fixes for distribution

Author: dmnfarrell

epitopepredict/app.py

@@ -217,6 +217,20 @@ def list_alleles():
         print ()
     return
 
+def test_run():
+    """Test run for a HIV sample file"""
+
+    path = os.path.dirname(os.path.abspath(__file__))
+    options = config.baseoptions
+    options['base']['sequence_file'] = os.path.join(path, 'testing','HIV-1.fa')
+    options['base']['mhc2_alleles'] = 'human_common_mhc2'
+    options['base']['path'] = 'hiv1_test'
+    options['base']['verbose'] = True
+    options = config.check_options(options)
+    W = WorkFlow(options)
+    st = W.setup()
+    W.run()
+
 def main():
     "Run the application"
 
@@ -232,7 +246,7 @@ def main():
     parser.add_option("-l", "--list-alleles", dest="list_alleles",  action="store_true",
                         default=False, help="List available alleles")
     parser.add_option("-t", "--test", dest="test",  action="store_true",
-                        default=False, help="Do quick test")
+                        default=False, help="Do test predictions")
     parser.add_option("-a", "--analysis", dest="analysis",
                         help="Analysis path", metavar="FILE")
     parser.add_option("-s", "--server", dest="server",  action="store_true",
@@ -266,6 +280,9 @@ def main():
         #webapp.run(port=5000, debug=True)
         import epitopepredict.tornado_serve
         epitopepredict.tornado_serve.main(opts.port)
+    elif opts.test == True:
+        test_run()
+        print ('these test predictions can be viewed in the web app')
     else:
         print_help()
 

epitopepredict/config.py

@@ -33,7 +33,8 @@
 path = os.path.dirname(os.path.abspath(__file__))
 datadir = os.path.join(path, 'data')
 
-baseoptions = {'base': {'predictors': 'tepitope',
+baseoptions = OrderedDict()
+baseoptions['base'] = {'predictors': 'tepitope',
                 'mhc2_alleles':'HLA-DRB1*01:01,HLA-DRB1*04:01',
                 'mhc1_alleles':'HLA-A*01:01',
                 'mhc1_length': 11,
@@ -49,12 +50,10 @@
                 'overwrite': 'no',
                 'plots': 'no', #whether to save plots
                 'genome_analysis': 'no',
-                'cpus': 1},
-              'iedbtools': {'iedbmhc1_path':'', 'iedbmhc2_path':'',
+                'cpus': 1}
+baseoptions['iedbtools'] = {'iedbmhc1_path':'', 'iedbmhc2_path':'',
                             'iedb_mhc1_method':'IEDB_recommended',
                             'iedb_mhc2_method':'IEDB_recommended'}
-                }
-#baseoptions = OrderedDict(baseoptions)
 
 def write_default_config(conffile='default.conf', defaults={}):
     """Write a default config file"""
@@ -76,8 +75,7 @@ def create_config_parser_from_dict(data=None, sections=['base','iedbtools'], **k
         cp.add_section(s)
         if not data.has_key(s):
             continue
-        for name in data[s]:
-            #name,val = i
+        for name in sorted(data[s]):
             val = data[s][name]
             if type(val) is list:
                 val = ','.join(val)

epitopepredict/static/custom.css

@@ -58,7 +58,7 @@ b.monospace{
   font-family: monospace;
 }
 div.warning{
-    background:#ffcccc;
+    background: #F7DDD8;
     padding: 5px 5px 5px 5px;
     font-size: 18px;
 }

epitopepredict/templates/base.html

@@ -36,8 +36,8 @@ <h3>epitopepredict</h3>
 
 	</body>
 
-	<div class="footer">
+	<!--<div class="footer">
 		<a href="https://github.com/dmnfarrell/epitopepredict/wiki">help page</a>
-	</div>
+	</div> -->
 
 </html>

epitopepredict/templates/makeconfig.html

@@ -58,12 +58,14 @@
 		  <div class="configform">
 				<table class="configform">
 					<tr>
-				<td>{{ form.presets.label}}</td>
-				<td>{{ form.presets}}</td>
-				<td>{{ form.mhc1_alleles.label }}</td>
-				<td>{{ form.mhc1_alleles }}</td>
-				<td>{{ form.mhc2_alleles.label }}</td>
-				<td>{{ form.mhc2_alleles}}</td></tr>
+				<td>{{ form.mhc1_presets.label}}
+				{{ form.mhc1_presets}}</td>
+				<td>{{ form.mhc2_presets.label}}
+				{{ form.mhc2_presets}}</td>
+				<td>{{ form.mhc1_alleles.label }}
+				{{ form.mhc1_alleles }}</td>
+				<td>{{ form.mhc2_alleles.label }}
+				{{ form.mhc2_alleles}}</td></tr>
 				</table>
 				</div>
 
@@ -73,11 +75,10 @@
 
 		<div class="floatright">
 			<p>
-				This page helps you generate a configuration file that can be used to then call the
-				command line interface to generate epitope predictions.
-				Select one or more predictors and appropriate alleles which are then run
-				for all the proteins in the chosen genome/sequence file. An entire proteome using
-				multiple methods may take some time to process. Selection of alleles should always
+				This page generates a configuration file from a form that can be used to then call the
+				command line interface to generate epitope predictions. You can then view the results in this
+				web application. Select one or more predictors and appropriate alleles which are then run
+				for all the proteins in the chosen genome/sequence file. Selection of alleles should always
 				be tailored to your own requirements.
 			</p>
 			<div class="monospace" style="background: #F7DDD8;">

epitopepredict/templates/sequence.html

@@ -24,10 +24,10 @@ <h3> epitopepredict:sequence view: {{name}} </h3>
 			{{ form.view.label }}
 			{{ form.view }}
 			<input type="submit" class="button">
-
 		</form>
 		</div>
 		{%if status == 0 %}
+	    </div>
 		<div class="warning">{{ msg }}</div>
 		{% else %}
 
@@ -54,6 +54,7 @@ <h3> epitopepredict:sequence view: {{name}} </h3>
 			{{ tables }}
 		</div>
 		{% end %}
+
 	  </div>
 
 {% end %}

epitopepredict/testing/HIV-1.fa

@@ -0,0 +1,66 @@
+>lcl|NC_001802.1_prot_NP_057849.4_1 [gene=gag-pol] [locus_tag=HIV1gp1] [db_xref=GeneID:155348] [protein=Gag-Pol] [exception=ribosomal slippage] [protein_id=NP_057849.4] [location=join(336..1637,1637..4642)] [gbkey=CDS]
+MGARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQPSLQT
+GSEELRSLYNTVATLYCVHQRIEIKDTKEALDKIEEEQNKSKKKAQQAAADTGHSNQVSQNYPIVQNIQG
+QMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAA
+EWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPT
+SILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTAC
+QGVGGPGHKARVLAEAMSQVTNSATIMMQRGNFRNQRKIVKCFNCGKEGHTARNCRAPRKKGCWKCGKEG
+HQMKDCTERQANFLREDLAFLQGKAREFSSEQTRANSPTRRELQVWGRDNNSPSEAGADRQGTVSFNFPQ
+VTLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAI
+GTVLVGPTPVNIIGRNLLTQIGCTLNFPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEK
+EGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGD
+AYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQY
+MDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWT
+VNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSK
+DLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPI
+QKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGR
+QKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYL
+AWVPAHKGIGGNEQVDKLVSAGIRKVLFLDGIDKAQDEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKC
+QLKGEAMHGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTI
+HTDNGSNFTGATVRAACWWAGIKQEFGIPYNPQSQGVVESMNKELKKIIGQVRDQAEHLKTAVQMAVFIH
+NFKRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRVYYRDSRNPLWKGPAKLLWKGEGAVVIQD
+NSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED
+>lcl|NC_001802.1_prot_NP_057850.1_2 [gene=gag] [locus_tag=HIV1gp2] [db_xref=GeneID:155030] [protein=Pr55(Gag)] [protein_id=NP_057850.1] [location=336..1838] [gbkey=CDS]
+MGARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQPSLQT
+GSEELRSLYNTVATLYCVHQRIEIKDTKEALDKIEEEQNKSKKKAQQAAADTGHSNQVSQNYPIVQNIQG
+QMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAA
+EWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPT
+SILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTAC
+QGVGGPGHKARVLAEAMSQVTNSATIMMQRGNFRNQRKIVKCFNCGKEGHTARNCRAPRKKGCWKCGKEG
+HQMKDCTERQANFLGKIWPSYKGRPGNFLQSRPEPTAPPEESFRSGVETTTPPQKQEPIDKELYPLTSLR
+SLFGNDPSSQ
+>lcl|NC_001802.1_prot_NP_057851.1_3 [gene=vif] [locus_tag=HIV1gp3] [db_xref=GeneID:155459] [protein=Vif] [protein_id=NP_057851.1] [location=4587..5165] [gbkey=CDS]
+MENRWQVMIVWQVDRMRIRTWKSLVKHHMYVSGKARGWFYRHHYESPHPRISSEVHIPLGDARLVITTYW
+GLHTGERDWHLGQGVSIEWRKKRYSTQVDPELADQLIHLYYFDCFSDSAIRKALLGHIVSPRCEYQAGHN
+KVGSLQYLALAALITPKKIKPPLPSVTKLTEDRWNKPQKTKGHRGSHTMNGH
+>lcl|NC_001802.1_prot_NP_057852.2_4 [gene=vpr] [locus_tag=HIV1gp4] [db_xref=GeneID:155807] [protein=Vpr] [exception=artificial frameshift] [protein_id=NP_057852.2] [location=join(5105..5319,5321..5396)] [gbkey=CDS]
+MEQAPEDQGPQREPHNEWTLELLEELKNEAVRHFPRIWLHGLGQHIYETYGDTWAGVEAIIRILQQLLFI
+HFRIGCRHSRIGVTRQRRARNGASRS
+>lcl|NC_001802.1_prot_NP_057853.1_5 [gene=tat] [locus_tag=HIV1gp5] [db_xref=GeneID:155871] [protein=Tat] [protein_id=NP_057853.1] [location=join(5377..5591,7925..7970)] [gbkey=CDS]
+MEPVDPRLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKALGISYGRKKRRQRRRAHQNSQTHQASLS
+KQPTSQPRGDPTGPKE
+>lcl|NC_001802.1_prot_NP_057854.1_6 [gene=rev] [locus_tag=HIV1gp6] [db_xref=GeneID:155908] [protein=Rev] [protein_id=NP_057854.1] [location=join(5516..5591,7925..8199)] [gbkey=CDS]
+MAGRSGDSDEELIRTVRLIKLLYQSNPPPNPEGTRQARRNRRRRWRERQRQIHSISERILGTYLGRSAEP
+VPLQLPPLERLTLDCNEDCGTSGTQGVGSPQILVESPTVLESGTKE
+>lcl|NC_001802.1_prot_NP_057855.1_7 [gene=vpu] [locus_tag=HIV1gp7] [db_xref=GeneID:155945] [protein=Vpu] [protein_id=NP_057855.1] [location=5608..5856] [gbkey=CDS]
+MQPIPIVAIVALVVAIIIAIVVWSIVIIEYRKILRQRKIDRLIDRLIERAEDSGNESEGEISALVEMGVE
+MGHHAPWDVDDL
+>lcl|NC_001802.1_prot_NP_057856.1_8 [gene=env] [locus_tag=HIV1gp8] [db_xref=GeneID:155971] [protein=Envelope surface glycoprotein gp160, precursor] [protein_id=NP_057856.1] [location=5771..8341] [gbkey=CDS]
+MRVKEKYQHLWRWGWRWGTMLLGMLMICSATEKLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWA
+THACVPTDPNPQEVVLVNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVSLKCTDLKNDTNT
+NSSSGRMIMEKGEIKNCSFNISTSIRGKVQKEYAFFYKLDIIPIDNDTTSYKLTSCNTSVITQACPKVSF
+EPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSVNFTDN
+AKTIIVQLNTSVEINCTRPNNNTRKRIRIQRGPGRAFVTIGKIGNMRQAHCNISRAKWNNTLKQIASKLR
+EQFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCNSTQLFNSTWFNSTWSTEGSNNTEGSDTITLPCRI
+KQIINMWQKVGKAMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPGGGDMRDNWRSELYKYKVVK
+IEPLGVAPTKAKRRVVQREKRAVGIGALFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQNNLLRAIE
+AQQHLLQLTVWGIKQLQARILAVERYLKDQQLLGIWGCSGKLICTTAVPWNASWSNKSLEQIWNHTTWME
+WDREINNYTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWFNITNWLWYIKLFIMIVGGLVGLRIVFA
+VLSIVNRVRQGYSPLSFQTHLPTPRGPDRPEGIEEEGGERDRDRSIRLVNGSLALIWDDLRSLCLFSYHR
+LRDLLLIVTRIVELLGRRGWEALKYWWNLLQYWSQELKNSAVSLLNATAIAVAEGTDRVIEVVQGACRAI
+RHIPRRIRQGLERILL
+>lcl|NC_001802.1_prot_NP_057857.2_9 [gene=nef] [locus_tag=HIV1gp9] [db_xref=GeneID:156110] [protein=Nef] [transl_except=(pos:370..372,aa:Trp)] [protein_id=NP_057857.2] [location=8343..8963] [gbkey=CDS]
+MGGKWSKSSVIGWPTVRERMRRAEPAADRVGAASRDLEKHGAITSSNTAATNAACAWLEAQEEEEVGFPV
+TPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPDWQNYTPGPGVRYPLTFG
+WCYKLVPVEPDKIEEANKGENTSLLHPVSLHGMDDPEREVLEWRFDSRLAFHHVARELHPEYFKNC
+

testing/zaire-ebolavirus.faa renamed to epitopepredict/testing/zaire-ebolavirus.faa

@@ -14,13 +14,17 @@
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
 
+path = os.path.dirname(os.path.abspath(__file__))
+testdir = os.path.join(path, 'testing')
+
 class PredictorTests(unittest.TestCase):
     """Basic tests for predictor"""
 
     def setUp(self):
-        genbankfile = 'testing/zaire-ebolavirus.gb'
-        self.df = sequtils.genbank_to_dataframe(genbankfile, cds=True)
-        self.testdir = 'testing'
+        self.genbankfile = os.path.join(testdir, 'zaire-ebolavirus.gb')
+        self.fastafile = os.path.join(testdir, 'zaire-ebolavirus.faa')
+        self.df = sequtils.genbank_to_dataframe(self.genbankfile, cds=True)
+        self.testdir = testdir
         if not os.path.exists(self.testdir):
             os.mkdir(self.testdir)
         return
@@ -105,8 +109,7 @@ def test_iedbmhc2(self):
     def test_fasta(self):
         """Test fasta predictions"""
 
-        fastafile = 'testing/zaire-ebolavirus.faa'
-        df = sequtils.fasta_to_dataframe(fastafile)
+        df = sequtils.fasta_to_dataframe(self.fastafile)
         alleles = ["HLA-DRB1*0101"]
         P = base.get_predictor('tepitope')
         P.predictProteins(df, length=11, alleles=alleles, path=self.testdir)
@@ -137,8 +140,7 @@ def test_analysis(self):
     def test_features(self):
         """Test genbank feature handling"""
 
-        fastafile = 'testing/zaire-ebolavirus.faa'
-        df = sequtils.fasta_to_dataframe(fastafile)
+        df = sequtils.fasta_to_dataframe(self.fastafile)
         name = 'ZEBOVgp1'
         sequtils.dataframe_to_fasta(df)
         sequtils.check_tags(df)

testing/zaire-ebolavirus.gb renamed to epitopepredict/testing/zaire-ebolavirus.gb

@@ -33,7 +33,7 @@
 opts = config.baseoptions.copy()
 
 def help_msg():
-    msg = '<a>path for results not found, enter an existing folder with your results. </a> '
+    msg = 'path for results not found, enter an existing folder with your results.  '
     msg += '<a href="%s"> see help page</a>' %wikipage
     return msg
 
@@ -67,6 +67,12 @@ def _is_seqfile(form, field):
             raise ValidationError(message)
     return _is_seqfile
 
+def exists(message=u'File does not exist'):
+    def _exists(form, field):
+        if not os.path.exists(field.data):
+            raise ValidationError(message)
+    return _exists
+
 class ControlsForm(Form):
     name = SelectField('name', choices=[])
     path = TextField('path', default='results')
@@ -88,13 +94,16 @@ class ConfigForm(Form):
                                      render_kw={"class": "combobox"})
     mhc1_length = IntegerField('mhc1 length', default=11)
     mhc2_length = IntegerField('mhc2 length', default=15)
-    sequence_file = FileField('sequence file',
-                              validators=[DataRequired(), is_seqfile()], default='')
-    overwrite = BooleanField('overwrite', default=True)
+    sequence_file = TextField('sequence file',
+                              validators=[DataRequired(), is_seqfile(), exists()], default='')
+    overwrite = BooleanField('overwrite', default=False, false_values={False, 'n', ''})
     cpus = IntegerField('cpus', default=1)
-    ps = [(i,i) for i in base.mhc1_presets+base.mhc2_presets]
-    ps.insert(0, ('',''))
-    presets = SelectField('Presets', choices=ps, default='')
+    ps1 = [(i,i) for i in base.mhc1_presets]
+    ps1.insert(0, ('',''))
+    mhc1_presets = SelectField('MHC-I presets', choices=ps1, default='')
+    ps2 = [(i,i) for i in base.mhc2_presets]
+    ps2.insert(0, ('',''))
+    mhc2_presets = SelectField('MHC-II presets', choices=ps2, default='')
     p1 = base.get_predictor('iedbmhc1')
     x = [(i,i) for i in p1.getAlleles()]
     mhc1_alleles = SelectMultipleField('MHC-I alleles', choices=x,
@@ -284,19 +293,21 @@ def get(self):
                     if a in opts[s]:
                         opts[s][a] = args[a]
 
-        if 'sequence_file' in args:
-            seqfile = args['sequence_file'][0]
-            #if os.path.exists(seqfile):
-            opts['base']['sequence_file'] = seqfile = os.path.abspath(seqfile)
-
+        #print (args)
+        o=opts['base']
+        if 'overwrite' not in args:
+            o['overwrite'] = 'no'
+        if 'mhc1_presets' in args and args['mhc1_presets'][0] != '':
+            o['mhc1_alleles'] = args['mhc1_presets']
+        if 'mhc2_presets' in args and args['mhc2_presets'][0] != '':
+            o['mhc2_alleles'] = args['mhc2_presets']
         #get configparser from args to make conf from form
         cp = config.create_config_parser_from_dict(opts)
         out = StringIO()
         cp.write(out)
         conftext = str_to_html(out.getvalue())
 
         form = ConfigForm(args)
-        #form.sequence_file.data = seqfile
         errors='no errors'
         if form.validate():
             pass

epitopepredict/tests.py

@@ -15,14 +15,14 @@
     author_email = 'farrell.damien[at]gmail.com',
     packages = ['epitopepredict'],
     package_data={'epitopepredict': ['mhcdata/*.csv', 'presets/*.csv',
-                  'tepitope/*.txt','tepitope/pssm/*',
+                  'tepitope/*.txt', 'tepitope/pssm/*', 'testing/*',
                   'templates/*.html','static/*',
                   'description.txt']
                  },
     install_requires=['numpy>=1.10',
                       'pandas>=0.20',
                       'biopython>=1.5',
-                      'bokeh>=0.12',
+                      'bokeh==0.12.9',
                       'wtforms>=2.1',
                       'wtforms_tornado',
                       'future'],