diff --git a/ariaec/__init__.pyc b/ariaec/__init__.pyc
index 0a688692da7f9ad1b88e6a73d21eb46c831377cc..42b779115f1d982b021de34a3c088eee58d048d0 100644
Binary files a/ariaec/__init__.pyc and b/ariaec/__init__.pyc differ
diff --git a/ariaec/base.pyc b/ariaec/base.pyc
index a2225329ee2801ba5b4989df43d92d0b97f98486..365e981ec59a720d21add9b113c4e20cdc1f84c5 100644
Binary files a/ariaec/base.pyc and b/ariaec/base.pyc differ
diff --git a/ariaec/commands.py b/ariaec/commands.py
index eda008cb93ca4d4c72f8e02e9c1413eb10fb039b..0ba025427effe7dd85401c468bdbb151f357fcff 100644
--- a/ariaec/commands.py
+++ b/ariaec/commands.py
@@ -177,6 +177,9 @@ class AriaEcCommand:
default=None, help="Do not use contact list "
"filter and select top n "
"contacts")
+ parser.add_argument("--onlyreport", dest="onlyreport",
+ action="store_true",
+ default=False, help="Generate only report file")
parser.add_argument("--ssidx", dest="ssidx", action="store_true",
default=False,
help="Use secondary structure index")
diff --git a/ariaec/commands.pyc b/ariaec/commands.pyc
index fe3093884131b3a59940f934fcdc43822ecc88e3..a38614cf856c3c4ad6a026166825a4c9e29811d7 100644
Binary files a/ariaec/commands.pyc and b/ariaec/commands.pyc differ
diff --git a/ariaec/maplot.py b/ariaec/maplot.py
index 18dee19188c7109298ea9b12d713aaea9e1273c5..645711f6bb0e2bb1d61f32aa6085803ba88ea5d6 100644
--- a/ariaec/maplot.py
+++ b/ariaec/maplot.py
@@ -90,7 +90,8 @@ class AriaEcContactMap(object):
outdir = self.settings.outdir
prefix = "_".join((self.outprefix, mapt, self.reftype))
- if 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",
@@ -128,26 +129,30 @@ class AriaEcContactMap(object):
# TODO: only one function for output files
# Write contact list in txt file
- cmpmap.write_contacts("_".join((self.outprefix, mapt)),
- scoremap=scoremap,
- outdir=outdir)
- # Write cmp stats
- cmpmap.compare_contactmap(refmap, cmplist, prefix,
- distmap=self.refmap["distmap"],
- human_idx=True,
- outdir=outdir)
refmap.report(cmpmap, scoremap=scoremap, outprefix=prefix,
- outdir=outdir, plotdir=self.settings.infra.get("graphics", outdir))
+ outdir=outdir,
+ plotag=not self.settings.contactmap.args.get(
+ "onlyreport"),
+ plotdir=self.settings.infra.get("graphics", outdir))
# Contact map comparison plot
# TODO: elementwise error with compare method
- refmap.compareplot(cmpmap, outprefix=prefix,
- outdir=outdir,
- save_fig=self.settings.contactmap.config.get(
- "save_fig"),
- alpha=self.settings.contactmap.config.get(
- "alpha"),
- **plotparams)
- # Contingency table
- # print(cmpmap.to_series())
- # logger.info(pd.crosstab(cmpmap.values, refmap.values,
- # rownames=[mapt], colnames=[self.reftype]))
+ # Write cmp stats
+ if not self.settings.contactmap.args.get("onlyreport", False):
+ cmpmap.write_contacts("_".join((self.outprefix, mapt)),
+ scoremap=scoremap,
+ outdir=outdir)
+ cmpmap.compare_contactmap(refmap, cmplist, prefix,
+ distmap=self.refmap["distmap"],
+ human_idx=True,
+ outdir=outdir)
+ refmap.compareplot(cmpmap, outprefix=prefix,
+ outdir=outdir,
+ save_fig=self.settings.contactmap.config.get(
+ "save_fig"),
+ alpha=self.settings.contactmap.config.get(
+ "alpha"),
+ **plotparams)
+ # Contingency table
+ # print(cmpmap.to_series())
+ # logger.info(pd.crosstab(cmpmap.values, refmap.values,
+ # rownames=[mapt], colnames=[self.reftype]))
diff --git a/ariaec/maplot.pyc b/ariaec/maplot.pyc
index 3474cdebf8089529afd56bbcf930a6ec6981bd15..8e2d7a1dde7431180f65dcb0d0c4c1faed158943 100644
Binary files a/ariaec/maplot.pyc and b/ariaec/maplot.pyc differ
diff --git a/ariaec/protein.pyc b/ariaec/protein.pyc
index 0fdf07a9316395e7555b137bf7d945d91e2ebe25..284b67088a7c769f0534a12991a39d4cbd2b4cf9 100644
Binary files a/ariaec/protein.pyc and b/ariaec/protein.pyc differ
diff --git a/ariaec/protmap.py b/ariaec/protmap.py
index ec12220c196627eed3f8f6feda95830f3aa4d37d..21ebafdaba7cde2d7193bb68b69a318c6afbb80b 100644
--- a/ariaec/protmap.py
+++ b/ariaec/protmap.py
@@ -294,7 +294,7 @@ class ProteinMap(Map):
self.saveplot(**kwargs)
def report(self, cmpmap, scoremap=None, outprefix="", outdir="", plotdir="",
- plot_ext="pdf"):
+ plot_ext="pdf", plotag=True):
reportpath = "%s/%s.report" % (outdir, outprefix)
logger.info("Generate report file (%s)" % reportpath)
with open(reportpath, 'w') as reportf:
@@ -320,36 +320,39 @@ class ProteinMap(Map):
allfpr, alltpr, rocthresholds = skm.roc_curve(y_true, y_scores,
pos_label=1)
roc_auc = skm.roc_auc_score(y_true, y_scores)
- 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)
allprec, allrec, prthresholds = skm.precision_recall_curve(
y_true, y_scores)
aver_prec = skm.average_precision_score(y_true, y_scores)
- plotpath = os.path.join(plotdir, "%s.precall.%s" % (outprefix,
+
+ if plotag:
+ plotpath = os.path.join(plotdir, "%s.roc.%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)
+ 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}
diff --git a/ariaec/protmap.pyc b/ariaec/protmap.pyc
index 6e5726397f52407b3bafcf63675c9133ccb4dd47..82d8147e5f4d45b223f11cd5d4ca80546517ad4d 100644
Binary files a/ariaec/protmap.pyc and b/ariaec/protmap.pyc differ
diff --git a/ariaec/setup.pyc b/ariaec/setup.pyc
index ddb0fe923f1b90ba63df12363dfd88aff5391197..bd6a1ed465b9192de27b9c0798e347979ff36b34 100644
Binary files a/ariaec/setup.pyc and b/ariaec/setup.pyc differ