Mercurial > repos > iuc > reprof

changeset 0:7c33ed152672 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reprof commit cc30e84dcc309a93f49f75250aa3344f926cee5e-dirty
author iuc
date Mon, 30 Nov 2015 20:10:58 -0500
parents
children 141da185be70
files macros.xml reprof.py reprof.xml test-data/P10.wig test-data/PACC.wig test-data/PREL.wig test-data/RI_A.wig test-data/RI_S.wig test-data/pE.wig test-data/pH.wig test-data/pL.wig test-data/secondary_structure.gff3 test-data/solvent_accessibility.gff3 test-data/test.fa test-data/test.fa.reprof tool_dependencies.xml
diffstat 16 files changed, 1637 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Nov 30 20:10:58 2015 -0500
@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+<macros>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="2.2.0">fann</requirement>
+      <requirement type="package" version="0.10">perl_ai_fann</requirement>
+      <requirement type="package" version="1.0.1">reprof</requirement>
+      <yield/>
+    </requirements>
+  </xml>
+  <token name="@WRAPPER_VERSION@">1.0.1</token>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reprof.py	Mon Nov 30 20:10:58 2015 -0500
@@ -0,0 +1,134 @@
+#!/usr/bin/env python
+import re
+import os
+import argparse
+import subprocess
+import tempfile
+from Bio import SeqIO
+from BCBio import GFF
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+from Bio.SeqFeature import SeqFeature, FeatureLocation
+
+def run_reprof(query_path, modeldir):
+    outtmp = tempfile.NamedTemporaryFile(delete=False)
+    cmd = [
+        './reprof/scripts/reprof',
+        '-i', query_path,
+        '--modeldir=%s' % modeldir,
+        '-o', outtmp.name
+    ]
+    subprocess.check_call(cmd)
+    outtmp.seek(0)
+    data = outtmp.read()
+    outtmp.close()
+    os.unlink(outtmp.name)
+    return data
+
+def process_reprof_report(data):
+    KEYS = ['idx', 'AA', 'PHEL', 'RI_S', 'pH', 'pE', 'pL', 'PACC', 'PREL', 'P10', 'RI_A', 'Pbe', 'Pbie']
+    data_tracks = {k: [] for k in KEYS}
+
+    for line in data.split('\n'):
+        if line.startswith('#') or line.startswith('No') or len(line.strip()) == 0:
+            continue
+
+        for idx, (key, value) in enumerate(zip(KEYS, line.strip().split('\t'))):
+            # numerical columns
+            if idx not in (1, 2, 11, 12):
+                value = int(value)
+
+            data_tracks[key].append(value)
+    return data_tracks
+
+def storeWigData(idx, data, id, path):
+    with open(path, 'a') as handle:
+        handle.write('variableStep chrom=%s\n' % id)
+        for (pos, val) in zip(idx, data):
+            handle.write('%s %s\n' % (pos, val))
+
+def storeGff3Data(path, id, positions, values, decodeMap):
+    merged = ''.join(values)
+    # http://stackoverflow.com/a/19683549
+    regions = [(x[0][0].upper(), len(x[0])) for x in re.findall('((.)(\\2*))', merged)]
+
+    location = 1
+
+    rec = SeqRecord(Seq("ACTG"), id=id)
+    for (region_char, region_length) in regions:
+        # If we don't wish to decode this region, skip it.
+        if region_char not in decodeMap:
+            location += region_length
+            continue
+
+        region_info = decodeMap[region_char]
+        # Create a feature representing this region
+        region_feat = SeqFeature(
+            FeatureLocation(location - 1, location - 1 + region_length),
+            type=region_info['type'], strand=0,
+            qualifiers={k: v for (k, v) in region_info.iteritems() if k != 'type'}
+        )
+        # Update our start location
+        location += region_length
+        rec.features.append(region_feat)
+
+    with open(path, 'a') as handle:
+        GFF.write([rec], handle)
+
+def main(fasta, modeldir):
+    for record in SeqIO.parse(fasta, 'fasta'):
+        tmp = tempfile.NamedTemporaryFile(delete=False)
+        SeqIO.write([record], tmp, 'fasta')
+        tmp.close()
+
+        # Run reprof
+        data = process_reprof_report(run_reprof(tmp.name, modeldir))
+        for col in ('RI_S', 'P10', 'RI_A', 'PACC', 'PREL', 'pH', 'pE', 'pL'):
+            storeWigData(data['idx'], data[col], record.id, col + '.wig')
+
+        storeGff3Data(
+            'secondary_structure.gff3', record.id, data['idx'], data['PHEL'],
+            {
+                'H': {
+                    'type': 'peptide_helix',
+                    'label': ['Helix'],
+                    'evidence': ['ECO:0000255']
+                },
+                'E': {
+                    'type': 'beta_strand',
+                    'label': ['Extended/Sheet'],
+                    'evidence': ['ECO:0000255']
+                },
+                'L': {
+                    'type': 'loop',
+                    'label': ['Loop'],
+                    'evidence': ['ECO:0000255']
+                }
+            }
+        )
+
+        storeGff3Data(
+            'solvent_accessibility.gff3', record.id, data['idx'], data['Pbe'],
+            {
+                'B': {
+                    'type': 'experimental_result_region',
+                    'label': ['Buried'],
+                    'evidence': ['ECO:0000255']
+                },
+                'E': {
+                    'type': 'experimental_result_region',
+                    'label': ['Exposed'],
+                    'evidence': ['ECO:0000255']
+                },
+            }
+        )
+
+
+if __name__ == '__main__':
+    # Grab all of the filters from our plugin loader
+    parser = argparse.ArgumentParser(description='Wrapper for reprof')
+    parser.add_argument('fasta', type=file, help='Fasta Input')
+    parser.add_argument('modeldir')
+    args = parser.parse_args()
+
+    main(**vars(args))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reprof.xml	Mon Nov 30 20:10:58 2015 -0500
@@ -0,0 +1,62 @@
+<?xml version="1.0"?>
+<tool id="rost_reprof" name="reprof" version="@WRAPPER_VERSION@">
+  <description>protein secondary structure and accessibility prediction</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="aggressive"><![CDATA[
+      ##if str($query.ext) == 'pssm':
+      ##end if
+
+      ln -s $query query.fa;
+      python $__tool_directory__/reprof.py query.fa $REPROF_MODEL_DIR
+]]></command>
+  <inputs>
+      <param name="query" label="Protein sequences" type="data" format="fasta" />
+  </inputs>
+  <outputs>
+      <data format="gff3" name="secondary_structure" from_work_dir="secondary_structure.gff3" label="Secondary Structure of ${on_string}"/>
+      <data format="wig" name="pE" from_work_dir="pE.wig" label="Probability of Extended/Sheet (${on_string})"/>
+      <data format="wig" name="pH" from_work_dir="pH.wig" label="Probability of Helix (${on_string})" />
+      <data format="wig" name="pL" from_work_dir="pL.wig" label="Probability of Loop (${on_string})" />
+      <data format="wig" name="RI_S" from_work_dir="RI_S.wig" label="Secondary Structure Reliability Index (${on_string})"/>
+
+      <data format="gff3" name="solvent_accessibility" from_work_dir="solvent_accessibility.gff3" label="Solvent Accessibile Regions of ${on_string}" />
+      <data format="wig" name="PACC" from_work_dir="PACC.wig" label="Absolute Solvent Accessibility of ${on_string}"/>
+      <data format="wig" name="PREL" from_work_dir="PREL.wig" label="Relative Solvent Accessibility of ${on_string}"/>
+      <data format="wig" name="P10" from_work_dir="P10.wig" label="Relative Solvent Accessibility (0-9) of ${on_string}"/>
+      <data format="wig" name="RI_A" from_work_dir="RI_A.wig" label="Solvent Accessibility Reliability Index (${on_string})"/>
+  </outputs>
+  <tests>
+      <test>
+          <param name="query" value="test.fa" />
+
+          <output name="secondary_structure" file="secondary_structure.gff3" />
+          <output name="solvent_accessibility" file="solvent_accessibility.gff3" />
+          <output name="pE" file="pE.wig" />
+          <output name="pH" file="pH.wig" />
+          <output name="pL" file="pL.wig" />
+          <output name="RI_S" file="RI_S.wig" />
+          <output name="PACC" file="PACC.wig" />
+          <output name="PREL" file="PREL.wig" />
+          <output name="P10" file="P10.wig" />
+          <output name="RI_A" file="RI_A.wig" />
+      </test>
+  </tests>
+  <help><![CDATA[
+reprof
+======
+
+Reprof is a protein secondary structure and accessibility predictor from the
+Rost Lab. Prediction is done from protein sequences.
+
+Three states of secondary structure are predicted: helix (H; includes alpha-,
+pi- and 3_10-helix), (beta-)strand (E = extended strand in beta-sheet
+conformation of at least two residues length) and loop (L).
+      ]]></help>
+  <citations>
+    <citation type="doi">10.1186/1471-2105-10-S13-O3</citation>
+    <citation type="doi">10.1002/pro.5560050824View</citation>
+  </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/P10.wig	Mon Nov 30 20:10:58 2015 -0500
@@ -0,0 +1,158 @@
+variableStep chrom=test
+1 9
+2 8
+3 8
+4 7
+5 8
+6 7
+7 0
+8 0
+9 0
+10 0
+11 0
+12 0
+13 0
+14 0
+15 7
+16 7
+17 0
+18 5
+19 8
+20 8
+21 4
+22 7
+23 8
+24 9
+25 7
+26 6
+27 4
+28 7
+29 7
+30 0
+31 6
+32 7
+33 7
+34 3
+35 8
+36 7
+37 0
+38 7
+39 7
+40 8
+41 0
+42 7
+43 7
+44 4
+45 7
+46 8
+47 7
+48 4
+49 8
+50 7
+51 5
+52 7
+53 7
+54 7
+55 0
+56 7
+57 7
+58 7
+59 7
+60 7
+61 8
+62 8
+63 7
+64 7
+65 0
+66 8
+67 7
+68 7
+69 7
+70 7
+71 9
+72 7
+73 7
+74 7
+75 8
+76 7
+77 7
+78 9
+variableStep chrom=test2
+1 9
+2 8
+3 8
+4 7
+5 7
+6 8
+7 7
+8 7
+9 0
+10 7
+11 7
+12 8
+13 0
+14 7
+15 7
+16 4
+17 7
+18 8
+19 7
+20 4
+21 8
+22 7
+23 0
+24 7
+25 7
+26 7
+27 0
+28 7
+29 7
+30 7
+31 8
+32 7
+33 8
+34 8
+35 7
+36 7
+37 0
+38 8
+39 7
+40 7
+41 2
+42 8
+43 9
+44 7
+45 7
+46 7
+47 7
+48 4
+49 6
+50 8
+51 0
+52 0
+53 0
+54 0
+55 0
+56 0
+57 0
+58 0
+59 8
+60 7
+61 7
+62 0
+63 5
+64 7
+65 8
+66 4
+67 7
+68 7
+69 9
+70 7
+71 6
+72 4
+73 7
+74 7
+75 8
+76 6
+77 9
+78 9
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/PACC.wig	Mon Nov 30 20:10:58 2015 -0500
@@ -0,0 +1,158 @@
+variableStep chrom=test
+1 169
+2 147
+3 76
+4 79
+5 147
+6 91
+7 0
+8 0
+9 0
+10 0
+11 0
+12 0
+13 0
+14 0
+15 72
+16 79
+17 0
+18 49
+19 76
+20 60
+21 27
+22 72
+23 93
+24 141
+25 59
+26 86
+27 33
+28 91
+29 110
+30 0
+31 54
+32 72
+33 91
+34 17
+35 142
+36 79
+37 0
+38 87
+39 59
+40 147
+41 0
+42 91
+43 110
+44 32
+45 72
+46 113
+47 91
+48 28
+49 113
+50 59
+51 56
+52 138
+53 72
+54 91
+55 0
+56 110
+57 59
+58 59
+59 114
+60 91
+61 117
+62 76
+63 59
+64 138
+65 0
+66 113
+67 110
+68 138
+69 91
+70 91
+71 141
+72 105
+73 59
+74 79
+75 147
+76 124
+77 138
+78 184
+variableStep chrom=test2
+1 169
+2 147
+3 76
+4 79
+5 114
+6 102
+7 110
+8 79
+9 0
+10 87
+11 59
+12 147
+13 0
+14 91
+15 110
+16 32
+17 72
+18 113
+19 91
+20 28
+21 113
+22 59
+23 0
+24 138
+25 72
+26 91
+27 0
+28 110
+29 59
+30 59
+31 147
+32 91
+33 117
+34 76
+35 59
+36 138
+37 0
+38 113
+39 110
+40 138
+41 9
+42 117
+43 141
+44 105
+45 59
+46 79
+47 114
+48 44
+49 104
+50 147
+51 0
+52 0
+53 0
+54 0
+55 0
+56 0
+57 0
+58 0
+59 60
+60 72
+61 79
+62 0
+63 49
+64 59
+65 60
+66 27
+67 72
+68 72
+69 141
+70 59
+71 86
+72 33
+73 91
+74 110
+75 118
+76 54
+77 117
+78 146
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/PREL.wig	Mon Nov 30 20:10:58 2015 -0500
@@ -0,0 +1,158 @@
+variableStep chrom=test
+1 90
+2 72
+3 72
+4 56
+5 72
+6 56
+7 0
+8 0
+9 0
+10 0
+11 0
+12 0
+13 0
+14 0
+15 56
+16 56
+17 0
+18 30
+19 72
+20 72
+21 20
+22 56
+23 72
+24 90
+25 56
+26 42
+27 20
+28 56
+29 56
+30 0
+31 42
+32 56
+33 56
+34 12
+35 72
+36 56
+37 0
+38 56
+39 56
+40 72
+41 0
+42 56
+43 56
+44 20
+45 56
+46 72
+47 56
+48 20
+49 72
+50 56
+51 30
+52 56
+53 56
+54 56
+55 0
+56 56
+57 56
+58 56
+59 56
+60 56
+61 72
+62 72
+63 56
+64 56
+65 0
+66 72
+67 56
+68 56
+69 56
+70 56
+71 90
+72 56
+73 56
+74 56
+75 72
+76 56
+77 56
+78 90
+variableStep chrom=test2
+1 90
+2 72
+3 72
+4 56
+5 56
+6 72
+7 56
+8 56
+9 0
+10 56
+11 56
+12 72
+13 0
+14 56
+15 56
+16 20
+17 56
+18 72
+19 56
+20 20
+21 72
+22 56
+23 0
+24 56
+25 56
+26 56
+27 0
+28 56
+29 56
+30 56
+31 72
+32 56
+33 72
+34 72
+35 56
+36 56
+37 0
+38 72
+39 56
+40 56
+41 6
+42 72
+43 90
+44 56
+45 56
+46 56
+47 56
+48 20
+49 42
+50 72
+51 0
+52 0
+53 0
+54 0
+55 0
+56 0
+57 0
+58 0
+59 72
+60 56
+61 56
+62 0
+63 30
+64 56
+65 72
+66 20
+67 56
+68 56
+69 90
+70 56
+71 42
+72 20
+73 56
+74 56
+75 72
+76 42
+77 90
+78 90
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RI_A.wig	Mon Nov 30 20:10:58 2015 -0500
@@ -0,0 +1,158 @@
+variableStep chrom=test
+1 3
+2 0
+3 0
+4 0
+5 0
+6 0
+7 0
+8 0
+9 1
+10 3
+11 0
+12 0
+13 0
+14 0
+15 0
+16 0
+17 1
+18 0
+19 0
+20 0
+21 0
+22 0
+23 0
+24 0
+25 0
+26 0
+27 0
+28 1
+29 0
+30 0
+31 0
+32 0
+33 0
+34 0
+35 0
+36 0
+37 0
+38 0
+39 0
+40 0
+41 0
+42 0
+43 0
+44 0
+45 0
+46 0
+47 0
+48 0
+49 0
+50 0
+51 0
+52 0
+53 0
+54 0
+55 0
+56 1
+57 1
+58 0
+59 0
+60 0
+61 0
+62 0
+63 0
+64 1
+65 0
+66 0
+67 1
+68 1
+69 0
+70 0
+71 0
+72 0
+73 0
+74 0
+75 1
+76 0
+77 0
+78 5
+variableStep chrom=test2
+1 3
+2 0
+3 0
+4 0
+5 0
+6 0
+7 1
+8 1
+9 0
+10 0
+11 0
+12 0
+13 0
+14 0
+15 0
+16 0
+17 0
+18 0
+19 0
+20 0
+21 0
+22 0
+23 0
+24 0
+25 0
+26 0
+27 0
+28 0
+29 1
+30 0
+31 0
+32 0
+33 1
+34 0
+35 0
+36 1
+37 0
+38 0
+39 1
+40 0
+41 0
+42 0
+43 0
+44 0
+45 0
+46 0
+47 0
+48 0
+49 0
+50 0
+51 0
+52 1
+53 0
+54 0
+55 3
+56 0
+57 0
+58 1
+59 0
+60 0
+61 0
+62 1
+63 0
+64 0
+65 0
+66 0
+67 0
+68 0
+69 0
+70 0
+71 0
+72 0
+73 1
+74 0
+75 0
+76 0
+77 0
+78 5
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RI_S.wig	Mon Nov 30 20:10:58 2015 -0500
@@ -0,0 +1,158 @@
+variableStep chrom=test
+1 9
+2 7
+3 1
+4 1
+5 4
+6 3
+7 3
+8 5
+9 6
+10 6
+11 6
+12 6
+13 6
+14 5
+15 6
+16 7
+17 7
+18 7
+19 3
+20 1
+21 6
+22 7
+23 6
+24 1
+25 0
+26 3
+27 6
+28 7
+29 7
+30 7
+31 6
+32 7
+33 6
+34 8
+35 8
+36 8
+37 8
+38 8
+39 8
+40 8
+41 8
+42 8
+43 7
+44 6
+45 5
+46 5
+47 6
+48 8
+49 8
+50 8
+51 7
+52 7
+53 6
+54 6
+55 8
+56 8
+57 8
+58 7
+59 8
+60 7
+61 8
+62 9
+63 9
+64 8
+65 8
+66 8
+67 8
+68 8
+69 8
+70 8
+71 8
+72 9
+73 8
+74 8
+75 7
+76 5
+77 3
+78 8
+variableStep chrom=test2
+1 9
+2 8
+3 3
+4 1
+5 4
+6 5
+7 6
+8 5
+9 7
+10 7
+11 8
+12 8
+13 8
+14 8
+15 7
+16 7
+17 6
+18 7
+19 7
+20 8
+21 8
+22 8
+23 7
+24 7
+25 5
+26 6
+27 8
+28 8
+29 8
+30 8
+31 8
+32 7
+33 8
+34 9
+35 9
+36 8
+37 8
+38 8
+39 8
+40 7
+41 8
+42 8
+43 8
+44 8
+45 8
+46 8
+47 8
+48 7
+49 7
+50 7
+51 7
+52 7
+53 7
+54 6
+55 6
+56 7
+57 7
+58 7
+59 6
+60 7
+61 7
+62 8
+63 7
+64 4
+65 0
+66 4
+67 6
+68 4
+69 0
+70 0
+71 3
+72 6
+73 6
+74 6
+75 4
+76 1
+77 6
+78 9
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pE.wig	Mon Nov 30 20:10:58 2015 -0500
@@ -0,0 +1,158 @@
+variableStep chrom=test
+1 2
+2 6
+3 10
+4 19
+5 18
+6 25
+7 23
+8 14
+9 9
+10 9
+11 12
+12 13
+13 8
+14 3
+15 4
+16 7
+17 8
+18 5
+19 4
+20 4
+21 2
+22 3
+23 3
+24 3
+25 3
+26 7
+27 4
+28 2
+29 2
+30 2
+31 1
+32 0
+33 0
+34 1
+35 1
+36 1
+37 1
+38 1
+39 1
+40 1
+41 1
+42 1
+43 1
+44 1
+45 1
+46 0
+47 0
+48 1
+49 1
+50 1
+51 1
+52 1
+53 1
+54 1
+55 1
+56 1
+57 1
+58 1
+59 1
+60 0
+61 1
+62 1
+63 1
+64 1
+65 1
+66 1
+67 1
+68 1
+69 1
+70 1
+71 1
+72 1
+73 1
+74 2
+75 2
+76 2
+77 1
+78 0
+variableStep chrom=test2
+1 2
+2 4
+3 10
+4 18
+5 20
+6 17
+7 13
+8 8
+9 4
+10 3
+11 2
+12 2
+13 1
+14 1
+15 1
+16 1
+17 1
+18 0
+19 0
+20 1
+21 1
+22 1
+23 1
+24 1
+25 1
+26 0
+27 1
+28 1
+29 1
+30 1
+31 1
+32 0
+33 1
+34 1
+35 1
+36 1
+37 1
+38 1
+39 1
+40 1
+41 1
+42 1
+43 1
+44 1
+45 1
+46 1
+47 1
+48 1
+49 1
+50 1
+51 1
+52 2
+53 2
+54 1
+55 2
+56 6
+57 7
+58 4
+59 2
+60 2
+61 4
+62 5
+63 4
+64 3
+65 3
+66 3
+67 3
+68 4
+69 5
+70 6
+71 13
+72 9
+73 7
+74 6
+75 5
+76 3
+77 1
+78 0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pH.wig	Mon Nov 30 20:10:58 2015 -0500
@@ -0,0 +1,158 @@
+variableStep chrom=test
+1 1
+2 8
+3 37
+4 48
+5 63
+6 61
+7 60
+8 70
+9 76
+10 79
+11 80
+12 80
+13 76
+14 76
+15 81
+16 82
+17 85
+18 84
+19 67
+20 40
+21 18
+22 11
+23 18
+24 43
+25 48
+26 65
+27 82
+28 86
+29 88
+30 86
+31 82
+32 84
+33 84
+34 93
+35 93
+36 92
+37 92
+38 92
+39 93
+40 92
+41 93
+42 90
+43 87
+44 81
+45 76
+46 79
+47 80
+48 90
+49 89
+50 92
+51 86
+52 85
+53 79
+54 80
+55 89
+56 91
+57 89
+58 89
+59 90
+60 87
+61 92
+62 95
+63 95
+64 93
+65 92
+66 91
+67 93
+68 90
+69 94
+70 94
+71 94
+72 94
+73 90
+74 89
+75 87
+76 74
+77 33
+78 4
+variableStep chrom=test2
+1 1
+2 5
+3 25
+4 33
+5 62
+6 70
+7 75
+8 75
+9 85
+10 87
+11 91
+12 91
+13 92
+14 90
+15 88
+16 84
+17 83
+18 84
+19 86
+20 91
+21 90
+22 92
+23 86
+24 85
+25 79
+26 79
+27 89
+28 91
+29 90
+30 89
+31 90
+32 86
+33 92
+34 95
+35 94
+36 93
+37 91
+38 90
+39 91
+40 86
+41 90
+42 90
+43 91
+44 93
+45 90
+46 92
+47 91
+48 88
+49 88
+50 88
+51 88
+52 87
+53 86
+54 82
+55 81
+56 84
+57 87
+58 83
+59 82
+60 84
+61 85
+62 87
+63 86
+64 71
+65 46
+66 23
+67 16
+68 25
+69 48
+70 47
+71 61
+72 76
+73 77
+74 78
+75 68
+76 39
+77 16
+78 3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pL.wig	Mon Nov 30 20:10:58 2015 -0500
@@ -0,0 +1,158 @@
+variableStep chrom=test
+1 96
+2 85
+3 52
+4 32
+5 17
+6 13
+7 15
+8 15
+9 14
+10 11
+11 7
+12 6
+13 14
+14 19
+15 14
+16 9
+17 6
+18 9
+19 28
+20 54
+21 79
+22 85
+23 78
+24 53
+25 47
+26 27
+27 13
+28 11
+29 8
+30 11
+31 16
+32 14
+33 14
+34 5
+35 5
+36 6
+37 5
+38 6
+39 5
+40 6
+41 5
+42 8
+43 10
+44 16
+45 22
+46 20
+47 18
+48 7
+49 9
+50 6
+51 12
+52 13
+53 18
+54 18
+55 8
+56 6
+57 8
+58 9
+59 8
+60 11
+61 6
+62 3
+63 3
+64 5
+65 6
+66 7
+67 5
+68 7
+69 4
+70 4
+71 4
+72 4
+73 7
+74 8
+75 10
+76 22
+77 64
+78 94
+variableStep chrom=test2
+1 96
+2 89
+3 63
+4 48
+5 17
+6 12
+7 11
+8 16
+9 9
+10 9
+11 6
+12 6
+13 5
+14 7
+15 9
+16 13
+17 15
+18 14
+19 12
+20 6
+21 8
+22 6
+23 12
+24 12
+25 19
+26 19
+27 8
+28 6
+29 7
+30 8
+31 8
+32 12
+33 6
+34 3
+35 3
+36 5
+37 7
+38 8
+39 7
+40 12
+41 8
+42 8
+43 7
+44 4
+45 7
+46 6
+47 6
+48 9
+49 9
+50 9
+51 9
+52 9
+53 10
+54 15
+55 15
+56 9
+57 5
+58 12
+59 14
+60 12
+61 9
+62 6
+63 8
+64 25
+65 49
+66 72
+67 79
+68 70
+69 45
+70 45
+71 25
+72 14
+73 14
+74 14
+75 25
+76 57
+77 81
+78 96
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/secondary_structure.gff3	Mon Nov 30 20:10:58 2015 -0500
@@ -0,0 +1,14 @@
+##gff-version 3
+##sequence-region test 1 4
+test	feature	loop	1	3	.	.	.	evidence=ECO:0000255;label=Loop
+test	feature	peptide_helix	4	19	.	.	.	evidence=ECO:0000255;label=Helix
+test	feature	loop	20	24	.	.	.	evidence=ECO:0000255;label=Loop
+test	feature	peptide_helix	25	76	.	.	.	evidence=ECO:0000255;label=Helix
+test	feature	loop	77	78	.	.	.	evidence=ECO:0000255;label=Loop
+##gff-version 3
+##sequence-region test2 1 4
+test2	feature	loop	1	4	.	.	.	evidence=ECO:0000255;label=Loop
+test2	feature	peptide_helix	5	64	.	.	.	evidence=ECO:0000255;label=Helix
+test2	feature	loop	65	68	.	.	.	evidence=ECO:0000255;label=Loop
+test2	feature	peptide_helix	69	75	.	.	.	evidence=ECO:0000255;label=Helix
+test2	feature	loop	76	78	.	.	.	evidence=ECO:0000255;label=Loop
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/solvent_accessibility.gff3	Mon Nov 30 20:10:58 2015 -0500
@@ -0,0 +1,38 @@
+##gff-version 3
+##sequence-region test 1 4
+test	feature	experimental_result_region	1	6	.	.	.	evidence=ECO:0000255;label=Exposed
+test	feature	experimental_result_region	7	14	.	.	.	evidence=ECO:0000255;label=Buried
+test	feature	experimental_result_region	15	16	.	.	.	evidence=ECO:0000255;label=Exposed
+test	feature	experimental_result_region	17	17	.	.	.	evidence=ECO:0000255;label=Buried
+test	feature	experimental_result_region	18	29	.	.	.	evidence=ECO:0000255;label=Exposed
+test	feature	experimental_result_region	30	30	.	.	.	evidence=ECO:0000255;label=Buried
+test	feature	experimental_result_region	31	33	.	.	.	evidence=ECO:0000255;label=Exposed
+test	feature	experimental_result_region	34	34	.	.	.	evidence=ECO:0000255;label=Buried
+test	feature	experimental_result_region	35	36	.	.	.	evidence=ECO:0000255;label=Exposed
+test	feature	experimental_result_region	37	37	.	.	.	evidence=ECO:0000255;label=Buried
+test	feature	experimental_result_region	38	40	.	.	.	evidence=ECO:0000255;label=Exposed
+test	feature	experimental_result_region	41	41	.	.	.	evidence=ECO:0000255;label=Buried
+test	feature	experimental_result_region	42	54	.	.	.	evidence=ECO:0000255;label=Exposed
+test	feature	experimental_result_region	55	55	.	.	.	evidence=ECO:0000255;label=Buried
+test	feature	experimental_result_region	56	64	.	.	.	evidence=ECO:0000255;label=Exposed
+test	feature	experimental_result_region	65	65	.	.	.	evidence=ECO:0000255;label=Buried
+test	feature	experimental_result_region	66	78	.	.	.	evidence=ECO:0000255;label=Exposed
+##gff-version 3
+##sequence-region test2 1 4
+test2	feature	experimental_result_region	1	8	.	.	.	evidence=ECO:0000255;label=Exposed
+test2	feature	experimental_result_region	9	9	.	.	.	evidence=ECO:0000255;label=Buried
+test2	feature	experimental_result_region	10	12	.	.	.	evidence=ECO:0000255;label=Exposed
+test2	feature	experimental_result_region	13	13	.	.	.	evidence=ECO:0000255;label=Buried
+test2	feature	experimental_result_region	14	22	.	.	.	evidence=ECO:0000255;label=Exposed
+test2	feature	experimental_result_region	23	23	.	.	.	evidence=ECO:0000255;label=Buried
+test2	feature	experimental_result_region	24	26	.	.	.	evidence=ECO:0000255;label=Exposed
+test2	feature	experimental_result_region	27	27	.	.	.	evidence=ECO:0000255;label=Buried
+test2	feature	experimental_result_region	28	36	.	.	.	evidence=ECO:0000255;label=Exposed
+test2	feature	experimental_result_region	37	37	.	.	.	evidence=ECO:0000255;label=Buried
+test2	feature	experimental_result_region	38	40	.	.	.	evidence=ECO:0000255;label=Exposed
+test2	feature	experimental_result_region	41	41	.	.	.	evidence=ECO:0000255;label=Buried
+test2	feature	experimental_result_region	42	50	.	.	.	evidence=ECO:0000255;label=Exposed
+test2	feature	experimental_result_region	51	58	.	.	.	evidence=ECO:0000255;label=Buried
+test2	feature	experimental_result_region	59	61	.	.	.	evidence=ECO:0000255;label=Exposed
+test2	feature	experimental_result_region	62	62	.	.	.	evidence=ECO:0000255;label=Buried
+test2	feature	experimental_result_region	63	78	.	.	.	evidence=ECO:0000255;label=Exposed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.fa	Mon Nov 30 20:10:58 2015 -0500
@@ -0,0 +1,5 @@
+>test
+MKATKLVLGAVILGSTLLAGCSSNAKIDQLSSDVQTLNAKVDQLSNDVNAMRSDVQAAKDDAARANQRLDNMATKYRK
+>test2
+MKATKVQTLNAKVDQLSNDVNAMRSDVQAAKDDAARANQRLDNMATKYRKLVLGAVILGSTLLAGCSSNAKIDQLSSD
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.fa.reprof	Mon Nov 30 20:10:58 2015 -0500
@@ -0,0 +1,96 @@
+##General
+# No	: Residue number (beginning with 1)
+# AA	: Amino acid
+##Secondary structure
+# PHEL	: Secondary structure (H = Helix, E = Extended/Sheet, L = Loop)
+# RI_S	: Reliability index (0 to 9 (most reliable))
+# pH	: Probability helix (0 to 1)
+# pE	: Probability extended (0 to 1)
+# pL	: Probability loop (0 to 1)
+##Solvent accessibility
+# PACC	: Absolute
+# PREL	: Relative
+# P10	: Relative in 10 states (0 - 9 (most exposed))
+# RI_A	: Reliability index (0 to 9 (most reliable))
+# Pbe	: Two states (b = buried, e = exposed)
+# Pbie	: Three states (b = buried, i = intermediate, e = exposed)
+# 
+No	AA	PHEL	RI_S	pH	pE	pL	PACC	PREL	P10	RI_A	Pbe	Pbie
+1	M	L	9	1	2	96	169	90	9	3	e	e
+2	K	L	7	8	6	85	147	72	8	0	e	e
+3	A	L	1	37	10	52	76	72	8	0	e	e
+4	T	H	1	48	19	32	79	56	7	0	e	e
+5	K	H	4	63	18	17	147	72	8	0	e	e
+6	L	H	3	61	25	13	91	56	7	0	e	e
+7	V	H	3	60	23	15	0	0	0	0	b	b
+8	L	H	5	70	14	15	0	0	0	0	b	b
+9	G	H	6	76	9	14	0	0	0	1	b	b
+10	A	H	6	79	9	11	0	0	0	3	b	b
+11	V	H	6	80	12	7	0	0	0	0	b	b
+12	I	H	6	80	13	6	0	0	0	0	b	b
+13	L	H	6	76	8	14	0	0	0	0	b	b
+14	G	H	5	76	3	19	0	0	0	0	b	b
+15	S	H	6	81	4	14	72	56	7	0	e	e
+16	T	H	7	82	7	9	79	56	7	0	e	e
+17	L	H	7	85	8	6	0	0	0	1	b	b
+18	L	H	7	84	5	9	49	30	5	0	e	i
+19	A	H	3	67	4	28	76	72	8	0	e	e
+20	G	L	1	40	4	54	60	72	8	0	e	e
+21	C	L	6	18	2	79	27	20	4	0	e	i
+22	S	L	7	11	3	85	72	56	7	0	e	e
+23	S	L	6	18	3	78	93	72	8	0	e	e
+24	N	L	1	43	3	53	141	90	9	0	e	e
+25	A	H	0	48	3	47	59	56	7	0	e	e
+26	K	H	3	65	7	27	86	42	6	0	e	e
+27	I	H	6	82	4	13	33	20	4	0	e	i
+28	D	H	7	86	2	11	91	56	7	1	e	e
+29	Q	H	7	88	2	8	110	56	7	0	e	e
+30	L	H	7	86	2	11	0	0	0	0	b	b
+31	S	H	6	82	1	16	54	42	6	0	e	e
+32	S	H	7	84	0	14	72	56	7	0	e	e
+33	D	H	6	84	0	14	91	56	7	0	e	e
+34	V	H	8	93	1	5	17	12	3	0	b	i
+35	Q	H	8	93	1	5	142	72	8	0	e	e
+36	T	H	8	92	1	6	79	56	7	0	e	e
+37	L	H	8	92	1	5	0	0	0	0	b	b
+38	N	H	8	92	1	6	87	56	7	0	e	e
+39	A	H	8	93	1	5	59	56	7	0	e	e
+40	K	H	8	92	1	6	147	72	8	0	e	e
+41	V	H	8	93	1	5	0	0	0	0	b	b
+42	D	H	8	90	1	8	91	56	7	0	e	e
+43	Q	H	7	87	1	10	110	56	7	0	e	e
+44	L	H	6	81	1	16	32	20	4	0	e	i
+45	S	H	5	76	1	22	72	56	7	0	e	e
+46	N	H	5	79	0	20	113	72	8	0	e	e
+47	D	H	6	80	0	18	91	56	7	0	e	e
+48	V	H	8	90	1	7	28	20	4	0	e	i
+49	N	H	8	89	1	9	113	72	8	0	e	e
+50	A	H	8	92	1	6	59	56	7	0	e	e
+51	M	H	7	86	1	12	56	30	5	0	e	i
+52	R	H	7	85	1	13	138	56	7	0	e	e
+53	S	H	6	79	1	18	72	56	7	0	e	e
+54	D	H	6	80	1	18	91	56	7	0	e	e
+55	V	H	8	89	1	8	0	0	0	0	b	b
+56	Q	H	8	91	1	6	110	56	7	1	e	e
+57	A	H	8	89	1	8	59	56	7	1	e	e
+58	A	H	7	89	1	9	59	56	7	0	e	e
+59	K	H	8	90	1	8	114	56	7	0	e	e
+60	D	H	7	87	0	11	91	56	7	0	e	e
+61	D	H	8	92	1	6	117	72	8	0	e	e
+62	A	H	9	95	1	3	76	72	8	0	e	e
+63	A	H	9	95	1	3	59	56	7	0	e	e
+64	R	H	8	93	1	5	138	56	7	1	e	e
+65	A	H	8	92	1	6	0	0	0	0	b	b
+66	N	H	8	91	1	7	113	72	8	0	e	e
+67	Q	H	8	93	1	5	110	56	7	1	e	e
+68	R	H	8	90	1	7	138	56	7	1	e	e
+69	L	H	8	94	1	4	91	56	7	0	e	e
+70	D	H	8	94	1	4	91	56	7	0	e	e
+71	N	H	8	94	1	4	141	90	9	0	e	e
+72	M	H	9	94	1	4	105	56	7	0	e	e
+73	A	H	8	90	1	7	59	56	7	0	e	e
+74	T	H	8	89	2	8	79	56	7	0	e	e
+75	K	H	7	87	2	10	147	72	8	1	e	e
+76	Y	H	5	74	2	22	124	56	7	0	e	e
+77	R	L	3	33	1	64	138	56	7	0	e	e
+78	K	L	8	4	0	94	184	90	9	5	e	e
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Nov 30 20:10:58 2015 -0500
@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="fann" version="2.2.0">
+        <repository changeset_revision="28d4ebb94540" name="package_fann_2_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="perl_ai_fann" version="0.10">
+        <repository changeset_revision="11045607d36d" name="package_perl_ai_fann_0_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="reprof" version="1.0.1">
+        <repository changeset_revision="c391423260a2" name="package_reprof_1_0_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>