y));
+                    print OUT "$fasta_ids[$cur_id]\t$pos_inc\t$mean\t$p\n";
+                } else {
+                    print OUT "$fasta_ids[$cur_id]\t$pos_inc\t$mean\n";
+                }
+            }
+            next;
+        }
+
+        # Case: array has $win size.
+        if (scalar(@scores) == $win) {
+            # Calculate avg array score.
+            my $mean = array_mean(@scores);
+            $c_out++;
+            $pos_inc++;
+            if ($add_p) {
+                my $y = exp(-1*(1 + ( ($mean-$distr_my)/$distr_sigma )*$distr_xi)**(-1/$distr_xi));
+                my $p = sprintf("%.8f", (1-$y));
+                print OUT "$fasta_ids[$cur_id]\t$pos_inc\t$mean\t$p\n";
+            } else {
+                print OUT "$fasta_ids[$cur_id]\t$pos_inc\t$mean\n";
+            }
+            # Remove old score from beginning.
+            shift(@scores);
+            next;
+        }
+    }
+}
+
+# Print remaining entries at the end of last section.
+while (scalar(@scores) >= ($ap_extlr + 1)) {
+    # Calculate avg array score.
+    my $mean = array_mean(@scores);
+    $c_out++;
+    $pos_inc++;
+    if ($add_p) {
+        my $y = exp(-1*(1 + ( ($mean-$distr_my)/$distr_sigma )*$distr_xi)**(-1/$distr_xi));
+        my $p = sprintf("%.8f", (1-$y));
+        print OUT "$fasta_ids[$cur_id]\t$pos_inc\t$mean\t$p\n";
+    } else {
+        print OUT "$fasta_ids[$cur_id]\t$pos_inc\t$mean\n";
+    }
+    # Remove old score from beginning.
+    shift(@scores);
+}
+close IN;
+close OUT;
+
+qx/rm -f $profile/;
+
+
+#########################
+# GET PEAK REGIONS.
+#########################
+
+
+my $p50_peaks_bed_out = $data_id . ".peak_regions_p50.bed";
+my $peaks_bed_out = $data_id . ".peak_regions.bed";
+
+# If p-values were calculated, use set p-value to get peak regions.
+if ($add_p) {
+    extract_peak_regions_from_p_values($average_profile, $peaks_bed_out, $max_merge_dist, $thr_p);
+    # If p50-out set.
+    if ($i_p50_out) {
+        # If p50 p-value present, also get peak regions file for this threshold.
+        if ($p50_p) {
+            extract_peak_regions_from_p_values($average_profile, $p50_peaks_bed_out, $max_merge_dist, $p50_p);
+        } else {
+            qx/touch $p50_peaks_bed_out/;
+        }
+    }
+} else {
+    # If no p-values available, use score threshold for defining peak regions.
+    extract_peak_regions_from_scores($average_profile, $peaks_bed_out, $max_merge_dist, $thr_sc);
+    # If p50-out set.
+    if ($i_p50_out) {
+        # If p50 score present, also get peak regions file for this threshold.
+        if ($p50_sc) {
+            extract_peak_regions_from_scores($average_profile, $p50_peaks_bed_out, $max_merge_dist, $p50_sc);
+        } else {
+            qx/touch $p50_peaks_bed_out/;
+        }
+    }
+}
+
+exit;
+
+
+
+################################################################################
+################################################################################
+# SUBROUTINES.
+################################################################################
+
+
+sub array_mean {
+
+  my $mean = sum(@_)/@_;
+  return sprintf("%.5f", $mean);
+
+}
+
+
+################################################################################
+
+sub extract_peak_regions_from_p_values {
+
+    my ($average_profile, $peak_regions_bed_file, $max_merge_dist, $max_p) = @_;
+
+    my $old_ref = "no";
+    my $in = "N";
+    my $ref_id;
+    my $start;
+    my $end;
+    my $best_p = 1;
+    my $best_sc = -1000;
+    my $region_s;
+    my $region_e;
+    my $zero_pos;
+
+    my $temp_bed_file = "peak_regions.tmp.bed";
+
+    open (IN, $average_profile) or die "Cannot open $average_profile: $!";
+    open (OUT, '>', $temp_bed_file) or die "Cannot open $temp_bed_file: $!";
+
+    while (<IN>) {
+        chomp;
+        my ($ref, $s, $sc, $p) = (split /\t/)[0,1,2,3];
+        # If file has zero-based positions.
+        if ($s == 0) {
+            $zero_pos = 1;
+        }
+        # If positions are one-based, make them zero-based.
+        unless ($zero_pos) {
+            $s -= 1;
+        }
+        # At transcript ends, if in positive region, write and reset.
+        if ($old_ref ne $ref) {
+            if ($in eq "Y") {
+                print OUT "$ref_id\t$region_s\t$region_e\t$end;$best_sc;$best_p\t0\t+\n";
+                $in = "N";
+            }
+        }
+        $old_ref = $ref;
+        # Deal with good p-value regions.
+        if ($p <= $max_p) {
+            # Start of a positive cluster.
+            if ($in eq "N") {
+                $start = $s;
+                $region_s = $s;
+                $region_e = $s + 1;
+                $end = $s + 1;
+                $best_p = $p;
+                $best_sc = $sc;
+                $ref_id = $ref;
+                $in = "Y";
+                next;
+            # Inside a positive cluster.
+            } elsif ($in eq "Y") {
+                if ($p < $best_p) {
+                    $start = $s;
+                    $end = $s + 1;
+                    $best_p = $p;
+                    $best_sc = $sc;
+                    $ref_id = $ref;
+                }
+                $region_e++;
+                next;
+            }
+        } else {
+            # If we were in positive cluster before.
+            if ($in eq "Y") {
+                print OUT "$ref_id\t$region_s\t$region_e\t$end;$best_sc;$best_p\t0\t+\n";
+                $in = "N";
+            }
+        }
+    }
+    # After last line processed.
+    if ($in eq "Y") {
+      print OUT "$ref_id\t$region_s\t$region_e\t$end;$best_sc;$best_p\t0\t+\n";
+      $in = "N";
+    }
+    close IN;
+    close OUT;
+    # If merge distance zero (i.e. end of one block is -1 from start of next block).
+    if ($max_merge_dist == 0) {
+        qx/cat $temp_bed_file > $peak_regions_bed_file/;
+    } else {
+        # Merge nearby regions.
+        open(IN, $temp_bed_file) or die "Cannot open $temp_bed_file: $!";
+        open(OUT, '>', $peak_regions_bed_file) or die "Cannot open $peak_regions_bed_file: $!";
+        # For storing current block stats.
+        my $block_chr = 0;
+        my ($block_s, $block_e, $block_best_pos, $block_best_p, $block_best_sc);
+        while (<IN>) {
+            chomp;
+            my ($chr, $s, $e, $id) = (split /\t/)[0,1,2,3];
+            my ($best_pos, $best_sc, $best_p) = (split /;/, $id);
+            if ($chr eq $block_chr) {
+                # If $block_e, $s within merge merge.
+                if ( ($s - $block_e) <= $max_merge_dist ) {
+                    # Update block stats.
+                    $block_e = $e;
+                    if ($block_best_p > $best_p) {
+                        $block_best_p = $best_p;
+                        $block_best_sc = $best_sc;
+                        $block_best_pos = $best_pos;
+                    }
+                } else {
+                    # If $e outside merge range, print block.
+                    print OUT "$block_chr\t$block_s\t$block_e\t$block_best_pos;$block_best_sc;$block_best_p\t0\t+\n";
+                    # Store new block.
+                    ($block_chr, $block_s, $block_e, $block_best_pos, $block_best_sc, $block_best_p) = ($chr, $s, $e, $best_pos, $best_sc, $best_p);
+                }
+
+            } else {
+                # If new chromosome, print last block, otherwise it is the first block.
+                if ($block_chr) {
+                    print OUT "$block_chr\t$block_s\t$block_e\t$block_best_pos;$block_best_sc;$block_best_p\t0\t+\n";
+                }
+                ($block_chr, $block_s, $block_e, $block_best_pos, $block_best_sc, $block_best_p) = ($chr, $s, $e, $best_pos, $best_sc, $best_p);
+            }
+        }
+        # Print last block.
+        if ($block_chr) {
+            print OUT "$block_chr\t$block_s\t$block_e\t$block_best_pos;$block_best_sc;$block_best_p\t0\t+\n";
+        }
+        close OUT;
+        close IN;
+    }
+    qx/rm -f $temp_bed_file/;
+}
+
+
+################################################################################
+
+sub extract_peak_regions_from_scores {
+
+    my ($average_profile, $peak_regions_bed_file, $max_merge_dist, $min_sc) = @_;
+
+    my $old_ref = "no";
+    my $in = "N";
+    my $ref_id;
+    my $start;
+    my $end;
+    my $best_sc = -1000;
+    my $region_s;
+    my $region_e;
+    my $zero_pos;
+
+    my $temp_bed_file = "peak_regions.tmp.bed";
+
+    open (IN, $average_profile) or die "Cannot open $average_profile: $!";
+    open (OUT, '>', $temp_bed_file) or die "Cannot open $temp_bed_file: $!";
+
+    while (<IN>) {
+        chomp;
+        my ($ref, $s, $sc) = (split /\t/)[0,1,2];
+        # If file has zero-based positions.
+        if ($s == 0) {
+            $zero_pos = 1;
+        }
+        # If positions are one-based, make them zero-based.
+        unless ($zero_pos) {
+            $s -= 1;
+        }
+        # At transcript ends, if in positive region, write and reset.
+        if ($old_ref ne $ref) {
+            if ($in eq "Y") {
+                print OUT "$ref_id\t$region_s\t$region_e\t$end;$best_sc\t0\t+\n";
+                $in = "N";
+            }
+        }
+        $old_ref = $ref;
+        # Deal with positive regions.
+        if ($sc > $min_sc) {
+            # Start of a positive cluster.
+            if ($in eq "N") {
+                $start = $s;
+                $region_s = $s;
+                $region_e = $s + 1;
+                $end = $s + 1;
+                $best_sc = $sc;
+                $ref_id = $ref;
+                $in = "Y";
+                next;
+            # Inside a positive cluster.
+            } elsif ($in eq "Y") {
+                if ($sc > $best_sc) {
+                    $start = $s;
+                    $end = $s + 1;
+                    $best_sc = $sc;
+                    $ref_id = $ref;
+                }
+                $region_e++;
+                next;
+            }
+        } else {
+            # If we were in positive cluster before.
+            if ($in eq "Y") {
+                print OUT "$ref_id\t$region_s\t$region_e\t$end;$best_sc\t0\t+\n";
+                $in = "N";
+            }
+        }
+    }
+    # After last line processed.
+    if ($in eq "Y") {
+      print OUT "$ref_id\t$region_s\t$region_e\t$end;$best_sc\t0\t+\n";
+      $in = "N";
+    }
+    close IN;
+    close OUT;
+    # If merge distance zero (i.e. end of one block is -1 from start of next block).
+    if ($max_merge_dist == 0) {
+        qx/cat $temp_bed_file > $peak_regions_bed_file/;
+    } else {
+        # Merge nearby regions.
+        open(IN, $temp_bed_file) or die "Cannot open $temp_bed_file: $!";
+        open(OUT, '>', $peak_regions_bed_file) or die "Cannot open $peak_regions_bed_file: $!";
+        # For storing current block stats.
+        my $block_chr = 0;
+        my ($block_s, $block_e, $block_best_pos, $block_best_sc);
+        while (<IN>) {
+            chomp;
+            my ($chr, $s, $e, $id) = (split /\t/)[0,1,2,3];
+            my ($best_pos, $best_sc) = (split /;/, $id);
+            if ($chr eq $block_chr) {
+                # If $block_e, $s within merge merge.
+                if ( ($s - $block_e) <= $max_merge_dist ) {
+                    # Update block stats.
+                    $block_e = $e;
+                    if ($block_best_sc < $best_sc) {
+                        $block_best_sc = $best_sc;
+                        $block_best_pos = $best_pos;
+                    }
+                } else {
+                    # If $e outside merge range, print block.
+                    print OUT "$block_chr\t$block_s\t$block_e\t$block_best_pos;$block_best_sc\t0\t+\n";
+                    # Store new block.
+                    ($block_chr, $block_s, $block_e, $block_best_pos, $block_best_sc) = ($chr, $s, $e, $best_pos, $best_sc);
+                }
+
+            } else {
+                # If new chromosome, print last block, otherwise it is the first block.
+                if ($block_chr) {
+                    print OUT "$block_chr\t$block_s\t$block_e\t$block_best_pos;$block_best_sc\t0\t+\n";
+                }
+                ($block_chr, $block_s, $block_e, $block_best_pos, $block_best_sc) = ($chr, $s, $e, $best_pos, $best_sc);
+            }
+
+        }
+        # Print last block.
+        if ($block_chr) {
+            print OUT "$block_chr\t$block_s\t$block_e\t$block_best_pos;$block_best_sc\t0\t+\n";
+        }
+        close OUT;
+        close IN;
+    }
+    qx/rm -f $temp_bed_file/;
+}
+
+
+################################################################################
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GraphProt_predict_profile_test_out1.average_profile	Fri May 25 12:17:44 2018 -0400
@@ -0,0 +1,4532 @@
+ENST00000620398	1	0.88223	0.08228291
+ENST00000620398	2	0.76226	0.09068277
+ENST00000620398	3	0.70164	0.09518219
+ENST00000620398	4	0.04769	0.15586177
+ENST00000620398	5	0.03856	0.15687939
+ENST00000620398	6	0.00464	0.16070393
+ENST00000620398	7	0.17725	0.14195340
+ENST00000620398	8	-0.08646	0.17132122
+ENST00000620398	9	-0.61662	0.24347692
+ENST00000620398	10	-1.24997	0.35314501
+ENST00000620398	11	-1.87072	0.48181594
+ENST00000620398	12	-2.09189	0.53096821
+ENST00000620398	13	-2.27211	0.57158527
+ENST00000620398	14	-2.74742	0.67782581
+ENST00000620398	15	-2.57531	0.63982927
+ENST00000620398	16	-2.63088	0.65218689
+ENST00000620398	17	-2.73678	0.67550300
+ENST00000620398	18	-3.17049	0.76596383
+ENST00000620398	19	-3.16859	0.76559075
+ENST00000620398	20	-2.77097	0.68295264
+ENST00000620398	21	-2.80243	0.68976911
+ENST00000620398	22	-2.42409	0.60590345
+ENST00000620398	23	-2.58751	0.64254848
+ENST00000620398	24	-2.88080	0.70657350
+ENST00000620398	25	-2.32299	0.58308238
+ENST00000620398	26	-1.83523	0.47404309
+ENST00000620398	27	-1.78105	0.46225287
+ENST00000620398	28	-1.55606	0.41445150
+ENST00000620398	29	-0.77370	0.26833083
+ENST00000620398	30	-1.08246	0.32174818
+ENST00000620398	31	-1.67262	0.43896511
+ENST00000620398	32	-1.58116	0.41968105
+ENST00000620398	33	-1.28700	0.36030150
+ENST00000620398	34	-0.87017	0.28437928
+ENST00000620398	35	-0.75886	0.26591482
+ENST00000620398	36	-0.45220	0.21917110
+ENST00000620398	37	-0.19484	0.18461904
+ENST00000620398	38	0.42151	0.11834288
+ENST00000620398	39	0.86845	0.08321446
+ENST00000620398	40	1.05424	0.07135026
+ENST00000620398	41	1.64441	0.04248276
+ENST00000620398	42	2.53989	0.01761073
+ENST00000620398	43	3.74771	0.00432059
+ENST00000620398	44	3.85191	0.00377309
+ENST00000620398	45	4.06806	0.00282450
+ENST00000620398	46	5.04742	0.00064169
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GraphProt_predict_profile_test_out1.peak_regions.bed	Fri May 25 12:17:44 2018 -0400
@@ -0,0 +1,41 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GraphProt_predict_profile_test_out1.peak_regions_p50.bed	Fri May 25 12:17:44 2018 -0400
@@ -0,0 +1,6 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GraphProt_predict_profile_test_out2.average_profile	Fri May 25 12:17:44 2018 -0400
@@ -0,0 +1,4532 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GraphProt_predict_profile_test_out2.peak_regions.bed	Fri May 25 12:17:44 2018 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GraphProt_predict_profile_test_out3.peak_regions.bed	Fri May 25 12:17:44 2018 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GraphProt_predict_profile_test_out4.average_profile	Fri May 25 12:17:44 2018 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GraphProt_predict_profile_test_out4.peak_regions.bed	Fri May 25 12:17:44 2018 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GraphProt_predict_profile_test_out4.peak_regions_p50.bed	Fri May 25 12:17:44 2018 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/structure_test.model	Fri May 25 12:17:44 2018 -0400
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16297:-1.1651790e+02 16298:2.3443216e+02 16299:-1.7045984e+02 16300:1.5198416e+01 16301:-1.9520554e+02 16302:3.9955811e+02 16303:-1.3044139e+02 16304:1.3230621e+02 16305:-1.5916510e+02 16306:-3.9482751e+02 16307:1.1108967e+02 16308:-1.7378566e+02 16309:-2.5667422e+02 16310:-1.0399294e+02 16311:-3.4011646e+01 16312:1.2511178e+02 16313:2.1757544e+02 16314:2.9530016e+01 16315:2.9884661e+01 16316:-5.2185001e+01 16317:-1.3335194e+02 16318:-4.6273777e+01 16319:-6.9023880e+01 16320:-1.4519902e+02 16321:8.7691116e+01 16322:-1.5744434e+02 16323:9.7839882e+01 16324:-4.1649670e+01 16325:2.0033319e+02 16326:5.5544514e+01 16327:7.1370956e+01 16328:1.5337119e+02 16329:6.7460289e+01 16330:-6.6159019e+01 16331:-2.4336459e+02 16332:-3.7881564e+02 16333:9.9232010e+01 16334:-4.3925926e+01 16335:2.2937117e+02 16336:2.3818100e+02 16337:3.7972620e+02 16338:-3.0985400e+02 16339:-1.0420200e+02 16340:-3.1460129e+01 16341:-1.9390654e+02 16342:2.4413045e+02 16343:-1.0303799e+02 16344:-9.4112808e+01 16345:-9.2702232e+01 16346:2.3670500e+02 16347:-1.5132767e+02 16348:3.1461002e+01 16349:-2.5901172e+02 16350:5.3989368e+01 16351:3.5555991e+02 16352:2.4456305e+02 16353:-1.7409081e+02 16354:7.3725153e+02 16355:-4.1369320e+01 16356:6.4980652e+01 16357:-2.8018726e+02 16358:3.3691666e+01 16359:3.0508701e+02 16360:-6.2882713e+01 16361:-2.2321880e+02 16362:-3.9429558e+01 16363:9.6953926e+01 16364:1.2708233e+02 16365:-5.4174554e+02 16366:-1.6106104e+02 16367:-2.3512967e+02 16368:-1.2259144e+02 16369:-7.5829514e+01 16370:1.4410321e+02 16371:2.0485582e+02 16372:4.0015186e+01 16373:3.8507840e+02 16374:4.2588135e+01 16375:-1.4845244e+02 16376:-1.6613632e+02 16377:1.8827328e+02 16378:-3.2113272e+02 16379:8.6524193e+01 16380:-4.6628574e+01 16381:2.9751631e+01 16382:4.3969955e+00 16383:-4.1308667e+02
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/structure_test.params	Fri May 25 12:17:44 2018 -0400
@@ -0,0 +1,6 @@
+epochs: 50
+lambda: 0.0001
+R: 4
+D: 0
+bitsize: 14
+abstraction: 3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.fa	Fri May 25 12:17:44 2018 -0400
@@ -0,0 +1,80 @@
+>ENST00000620398
+ACTCTGGGAGGGCTAAGGAGCCATCATGATCCCTAAGCTGCTTTCCCTCCTCTGTTTCAG
+ACTGTGCGTGGGCCAAGGAGACACAAGGGGAGATGGGTCACTGCCCAAGCCGTCCCTCAG
+TGCCTGGCCCAGCTCGGTGGTCCCTGCCAACAGCAATGTGACGCTGCGATGTTGGACTCC
+TGCCAGAGGTGTGAGCTTTGTTCTCAGGAAGGGAGGAATTATTCTGGAGTCCCCGAAGCC
+CCTTGATTCTACAGAGGGCGCGGCCGAATTTCACCTCAATAATCTAAAAGTCAGAAATGC
+TGGAGAGTACACCTGTGAATACTACAGAAAAGCATCCCCCCACATCCTTTCACAGCGCAG
+TGACGTCCTTCTACTGTTGGTGACAGGACATTTATCTAAACCTTTCCTCCGAACCTACCA
+AAGGGGTACAGTGACCGCAGGTGGAAGGGTGACTCTGCAGTGCCAGAAGCGAGACCAATT
+GTTTGTGCCTATCATGTTCGCTCTACTGAAGGCAGGGACGCCATCACCCATCCAGCTGCA
+GAGTCCAGCGGGGAAGGAGATAGACTTCTCTCTGGTGGACGTGACAGCCGGCGATGCTGG
+GAACTACAGCTGCATGTACTACCAGACAAAGTCTCCCTTCTGGGCCTCAGAACCCAGTGA
+TCAGCTTGAGATATTGGTGACAGTTCCCCCAGGTACCACATCGAGCAACTACTCCCTGGG
+TAACTTCGTACGACTGGGTCTGGCTGCCGTAATTGTGGTTATCATGGGAGCTTTCCTGGT
+GGAGGCCTGGTACAGCCGGAATGTGTCTCCAGGTGAATCAGAGGCCTTCAAACCAGAGTG
+ACTCCATCTTGAACCGGGGCTGGGTAAACTGAGGCTGCAACCTGCTGGACTGCATTC
+>ENST00000550775
+TCATGACTACACAGTTAAGGGTCGTCCATCTGCTTCCCCTTCTCCTAGCCTGCTTTGTGC
+AAACAAGTCCCAAGCAGGAGAAGATGAAGATGGATTGCCACAAAGACGAGAAAGGCACCA
+TCTATGACTATGAGGCCATCGCACTTAATAAGAATGAATATGTTTCCTTCAAGCAGTATG
+TGGGCAAGCACATCCTCTTCGTCAACGTGGCCACCTACTGTGGTCTGACAGCGCAATATC
+CTGAACTAAATGCACTCCAGGAGGAGCTGAAGCCCTATGGTCTAGTTGTGTTGGGCTTTC
+CCTGCAACCAATTTGGAAAGCAAGAACCAGGAGATAACAAAGAGATTCTTCCTGGGCTCA
+AGTATGTCCGTCCAGGGGGAGGATTTGTACCTAGTTTCCAGCTTTTTGAGAAAGGGGATG
+TGAATGGTGAAAAAGAACAGAAAGTCTTCAGTTTCTTGAAGCACTCCTGTCCTCATCCCT
+CTGAGATTTTGGGCACATTCAAATCTATATCCTGGGACCCTGTAAAGGTCCATGACATCC
+GTTGGAACTTTGAAAAGTTCCTGGTGGGGCCTGATGGAATCCCTGTCATGCGCTGGTCCC
+ACCGGGCTACGGTCAGCTCAGTCAAGACAGACATCCTGGCGTACTTGAAGCAATTCAAAA
+CCAAATAGGAAGGTGGAGTTAAGGGCAGGAGCAACCCTACTTCTCACCTAATGACTTGCT
+CTCCCCACCCCTCCAAAAAAAAGGAATACCCATCTTCTCACCACACTCTCTTCCTGCATG
+GGCTCCACCTGAGTAAATCACCGCCACATACTGCCAGAATTCCCACTCTCCACAAACTAG
+ATTTATATTTGGAAGGCTACTGCTCTTTTGCCTCTCAAGAGTATGTGGGTGAAGACTGAA
+ACAAATGGAAACCTAAAATCCCCAGACCTCTGTTACAGGTTGAATCATTCATATCCACCA
+GAGGGAAATCATCCTTCCACGACAATGGTTCAGTCGGCCATCACATCCTGAAGAACATTC
+CTAGACATTCTGACTCTTCCATCTCTCTCTACCCTGGAGGTGTAGAAATAGCAATGGGGT
+CACAGTCACACAATTTAGGTTCCACTTCATAACATTTTTTGTCTCCTAGGACAAACGTGT
+ATCATCAGTTTCCAACTGTTTTGGCTCAGTTTTCATCCATGACACCTCCCCCTACCAGCC
+ATTCTCCTGTGGGAGCAAGAACATTGCTTCAAAAGAAGAGAGGGCATCTCCATGCTTGTG
+GGACCCAAAACCTATCTCTGGCCCTACAAAAGTTTTCCTAATTGTCTGATCTTTAGTGCA
+TTCAGGTTATGGCACCTGGAGAGGAATGCCCTTTATCTTTTGAAGGATGGGATTTCCCAT
+CTCAACCCTGGATTCCTCACCTTCAGAACGAGCCCTGCCACTGTCTCCAATAAAATGTTT
+TCTGCAGCATCG
+>ENST00000622300
+TAGTTTCCTGTTTCCGGCTTCGCTTCGGCCCACCCCCACGTCCACCCCGAATCCCTGCTT
+AAAGGCCTTGCTTTCTTGTCTAACGCCGCAACCAGTCCTCTGAGTTGCCAACGTCTTTCT
+TCTTGTCTCGACGCCCCGTCGTCCGGCCACAGCGATTCTCTGCTTAGCAGGATCGGTCCA
+CAGCGGGACGTGAGTCCCTTTCCTCCTCGCGGCTTACCGCCTCTCTCCGCCTAGTGCCAG
+GTGCTAATAAAGTTGTTGTTTCAAATGCGGCCAGGAACATCGCGAGCGGGGACCAATCAG
+AGAGTAGCTTTGCCTCTATAACGGCGCGAGAGTGAGACGTCATCGGTGAGCGACTAACGC
+TAGAAACAGTGGTGCGCGGAGAGGAGAGGCCTCGGGATGTCTCTGGCAGATGAGCTCTTA
+GCTGATCTCGAAGAGGCAGCAGAAGAGGAGGAAGGAGGAAGCTATGGGGAGGAAGAAGAG
+GAGCCAGCGATCGAGGATGTGCAGGAGGAGACACAGCTGGATCTTTCCGGGGATTCAGTC
+AAGACCATCGCCAAGCTATGGGATAGTAAGATGTTTGCTGAGATTATGATGAAGATTGAG
+GAGTATATCAGCAAGCAAGCCAAAGCTTCAGAAGTGATGGGACCAGTGGAGGCCGCGCCT
+GAATACCGCGTCATCGTGGATGCCAACAACCTGACCGTGGAGATCGAAAACGAGCTGAAC
+ATCATCCATAAGTTCATCCGGGATAAGTACTCAAAGAGATTCCCTGAACTGGAGTCCTTG
+GTCCCCAATGCACTGGATTACATCCGCACGGTCAAGGAGCTGGGCAACAGCCTGGACAAG
+TGCAAGAACAATGAGAACCTGCAGCAGATCCTCACCAATGCCACCATCATGGTCGTCAGC
+GTCACCGCCTCCACCACCCAGGGGCAGCAGCTGTCGGAGGAGGAGCTGGAGCGGCTGGAG
+GAGGCCTGCGACATGGCGCTGGAGCTGAACGCCTCCAAGCACCGCATCTACGAGTATGTG
+GAGTCCCGGATGTCCTTCATCGCACCCAACCTGTCCATCATTATCGGGGCATCCACGGCC
+GCCAAGATCATGGGTGTGGCCGGCGGCCTGACCAACCTCTCCAAGATGCCCGCCTGCAAC
+ATCATGCTGCTCGGGGCCCAGCGCAAGACGCTGTCGGGCTTCTCGTCTACCTCAGTGCTG
+CCCCACACCGGCTACATCTACCACAGTGACATCGTGCAGTCCCTGCCACCGGATCTGCGG
+CGGAAAGCGGCCCGGCTGGTGGCCGCCAAGTGCACACTGGCAGCCCGTGTGGACAGTTTC
+CACGAGAGCACAGAAGGGAAGGTGGGCTACGAACTGAAGGATGAGATCGAGCGCAAATTC
+GACAAGTGGCAGGAGCCGCCGCCTGTGAAGCAGGTGAAGCCGCTGCCTGCGCCCCTGGAT
+GGACAGCGGAAGAAGCGAGGCGGCCGCAGGTACCGCAAGATGAAGGAGCGGCTGGGGCTG
+ACGGAGATCCGGAAGCAGGCCAACCGTATGAGCTTCGGAGAGATCGAGGAGGACGCCTAC
+CAGGAGGACCTGGGATTCAGCCTGGGCCACCTGGGCAAGTCGGGCAGTGGGCGTGTGCGG
+CAGACACAGGTAAACGAGGCCACCAAGGCCAGGATCTCCAAGACGCTGCAGCGGACCCTG
+CAGAAGCAGAGCGTCGTATATGGCGGGAAGTCCACCATCCGCGACCGCTCCTCGGGCACG
+GCCTCCAGCGTGGCCTTCACCCCACTCCAGGGCCTGGAGATTGTGAACCCACAGGCGGCA
+GAGAAGAAGGTGGCTGAGGCCAACCAGAAGTATTTCTCCAGCATGGCTGAGTTCCTCAAG
+GTCAAGGGCGAGAAGAGTGGCCTTATGTCCACCTGAATGACTGCGTGTGTCCAAGGTGGC
+TTCCCACTGAAGGGACACAGAGGTCCAGTCCTTCTGAAGGGCTAGGATCGGGTTCTGGCA
+GGGAGAACCTGCCCTGCCACTGGCCCCATTGCTGGGACTGCCCAGGGAGGAGGCCTTGGA
+AGAGTCCGGCCTGGCCTCCCCCAGGACCGAGATCACCGCCCAGTATGGGCTAGAGCAGGT
+CTTCATCATGCCTTGTCTTTTTTAACTGAGAAAGGAGATTTTTTGAAAAGAGTACAATTA
+AAAGGACATTGTCAAGATCTGTC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.model	Fri May 25 12:17:44 2018 -0400
@@ -0,0 +1,3 @@
+bias 0.0990594
+wscale 0.000419047
+w  3:-2.6323795e+02 7:-1.5498299e+02 39:3.2710247e+01 90:-9.6892609e+01 92:-6.2059918e+02 102:2.7361217e+01 108:-1.8683072e+02 111:9.2224388e+01 121:4.4261597e+01 127:-2.9686353e+02 148:-2.4798018e+02 155:1.0929895e+02 212:-3.0733829e+02 217:-3.6330551e+02 219:4.3392648e+02 220:-4.3969490e+01 223:-1.2370902e+03 235:-2.5857092e+02 286:-4.4877792e+01 306:-3.2496075e+02 308:-2.0045505e+02 375:-2.3125467e+02 396:-6.7614136e+02 400:1.1828072e+02 408:4.3950644e+00 414:2.0196147e+03 421:-3.3002304e+01 431:-4.0940579e+02 432:-5.0269598e+02 434:-1.4379294e+02 469:-4.2782242e+02 486:1.9116473e+02 492:-1.6351070e+02 496:-3.4013925e+02 502:1.6938168e+02 524:9.0154556e+01 541:-3.2447818e+02 542:-3.8114508e+02 546:1.8973650e+02 605:2.8628244e+02 609:-2.4498466e+02 615:4.9888785e+02 617:-7.0967567e+01 626:-7.4189880e+01 635:-4.8810840e+02 638:-3.8662479e+02 703:-6.1965290e+01 718:-2.5008917e+02 752:4.7394373e+02 778:3.6091281e+02 780:-7.1200995e+02 800:-7.9289467e+01 802:1.0135097e+03 805:6.8798347e+01 862:2.0908080e+02 890:-1.3723445e+03 892:-3.4540729e+02 902:3.8364291e+02 904:7.1494586e+02 919:-3.6798563e+02 921:-4.8533035e+02 932:-4.9616232e+00 934:7.6746864e+01 947:-3.0528450e+01 962:2.0308733e+02 982:-8.8417072e+02 1010:2.7702023e+02 1012:-6.7064438e+01 1042:1.5783516e+03 1043:7.6573596e+02 1052:-3.1112509e+02 1053:5.5852393e+02 1057:-1.7441716e+02 1061:-8.1911877e+02 1072:-8.0545190e+02 1097:3.0343884e+01 1101:-9.3145149e+01 1146:-1.4208945e+02 1170:-1.5208934e+02 1185:-5.1659613e+02 1188:7.9852242e+00 1191:2.7740912e+02 1226:-6.5887558e+01 1233:-7.5957849e+02 1240:6.7184441e+01 1268:-1.6966364e+01 1270:7.1152705e-01 1278:-2.6539410e+02 1281:-5.3602417e+02 1291:-7.0432999e+01 1293:-3.1627484e+02 1324:5.9499172e+01 1327:-2.5026250e+02 1338:-4.3128751e+02 1341:1.2852692e+02 1400:-1.8205722e+02 1445:8.7823769e+01 1448:-2.2847488e+02 1477:-1.8806841e+01 1478:-2.2553993e+02 1519:-4.3346246e+02 1521:1.9021851e+03 1525:9.8176186e+01 1532:1.8415245e+03 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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.params	Fri May 25 12:17:44 2018 -0400
@@ -0,0 +1,19 @@
+epochs: 20
+lambda: 0.001
+R: 1
+D: 4
+bitsize: 14
+model_type: sequence
+#ADDITIONAL MODEL PARAMETERS
+ap_extlr: 5
+gev_my: -2.5408
+gev_sigma: 1.6444
+gev_xi: -0.1383
+p50_score: 6.51534
+p50_p_val: 0.0009059744
+# ADDITIONAL MODEL INFO
+organism: hsa
+rbp_ens_gene_id: ENSG00000011304
+rbp_gene_name: PTBP1
+clip_method: eCLIP
+pubmed_id: 27018577