def test_enable_import_with_ext():
"""Using exts any file extension can be importable."""
ext = ".html,.kid.html"
sys.path.insert(0, tmpdir)
try:
raises(ImportError, "import test_suffixes1")
raises(ImportError, "import test_suffixes2")
raises(ImportError, "import test_suffixes3")
kid.enable_import(ext=ext)
dest = joinpath(tmpdir, "test_suffixes1.kid")
copyfile(tfile, dest)
import test_suffixes1 # *.kid files are always importable
dest = joinpath(tmpdir, "test_suffixes2.html")
copyfile(tfile, dest)
import test_suffixes2
dest = joinpath(tmpdir, "test_suffixes3.kid.html")
copyfile(tfile, dest)
import test_suffixes3
dest = joinpath(tmpdir, "test_suffixes4.xhtml")
copyfile(tfile, dest)
raises(ImportError, "import test_suffixes4")
kid.disable_import()
finally:
sys.path.remove(tmpdir)
def test_import_hook():
kid.enable_import()
import test.test_if
assert_template_interface(test.test_if)
assert sys.modules.has_key("test.test_if")
kid.disable_import()
def test_pyc_generation():
# if this exists, the test is worthless. make sure this test runs before
# anything else import test_content
from kid.test import template_dir
kid.enable_import()
assert not exists(joinpath(template_dir, 'test_content.pyc'))
import test.test_content
assert exists(joinpath(template_dir, 'test_content.pyc'))
assert sys.modules.has_key('test.test_content')
def test_pyc_generation():
# if this exists, the test is worthless. make sure this test runs before
# anything else import test_content
from kid.test import template_dir
kid.enable_import()
assert not exists(joinpath(template_dir, 'test_content.pyc'))
import test.test_content
assert exists(joinpath(template_dir, 'test_content.pyc'))
assert sys.modules.has_key('test.test_content')
def _create_report(self, pwm, background, stats={}, best_id={}):
self.logger.info("Creating graphical report")
class ReportMotif:
pass
motifs = pwmfile_to_motifs(pwm)
for m,match in self.closest_match.items():
match[0].to_img(os.path.join(self.imgdir,"%s.png" % match[0].id), format="PNG")
sort_key = background[0]
if "gc" in background:
sort_key = "gc"
roc_img_file = "%s_%s_roc"
report_motifs = []
sorted_motifs = sorted(motifs,
cmp= lambda x,y: cmp(self.mncp[sort_key][y.id], self.mncp[sort_key][x.id])
)
for motif in sorted_motifs:
rm = ReportMotif()
rm.id = motif.id
rm.id_href = {"href": "#%s" % motif.id}
rm.id_name = {"name": motif.id}
rm.img = {"src": os.path.join("images", "%s.png" % motif.id)}
rm.best = best_id[motif.id]
rm.consensus = motif.to_consensus()
rm.stars = stats["%s_%s" % (motif.id, motif.to_consensus())]["stars"]
rm.bg = {}
for bg in background:
rm.bg[bg] = {}
rm.bg[bg]["e"] = "%0.2f" % self.e[bg].setdefault(motif.id, 0.0)
rm.bg[bg]["p"] = "%0.2f" % self.p[bg].setdefault(motif.id, 1.0)
rm.bg[bg]["auc"] = "%0.3f" % self.auc[bg][motif.id]
rm.bg[bg]["mncp"] = "%0.3f" % self.mncp[bg][motif.id]
rm.bg[bg]["roc_img"] = {"src": "images/" + os.path.basename(roc_img_file % (motif.id, bg)) + ".png"}
rm.bg[bg]["roc_img_link"] = {"href": "images/" + os.path.basename(roc_img_file % (motif.id, bg)) + ".png"}
rm.histogram_img = {"data":"images/%s_histogram.svg" % motif.id}
rm.histogram_link= {"href":"images/%s_histogram.svg" % motif.id}
rm.match_img = {"src": "images/%s.png" % self.closest_match[motif.id][0].id}
rm.match_id = self.closest_match[motif.id][0].id
rm.match_pval = "%0.2e" % self.closest_match[motif.id][1]
report_motifs.append(rm)
total_report = self.motif_report
kid.enable_import()
template_file = os.path.join(self.config.get_template_dir(), "report_template_v2.kid")
template = kid.Template(file=template_file, expname=self.name, motifs=report_motifs, inputfile=self.inputfile, date=datetime.today().strftime("%d/%m/%Y"), version=GM_VERSION)
f = open(total_report, "w")
f.write(template.serialize())
f.close()
def _cluster_motifs(self, pfm_file, cluster_pwm, dir, threshold):
self.logger.info("Clustering significant motifs.")
trim_ic = 0.2
clusters = []
motifs = pwmfile_to_motifs(pfm_file)
if len(motifs) == 1:
clusters = [[motifs[0], motifs]]
else:
tree = cluster_motifs(pfm_file, "total", "wic", "mean", True, threshold=float(threshold), include_bg=True)
clusters = tree.getResult()
ids = []
mc = MotifComparer()
for cluster,members in clusters:
cluster.trim(trim_ic)
cluster.to_img(os.path.join(self.imgdir,"%s.png" % cluster.id), format="PNG")
ids.append([cluster.id, {"src":"images/%s.png" % cluster.id},[]])
if len(members) > 1:
scores = {}
for motif in members:
scores[motif] = mc.compare_motifs(cluster, motif, "total", "wic", "mean", pval=True)
add_pos = sorted(scores.values(),cmp=lambda x,y: cmp(x[1], y[1]))[0][1]
for motif in members:
score, pos, strand = scores[motif]
add = pos - add_pos
if strand in [1,"+"]:
pass
else:
#print "RC %s" % motif.id
rc = motif.rc()
rc.id = motif.id
motif = rc
#print "%s\t%s" % (motif.id, add)
motif.to_img(os.path.join(self.imgdir, "%s.png" % motif.id.replace(" ", "_")), format="PNG", add_left=add)
ids[-1][2] = [dict([("src", "images/%s.png" % motif.id.replace(" ", "_")), ("alt", motif.id.replace(" ", "_"))]) for motif in members]
kid.enable_import()
template_file = os.path.join(self.config.get_template_dir(), "cluster_template_v2.kid")
template = kid.Template(file=template_file, expname=self.name, motifs=ids, inputfile=self.inputfile, date=datetime.today().strftime("%d/%m/%Y"), version=GM_VERSION)
f = open(self.cluster_report, "w")
f.write(template.serialize())
f.close()
f = open(cluster_pwm, "w")
if len(clusters) == 1 and len(clusters[0][1]) == 1:
f.write("%s\n" % clusters[0][0].to_pwm())
else:
for motif in tree.get_clustered_motifs():
f.write("%s\n" % motif.to_pwm())
f.close()
self.logger.info("Clustering done. See the result in %s" % self.cluster_report)
return clusters
def _cluster_motifs(self, pfm_file, cluster_pwm, dir, threshold):
self.logger.info("Clustering significant motifs.")
trim_ic = 0.2
clusters = []
motifs = pwmfile_to_motifs(pfm_file)
if len(motifs) == 1:
clusters = [[motifs[0], motifs]]
else:
tree = cluster_motifs(pfm_file, "total", "wic", "mean", True, threshold=float(threshold), include_bg=True)
clusters = tree.getResult()
ids = []
mc = MotifComparer()
for cluster,members in clusters:
cluster.trim(trim_ic)
cluster.to_img(os.path.join(self.imgdir,"%s.png" % cluster.id), format="PNG")
ids.append([cluster.id, {"src":"images/%s.png" % cluster.id},[]])
if len(members) > 1:
scores = {}
for motif in members:
scores[motif] = mc.compare_motifs(cluster, motif, "total", "wic", "mean", pval=True)
add_pos = sorted(scores.values(),cmp=lambda x,y: cmp(x[1], y[1]))[0][1]
for motif in members:
score, pos, strand = scores[motif]
add = pos - add_pos
if strand in [1,"+"]:
pass
else:
#print "RC %s" % motif.id
rc = motif.rc()
rc.id = motif.id
motif = rc
#print "%s\t%s" % (motif.id, add)
motif.to_img(os.path.join(self.imgdir, "%s.png" % motif.id.replace(" ", "_")), format="PNG", add_left=add)
ids[-1][2] = [dict([("src", "images/%s.png" % motif.id.replace(" ", "_")), ("alt", motif.id.replace(" ", "_"))]) for motif in members]
kid.enable_import()
template_file = os.path.join(self.config.get_template_dir(), "cluster_template_v2.kid")
template = kid.Template(file=template_file, expname=self.name, motifs=ids, inputfile=self.inputfile, date=datetime.today().strftime("%d/%m/%Y"), version=GM_VERSION)
f = open(self.cluster_report, "w")
f.write(template.serialize())
f.close()
f = open(cluster_pwm, "w")
if len(clusters) == 1 and len(clusters[0][1]) == 1:
f.write("%s\n" % clusters[0][0].to_pwm())
else:
for motif in tree.get_clustered_motifs():
f.write("%s\n" % motif.to_pwm())
f.close()
self.logger.info("Clustering done. See the result in %s" % self.cluster_report)
return clusters
def _create_report(self, pwm, background):
class ReportMotif:
pass
motifs = pwmfile_to_motifs(pwm)
for m,match in self.closest_match.items():
match[0].to_img(os.path.join(self.imgdir,"%s.png" % match[0].id), format="PNG")
random = "random" in background
genomic = "genomic_matched" in background
sort_key = "random"
if genomic:
sort_key = "genomic_matched"
roc_img_file = "%s_%s_roc"
report_motifs = []
for motif in sorted(motifs, cmp=lambda x,y: cmp(self.mncp[sort_key][y.id], self.mncp[sort_key][x.id])):
rm = ReportMotif()
rm.id = motif.id
rm.id_href = {"href": "#%s" % motif.id}
rm.id_name = {"name": motif.id}
rm.img = {"src": os.path.join("images", "%s.png" % motif.id)}
rm.consensus = motif.to_consensus()
if random:
rm.random_e = "%0.2f" % self.e["random"][motif.id]
rm.random_p = "%0.2f" % self.p["random"][motif.id]
rm.random_auc = "%0.3f" % self.auc["random"][motif.id]
rm.random_mncp = "%0.3f" % self.mncp["random"][motif.id]
rm.random_roc_img = {"src": "images/" + os.path.basename(roc_img_file % (motif.id, "random")) + ".png"}
rm.random_roc_img_link = {"href": "images/" + os.path.basename(roc_img_file % (motif.id, "random")) + ".png"}
if genomic:
rm.genomic_e = "%0.2f" % self.e["genomic_matched"][motif.id]
rm.genomic_p = "%0.2f" % self.p["genomic_matched"][motif.id]
rm.genomic_auc = "%0.3f" % self.auc["genomic_matched"][motif.id]
rm.genomic_mncp = "%0.3f" % self.mncp["genomic_matched"][motif.id]
rm.genomic_roc_img = {"src": "images/" + os.path.basename(roc_img_file % (motif.id, "genomic_matched")) + ".png"}
rm.genomic_roc_img_link = {"href": "images/" + os.path.basename(roc_img_file % (motif.id, "genomic_matched")) + ".png"}
rm.histogram_img = {"data":"images/%s_histogram.svg" % motif.id}
rm.histogram_link= {"href":"images/%s_histogram.svg" % motif.id}
rm.match_img = {"src": "images/%s.png" % self.closest_match[motif.id][0].id}
rm.match_id = self.closest_match[motif.id][0].id
rm.match_pval = "%0.2e" % self.closest_match[motif.id][1]
report_motifs.append(rm)
total_report = self.motif_report
kid.enable_import()
template_file = os.path.join(self.config.get_template_dir(), "report_template_v2.kid")
template = kid.Template(file=template_file, expname=self.name, motifs=report_motifs, random=random, genomic=genomic, inputfile=self.inputfile, date=datetime.today().strftime("%d/%m/%Y"), version=self.VERSION)
f = open(total_report, "w")
f.write(template.serialize())
f.close()
def test_import_and_expand():
from kid.test import output_dir
kid.enable_import()
import test.context as c
C = c.Template
out = joinpath(output_dir, 'context.out')
t = C(foo=10, bar='bla bla')
it = t.pull()
for e in it:
pass
t.write(out)
check_xml_file(out)
def test_enable_import_empty():
"""By default *.kid files are imported."""
sys.path.insert(0, tmpdir)
try:
kid.disable_import()
raises(ImportError, "import test_suffixes0")
kid.enable_import()
import test_suffixes0
raises(ImportError, "import test_suffixes1")
kid.disable_import()
finally:
sys.path.remove(tmpdir)
def test_enable_import_with_path():
"""Using path any template directory can be importable."""
assert tmpdir not in sys.path
raises(ImportError, "import test_suffixes4")
kid.enable_import(path=tmpdir)
dest = joinpath(tmpdir, "test_suffixes4.kid")
copyfile(tfile, dest)
import test_suffixes4
kid.disable_import(path=tmpdir)
dest = joinpath(tmpdir, "test_suffixes5.kid")
copyfile(tfile, dest)
raises(ImportError, "import test_suffixes5")
def test_import_and_expand():
from kid.test import output_dir
kid.enable_import()
import test.context as c
C = c.Template
out = joinpath(output_dir, 'context.out')
t = C(foo=10, bar='bla bla')
it = t.pull()
for e in it:
pass
t.write(out)
check_xml_file(out)
def test_enable_import_with_path():
"""Using path any template directory can be importable."""
assert tmpdir not in sys.path
raises(ImportError, "import test_suffixes4")
kid.enable_import(path=tmpdir)
dest = joinpath(tmpdir, "test_suffixes4.kid")
copyfile(tfile, dest)
import test_suffixes4
kid.disable_import(path=tmpdir)
dest = joinpath(tmpdir, "test_suffixes5.kid")
copyfile(tfile, dest)
raises(ImportError, "import test_suffixes5")
def test_enable_import_empty():
"""By default *.kid files are imported."""
sys.path.insert(0, tmpdir)
try:
kid.disable_import()
raises(ImportError, "import test_suffixes0")
kid.enable_import()
import test_suffixes0
raises(ImportError, "import test_suffixes1")
kid.disable_import()
finally:
sys.path.remove(tmpdir)
def _create_report(self, pwm, background):
self.logger.info("Creating graphical report")
class ReportMotif:
pass
motifs = pwmfile_to_motifs(pwm)
for m,match in self.closest_match.items():
match[0].to_img(os.path.join(self.imgdir,"%s.png" % match[0].id), format="PNG")
sort_key = background[0]
if "genomic_matched" in background:
sort_key = "genomic_matched"
roc_img_file = "%s_%s_roc"
report_motifs = []
for motif in sorted(motifs, cmp=lambda x,y: cmp(self.mncp[sort_key][y.id], self.mncp[sort_key][x.id])):
rm = ReportMotif()
rm.id = motif.id
rm.id_href = {"href": "#%s" % motif.id}
rm.id_name = {"name": motif.id}
rm.img = {"src": os.path.join("images", "%s.png" % motif.id)}
rm.consensus = motif.to_consensus()
rm.bg = {}
for bg in background:
rm.bg[bg] = {}
rm.bg[bg]["e"] = "%0.2f" % self.e[bg][motif.id]
rm.bg[bg]["p"] = "%0.2f" % self.p[bg][motif.id]
rm.bg[bg]["auc"] = "%0.3f" % self.auc[bg][motif.id]
rm.bg[bg]["mncp"] = "%0.3f" % self.mncp[bg][motif.id]
rm.bg[bg]["roc_img"] = {"src": "images/" + os.path.basename(roc_img_file % (motif.id, bg)) + ".png"}
rm.bg[bg]["roc_img_link"] = {"href": "images/" + os.path.basename(roc_img_file % (motif.id, bg)) + ".png"}
rm.histogram_img = {"data":"images/%s_histogram.svg" % motif.id}
rm.histogram_link= {"href":"images/%s_histogram.svg" % motif.id}
rm.match_img = {"src": "images/%s.png" % self.closest_match[motif.id][0].id}
rm.match_id = self.closest_match[motif.id][0].id
rm.match_pval = "%0.2e" % self.closest_match[motif.id][1]
report_motifs.append(rm)
total_report = self.motif_report
kid.enable_import()
template_file = os.path.join(self.config.get_template_dir(), "report_template_v2.kid")
template = kid.Template(file=template_file, expname=self.name, motifs=report_motifs, inputfile=self.inputfile, date=datetime.today().strftime("%d/%m/%Y"), version=GM_VERSION)
f = open(total_report, "w")
f.write(template.serialize())
f.close()
def test_import_and_expand():
try:
del sys.modules['test.context']
except KeyError:
pass
kid.disable_import()
try:
import test.context as c
except ImportError:
c = None
assert c is None
kid.enable_import()
import test.context as c
kid.disable_import()
C = c.Template
out = joinpath(output_dir, 'context.out')
t = C(foo=10, bar='bla bla')
it = t.pull()
for e in it:
pass
t.write(out)
check_xml_file(out)
def test_import_and_expand():
try:
del sys.modules['test.context']
except KeyError:
pass
kid.disable_import()
try:
import test.context as c
except ImportError:
c = None
assert c is None
kid.enable_import()
import test.context as c
kid.disable_import()
C = c.Template
out = joinpath(output_dir, 'context.out')
t = C(foo=10, bar='bla bla')
it = t.pull()
for e in it:
pass
t.write(out)
check_xml_file(out)
def test_enable_import_with_ext():
"""Using exts any file extension can be importable."""
ext = ".html,.kid.html"
sys.path.insert(0, tmpdir)
try:
raises(ImportError, "import test_suffixes1")
raises(ImportError, "import test_suffixes2")
raises(ImportError, "import test_suffixes3")
kid.enable_import(ext=ext)
dest = joinpath(tmpdir, "test_suffixes1.kid")
copyfile(tfile, dest)
import test_suffixes1 # *.kid files are always importable
dest = joinpath(tmpdir, "test_suffixes2.html")
copyfile(tfile, dest)
import test_suffixes2
dest = joinpath(tmpdir, "test_suffixes3.kid.html")
copyfile(tfile, dest)
import test_suffixes3
dest = joinpath(tmpdir, "test_suffixes4.xhtml")
copyfile(tfile, dest)
raises(ImportError, "import test_suffixes4")
kid.disable_import()
finally:
sys.path.remove(tmpdir)
# # Copyright (c) SAS Institute Inc. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # import kid kid.enable_import()
#! /usr/bin/env python
# -*- coding: utf-8 -*-
"""
Filename: index.py
Authors: Han Lin Yap and Alexander Östman
Course: TDP003 - Projekt: Egna datormiljön
Date: HT09 - 2009-10-07
Program: LiU/IP1
Desciption: This is the startpage.
"""
import kid
import os
from config import *
kid.enable_import(path=os.path.dirname(__file__) + "/" + "templates")
def index():
template = kid.Template(name='home',
headline=get_text('startpage'),
title=get_text('sitename'),
**common_language[DEFAULT_LANGUAGE])
template.cache = False
return template.serialize(output='xhtml-strict')
#! -*- coding: utf-8 -*-
# Returns a project with specified id
# Whenever exceptions is caught the user is redirected to a page telling a error has occured.
import site
import kid
import os
import sys
import data
path = os.getcwd() + "/"
sys.path.append(path)
kid.enable_import(path=path)
def index(id):
try:
id = int(id)
except ValueError:
pass
project = data.lookup_project(id)[1]
if project is not None:
template = kid.Template(file=os.path.dirname(__file__) + os.sep + 'templates' + os.sep + 'project',project_id=project)
else:
template = kid.Template(file=os.path.dirname(__file__) + os.sep + 'templates' + os.sep + 'error',project_id=project)
template.cache = False
site.cache = False
return template.serialize(output='xhtml-strict')
add_pos = sorted(scores.values(),cmp=lambda x,y: cmp(x[1], y[1]))[0][1]
for motif in members:
score, pos, strand = scores[motif]
add = pos - add_pos
if strand in [1,"+"]:
pass
else:
#print "RC %s" % motif.id
rc = motif.rc()
rc.id = motif.id
motif = rc
#print "%s\t%s" % (motif.id, add)
motif.to_img(os.path.join(outdir, "%s.png" % motif.id.replace(" ", "_")), format="PNG", add_left=add)
ids[-1][2] = [dict([("src", "%s.png" % motif.id.replace(" ", "_")), ("alt", motif.id.replace(" ", "_"))]) for motif in members]
kid.enable_import()
template_file = os.path.join(sys.prefix, "share/gimmemotifs/templates/cluster_template.kid")
template = kid.Template(file=template_file, motifs=ids)
f = open(os.path.join(outdir, "cluster_report.html"), "w")
f.write(template.serialize())
f.close()
f = open(os.path.join(outdir, "clustered_motifs.pwm"), "w")
if len(clusters) == 1 and len(clusters[0][1]) == 1:
f.write("%s\n" % clusters[0][0].to_pwm())
else:
for motif in tree.get_clustered_motifs():
f.write("%s\n" % motif.to_pwm())
f.close()
def test_import_hook():
kid.enable_import()
import test.test_if
assert_template_interface(test.test_if)
assert sys.modules.has_key('test.test_if')
kid.disable_import()
def cluster(args):
revcomp = not args.single
outdir = os.path.abspath(args.outdir)
if not os.path.exists(outdir):
os.mkdir(outdir)
trim_ic = 0.2
clusters = []
motifs = pwmfile_to_motifs(args.inputfile)
if len(motifs) == 1:
clusters = [[motifs[0], motifs]]
else:
tree = cluster_motifs(args.inputfile, "total", "wic", "mean", True, threshold=args.threshold, include_bg=True)
clusters = tree.getResult()
ids = []
mc = MotifComparer()
sys.stderr.write("Creating images\n")
for cluster,members in clusters:
cluster.trim(trim_ic)
cluster.to_img(os.path.join(outdir,"%s.png" % cluster.id), format="PNG")
ids.append([cluster.id, {"src":"%s.png" % cluster.id},[]])
if len(members) > 1:
scores = {}
for motif in members:
scores[motif] = mc.compare_motifs(cluster, motif, "total", "wic", "mean", pval=True)
add_pos = sorted(scores.values(),cmp=lambda x,y: cmp(x[1], y[1]))[0][1]
for motif in members:
score, pos, strand = scores[motif]
add = pos - add_pos
if strand in [1,"+"]:
pass
else:
#print "RC %s" % motif.id
rc = motif.rc()
rc.id = motif.id
motif = rc
#print "%s\t%s" % (motif.id, add)
motif.to_img(os.path.join(outdir, "%s.png" % motif.id.replace(" ", "_")), format="PNG", add_left=add)
ids[-1][2] = [dict([("src", "%s.png" % motif.id.replace(" ", "_")), ("alt", motif.id.replace(" ", "_"))]) for motif in members]
kid.enable_import()
template_file = os.path.join(sys.prefix, "share/gimmemotifs/templates/cluster_template.kid")
template = kid.Template(file=template_file, motifs=ids)
f = open(os.path.join(outdir, "cluster_report.html"), "w")
f.write(template.serialize())
f.close()
f = open(os.path.join(outdir, "cluster_key.txt"), "w")
for id in ids:
f.write("%s\t%s\n" % (id[0], ",".join([x["alt"] for x in id[2]])))
f.close()
f = open(os.path.join(outdir, "clustered_motifs.pwm"), "w")
if len(clusters) == 1 and len(clusters[0][1]) == 1:
f.write("%s\n" % clusters[0][0].to_pwm())
else:
for motif in tree.get_clustered_motifs():
f.write("%s\n" % motif.to_pwm())
f.close()
