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Commit 3108a9c6 authored by fabrice's avatar fabrice
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Setting position filter mandatory in contactmap section (have to do the same in setup section)

parent 3e7e1ca5
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ariaec/__init__.pyc
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ariaec/base.pyc
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ariaec/commands.pyc
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ariaec/econverter.pyc
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ariaec/ecsettings.pyc
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ariaec/maplot.py
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......@@ -72,6 +72,12 @@ class AriaEcContactMap(object):
self.protein, clashlist=fo.clashlist,
outprefix=self.outprefix,
outdir=self.settings.outdir)
else:
# Use only position filter
self.filter(fo.mapdict, fo.filetype, fo.contactlist,
self.protein, clashlist=fo.clashlist,
outprefix=self.outprefix,
outdir=self.settings.outdir, mapfilters="pos")
self.allresmap[fo.filetype] = fo.mapdict
try:
......@@ -84,22 +90,22 @@ class AriaEcContactMap(object):
self.settings.setup.config.get("n_factor"))
plotparams = {k: self.settings.contactmap.config.get(k, None)
for k in ('size_fig', 'plot_ext', 'plot_dpi')}
outdir = self.settings.outdir
if self.settings.contactmap.config.get("save_fig"):
refmap.saveplot(outdir=outdir,
outprefix="_".join((self.outprefix, "pdb")),
**plotparams)
for mapt in self.allresmap.keys():
outdir = self.settings.outdir
prefix = "_".join((self.outprefix, mapt, self.reftype))
if mapt == self.reftype and not \
self.settings.contactmap.args.get("onlyreport", False):
refmap.write_contacts("_".join((self.outprefix, mapt)),
outdir=outdir,
scoremap=self.refmap.get("scoremap",
None))
if self.settings.contactmap.config.get("save_fig"):
refmap.saveplot(outdir=outdir,
outprefix="_".join((self.outprefix, mapt)),
**plotparams)
continue
scoremap = self.allresmap[mapt].get('scoremap', None)
......@@ -107,7 +113,7 @@ class AriaEcContactMap(object):
self.allresmap[mapt].get("scoremap") is not None:
if not self.settings.contactmap.args.get("nofilter"):
# Get filtered contact map/list
# Get top contact map/list
cmpmap = self.allresmap[mapt]["contactmap"].topmap(
self.allresmap[mapt]["scoremap"], nb_c)
cmplist = self.allresmap[mapt]['scoremap'].sortedset(
......
ariaec/maplot.pyc
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ariaec/protein.pyc
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ariaec/protmap.py
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......@@ -9,6 +9,7 @@ matplotlib.use("Agg", warn=False)
import os
import re
import csv
import logging
import collections
import itertools
......@@ -68,6 +69,12 @@ class Map(pd.DataFrame):
self.sym = sym
self.desc = desc
@staticmethod
def plotflush():
plt.clf()
plt.cla()
plt.close()
def sortedset(self, human_idx=False):
# Remove duplicate in sort_list
n = 1 if human_idx else 0
......@@ -187,6 +194,9 @@ class ProteinMap(Map):
def maplot(self):
# Contact map Plot
if not self._maplot:
# Flush matplot
logger.debug("Build maplot")
self.plotflush()
minticks = tickmin(self, shift=1) # Nb graduations
self._maplot = sns.heatmap(self, square=True, cbar=False,
......@@ -252,6 +262,7 @@ class ProteinMap(Map):
raise NotImplementedError
def compareplot(self, protmap, save_fig=True, alpha=None, **kwargs):
self.plotflush()
# Contact map plot
if getattr(protmap, "shape") and self.shape != protmap.shape:
logging.error("Cant't compare %s map with %s" % (
......@@ -261,7 +272,6 @@ class ProteinMap(Map):
cmplist = protmap.contact_list()
ymax = len(self.sequence) - 1
if protmap.contact_flags:
flags = set(protmap.contact_flags.values())
# Color palette
......@@ -325,35 +335,6 @@ class ProteinMap(Map):
y_true, y_scores)
aver_prec = skm.average_precision_score(y_true, y_scores)
if plotag:
plotpath = os.path.join(plotdir, "%s.roc.%s" % (outprefix,
plot_ext))
plt.figure()
plt.plot(allfpr, alltpr, label='ROC curve (area = %0.2f)' % roc_auc)
plt.plot([0, 1], [0, 1], 'k--')
plt.xlim([0.0, 1.0])
plt.ylim([0.0, 1.0])
plt.xlabel('False Positive Rate')
plt.ylabel('True Positive Rate')
plt.title('Receiver operating characteristic %s vs. %s' % (
map1name, map2name))
plt.legend(loc="lower right")
plt.savefig(plotpath)
plotpath = os.path.join(plotdir, "%s.precall.%s" % (outprefix,
plot_ext))
# Precision recall curve
plt.clf()
plt.plot(allrec, allprec, label='Precision-Recall curve')
plt.xlabel('Recall')
plt.ylabel('Precision')
plt.ylim([0.0, 1.0])
plt.xlim([0.0, 1.0])
plt.title('Precision-Recall {1} vs. {2}: AUC={0:0.2f}'.format(
aver_prec, map1name, map2name))
plt.legend(loc="lower left")
plt.savefig(plotpath)
msg = """\
## Report {map1name} vs. {map2name}
##
......@@ -418,6 +399,51 @@ class ProteinMap(Map):
logger.debug("\n" + msg)
reportf.write(msg)
if plotag and scoremap is not None:
csv_roc = os.path.join(plotdir, "%s.roc.csv" % outprefix)
logger.info("Generate roc file (%s)" % csv_roc)
with open(csv_roc, "w") as f:
f.write("TPR,FPR,Treshold\n")
writer = csv.writer(f)
writer.writerows(zip(alltpr, allfpr, rocthresholds))
plotpath = os.path.join(plotdir, "%s.roc.%s" % (outprefix,
plot_ext))
logger.info("Generate roc plot (%s)" % plotpath)
plt.figure()
plt.plot(allfpr, alltpr, label='ROC curve (area = %0.2f)' % roc_auc)
plt.plot([0, 1], [0, 1], 'k--')
plt.xlim([0.0, 1.0])
plt.ylim([0.0, 1.0])
plt.xlabel('False Positive Rate')
plt.ylabel('True Positive Rate')
plt.title('Receiver operating characteristic %s vs. %s' % (
map1name, map2name))
plt.legend(loc="lower right")
plt.savefig(plotpath)
csv_precall = os.path.join(plotdir, "%s.roc.csv" % outprefix)
logger.info("Generate precall file (%s)" % csv_precall)
with open(csv_precall, "w") as f:
f.write("Precision,Recall,Treshold\n")
writer = csv.writer(f)
writer.writerows(zip(allprec, allrec, prthresholds))
plotpath = os.path.join(plotdir, "%s.precall.%s" % (outprefix,
plot_ext))
logger.info("Generate precall plot (%s)" % plotpath)
# Precision recall curve
plt.clf()
plt.plot(allrec, allprec, label='Precision-Recall curve')
plt.xlabel('Recall')
plt.ylabel('Precision')
plt.ylim([0.0, 1.0])
plt.xlim([0.0, 1.0])
plt.title('Precision-Recall {1} vs. {2}: AUC={0:0.2f}'.format(
aver_prec, map1name, map2name))
plt.legend(loc="lower left")
plt.savefig(plotpath)
def compare_contactmap(self, cmpmap, contactlist, outprefix,
outdir="", distmap=None, human_idx=True):
# CSV file giving TP/FP contacts
......@@ -1101,6 +1127,8 @@ class MapFilter:
mapfilters = [elm for elm in mapfilters if elm in self.filter_types]
else:
mapfilters = [mapfilters]
if "pos" not in mapfilters:
mapfilters.insert(0, "pos")
logger.info("Filtering %s contact map" % mtype)
for flt in mapfilters:
# /!\ cys unicity filter must be the last filter !
......
ariaec/protmap.pyc
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ariaec/reader.pyc
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ariaec/setup.pyc
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version.py
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# Do not edit this file, pipeline versioning is governed by git tags
__version__=v0.1.4-dev1-1-gf2ac0b3
\ No newline at end of file
__version__=v0.1.8-dev2
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