def test_simple_assembly(self):
"""
Simple test if everything works. Solution manually tested for optimality.
:return:
"""
pred = CleavageSitePredictorFactory("PCM")
assembler = EpitopeAssembly(self.peptides, pred, solver="glpk", verbosity=0)
r = assembler.solve()
self.assertEqual(r, [Peptide("YLYDHLAPM"), Peptide("ALYDVVSTL"), Peptide("KLLPRLPGV")])
def main():
parser = argparse.ArgumentParser(description="Reads peptide sequences and predicts best arrangement "+
"for a string-of-beats peptide vaccine based on proteasomal cleavage prediction.")
parser.add_argument("-i", "--input",
nargs="+",
required=True,
help="peptide file (one peptide per line),"
+" or peptide sequences as sequences (max 50)"
)
input_types = parser.add_mutually_exclusive_group(required=True)
input_types.add_argument("-pf","--pepfile",
action="store_true",
help= "Specifies the input as peptide file")
input_types.add_argument("-p","--peptide",
action="store_true",
help= "Specifies the input as peptide sequences")
parser.add_argument("-m", "--method",
default="PCM",
help="Specifies the Cleavage Site prediction tool to use - default PCM."
)
parser.add_argument("-s", "--solver",
default="glpk",
help="Specifies the ILP solver to use (must be installed) - default glpk"
)
parser.add_argument("-o", "--output",
required=True,
help="Specifies the output path. Results will be written to CSV")
parser.add_argument("-v", "--verbose",
action="store_true",
help="Specifies verbose run."
)
parser.add_argument("-am", "--available",
required=False,
action="store_true",
help="Returns all available methods and their allele models.")
#COMMENT: These options are hidden and only used for ETK2
parser.add_argument("-html", "--html",
required=False,
action="store_true",
help=argparse.SUPPRESS)
parser.add_argument("-od", "--outdir",
required=False,
default="",
help=argparse.SUPPRESS)
args = parser.parse_args()
if args.available:
for pred, obj in ACleavageSitePrediction.registry.iteritems():
if pred not in ["ACleavageSitePrediction", "APSSMCleavageSitePredictor"]:
print "Method: ",pred
print "Supported Length: ", " ".join(map(str, getattr(obj, "_"+pred+"__supported_length")))
print
sys.exit(0)
if args.pepfile:
peptides = read_lines(args.input, type="Peptide")
else:
peptides = [Peptide(s) for s in args.input]
cleav_pred = CleavageSitePredictorFactory(args.method)
assembler = EpitopeAssembly(peptides, cleav_pred, solver=args.solver, verbosity=1 if args.verbose else 0)
result = assembler.solve()
output = args.output if args.outdir == "" else args.outdir + os.path.basename(args.output)
with open(output, "w") as out:
out.write("Order,Peptide\n")
out.write("\n".join("%i,%s"%(i+1,str(p)) for i, p in enumerate(result)))
if args.html:
begin_html = """<?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<link rel="stylesheet" href="/static/style/etk.css" type="text/css" />
<script type="text/javascript" src="/static/scripts/libs/jquery/jquery.js"></script>
<script type="text/javascript" src="/static/scripts/libs/jquery/jquery.tablesorter.js"></script>
<script type="text/javascript" src="/static/scripts/libs/etk.js"></script>
</head>
<body>
<div class="document">"""
setting = """ <h2 class="etk-heading">Peptide String-of-Beats Design</h2>
<table class="etk-parameterT">
<tr> <th class ="etk-innerHeading" colspan="2"> Parameters </th></tr>
<tr>
<th>Cleave Site Prediction Method:</th>
<td>%s</td>
</tr>
</table>"""%args.method
table="""
<input id="etk-search" placeholder=" filter">
<table class="etk-sortT etk-resultsT etk-filterT">
<thead>
<tr>
<th>Order</th><th>Peptide</th>
</tr>
</thead>"""+"".join("<tr><td>%i</td><td>%s</td></tr>"%(i+1,p) for i, p in enumerate(result))+"</table>"
end_html = "</div></body></html>"
html_out = ".".join(output.split(".")[:-1])+".html"
with open(html_out, "w") as html_o:
html_o.write(begin_html+setting+table+end_html)
