Fix of line-end for clustering utility

CHANGES

@@ -1,3 +1,6 @@
+## 0.12.3 (2020-10-23)
+- Fix of windows /r line-end in "cluster_sites_by_overlap.py"
+
 ## 0.12.2 (2020-10-23)
 - Fix to BINDetect bug occurring in case of duplicates in --motif input. Motifs are now given unique names if duplicated. 
 - Change of "Transcription factor similarities" to "Transcription factor distance" in BINDetect.

tobias/__init__.py

@@ -1 +1 @@
-__version__ = "0.12.2"
+__version__ = "0.12.3"

tobias/scripts/cluster_sites_by_overlap.py

@@ -1,74 +1,74 @@
-#!/usr/bin/env python
-
-"""
-cluster_sites_by_overlap.py: Utility script to cluster .bed-file input and create a distance-matrix and dendrogram similar to the BINDetect output.
-
-@author: Mette Bentsen
-@contact: mette.bentsen (at) mpi-bn.mpg.de
-@license: MIT
-"""
-
-import os
-import argparse
-import matplotlib.pyplot as plt
-from scipy.cluster.hierarchy import dendrogram
-from tobias.utils.regions import RegionList, RegionCluster
-from tobias.utils.logger import TobiasLogger
-from tobias.utils.utilities import check_required, make_directory
-from tobias.utils.logger import TobiasLogger
-
-#----------------------------- Input arguments -----------------------------#
-
-parser = argparse.ArgumentParser()
-parser.add_argument("--bedfiles", nargs="*", help="Bedfiles with ID in the 4th column")
-parser.add_argument("--outdir", help="Output directory (default: bedfile_clustering_output)", default="bedfile_clustering_output")
-args = parser.parse_args()
-check_required(args, ["bedfiles"])
-
-logger = TobiasLogger()
-make_directory(args.outdir) #Create dir if not existing
-
-#------------------------- Read bedfiles to cluster ------------------------#
-
-all_sites = RegionList()
-for bedfile in args.bedfiles:
-	with open(bedfile) as f:
-		sites = RegionList().from_bed(bedfile)
-		all_sites.extend(sites)
-
-logger.info("Read {0} regions from {1} files".format(len(all_sites), len(args.bedfiles)))
-
-
-#---------- Calculate distances between sites in RegionList object ---------#
-
-logger.info("Calculating distances between regions")
-overlaps = all_sites.count_overlaps()
-clustering = RegionCluster(overlaps)
-clustering.overlap_to_distance()
-
-f_out = os.path.join(args.outdir, "distance_matrix.txt")
-clustering.write_distance_mat(f_out)
-logger.info("Wrote distance matrix to: {0}".format(f_out))
-
-
-#------------------------------ Plot dendrogram ----------------------------#
-
-logger.info("Plotting dendrogram")
-clustering.cluster()	#provides linkage matrix
-
-#Plot figure
-fig = plt.figure(figsize = (5, len(clustering.names)/7))
-dendro_dat = dendrogram(clustering.linkage_mat, 
-						labels=clustering.names, 
-						orientation="right", 
-						above_threshold_color="black", 
-						)
-
-plt.title("Clustering of input regions")
-plt.xlabel("Distance\n(based on overlap of .bed-file regions)")
-plt.ylabel("Region names")
-
-f_out = os.path.join(args.outdir, "dendrogram.pdf")
-plt.savefig(f_out, bbox_inches="tight")
-logger.info("Plotted dendrogram to: {0}".format(f_out))
+#!/usr/bin/env python
+
+"""
+cluster_sites_by_overlap.py: Utility script to cluster .bed-file input and create a distance-matrix and dendrogram similar to the BINDetect output.
+
+@author: Mette Bentsen
+@contact: mette.bentsen (at) mpi-bn.mpg.de
+@license: MIT
+"""
+
+import os
+import argparse
+import matplotlib.pyplot as plt
+from scipy.cluster.hierarchy import dendrogram
+from tobias.utils.regions import RegionList, RegionCluster
+from tobias.utils.logger import TobiasLogger
+from tobias.utils.utilities import check_required, make_directory
+from tobias.utils.logger import TobiasLogger
+
+#----------------------------- Input arguments -----------------------------#
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--bedfiles", nargs="*", help="Bedfiles with ID in the 4th column")
+parser.add_argument("--outdir", help="Output directory (default: bedfile_clustering_output)", default="bedfile_clustering_output")
+args = parser.parse_args()
+check_required(args, ["bedfiles"])
+
+logger = TobiasLogger()
+make_directory(args.outdir) #Create dir if not existing
+
+#------------------------- Read bedfiles to cluster ------------------------#
+
+all_sites = RegionList()
+for bedfile in args.bedfiles:
+	with open(bedfile) as f:
+		sites = RegionList().from_bed(bedfile)
+		all_sites.extend(sites)
+
+logger.info("Read {0} regions from {1} files".format(len(all_sites), len(args.bedfiles)))
+
+
+#---------- Calculate distances between sites in RegionList object ---------#
+
+logger.info("Calculating distances between regions")
+overlaps = all_sites.count_overlaps()
+clustering = RegionCluster(overlaps)
+clustering.overlap_to_distance()
+
+f_out = os.path.join(args.outdir, "distance_matrix.txt")
+clustering.write_distance_mat(f_out)
+logger.info("Wrote distance matrix to: {0}".format(f_out))
+
+
+#------------------------------ Plot dendrogram ----------------------------#
+
+logger.info("Plotting dendrogram")
+clustering.cluster()	#provides linkage matrix
+
+#Plot figure
+fig = plt.figure(figsize = (5, len(clustering.names)/7))
+dendro_dat = dendrogram(clustering.linkage_mat, 
+						labels=clustering.names, 
+						orientation="right", 
+						above_threshold_color="black", 
+						)
+
+plt.title("Clustering of input regions")
+plt.xlabel("Distance\n(based on overlap of .bed-file regions)")
+plt.ylabel("Region names")
+
+f_out = os.path.join(args.outdir, "dendrogram.pdf")
+plt.savefig(f_out, bbox_inches="tight")
+logger.info("Plotted dendrogram to: {0}".format(f_out))
 logger.info("Done!")