coolbox 0.3.7__py3-none-any.whl → 0.3.9__py3-none-any.whl

coolbox/utilities/hic/wrap.py

@@ -35,7 +35,7 @@ class StrawWrap(object):
         self.chromosomes, self.resolutions, self.masterindex, self.genome, self.metadata = self.__info()
         self.fetched_binsize = None
 
-    def fetch(self, genome_range1, genome_range2=None):
+    def fetch(self, gr1, gr2=None):
         """
         Return
         ------
@@ -43,26 +43,34 @@ class StrawWrap(object):
         """
         from coolbox.utilities.genome import GenomeRange
 
-        if genome_range2 is None:
-            genome_range2 = genome_range1
-        genome_range1 = to_gr(genome_range1)
-        genome_range2 = to_gr(genome_range2)
+        flip = False
 
-        if isinstance(genome_range1, str):
-            genome_range1 = GenomeRange(genome_range1)
-        if isinstance(genome_range2, str):
-            genome_range2 = GenomeRange(genome_range2)
+        if gr2 is None:
+            gr2 = gr1
+        gr1 = to_gr(gr1)
+        gr2 = to_gr(gr2)
+        if gr2.start < gr1.start:
+            flip = True
+            gr1, gr2 = gr2, gr1
 
-        if genome_range1.chrom.startswith("chr"):
-            genome_range1.change_chrom_names()
-        if genome_range2.chrom.startswith("chr"):
-            genome_range2.change_chrom_names()
+        if isinstance(gr1, str):
+            gr1 = GenomeRange(gr1)
+        if isinstance(gr2, str):
+            gr2 = GenomeRange(gr2)
 
-        binsize = self.infer_binsize(genome_range1)
+        if gr1.chrom.startswith("chr"):
+            gr1.change_chrom_names()
+        if gr2.chrom.startswith("chr"):
+            gr2.change_chrom_names()
+
+        binsize = self.infer_binsize(gr1)
         self.fetched_binsize = binsize  # expose fetched binsize
 
-        straw_list = self.__fetch_straw_list(genome_range1, genome_range2, binsize)
-        return self.__list_to_matrix(straw_list, genome_range1, genome_range2, binsize)
+        straw_iter = self.__fetch_straw_iter(gr1, gr2, binsize)
+        mat = self.__straw_to_matrix(straw_iter, gr1, gr2, binsize)
+        if flip:
+            mat = mat.T
+        return mat
 
     def infer_binsize(self, genome_range):
         from .tools import infer_resolution
@@ -71,13 +79,36 @@ class StrawWrap(object):
         else:
             return self.binsize
 
-    def __fetch_straw_list(self, genome_range1, genome_range2, binsize):
+    def __fetch_straw_iter(self, genome_range1, genome_range2, binsize):
+        try:
+            slist = self.__fetch_straw_list_strawc(genome_range1, genome_range2, binsize)
+            siter = ((r.binX, r.binY, r.counts) for r in slist)
+        except ImportError:
+            log.warning("strawC is not installed. Install strawC to achieve faster read speed: $ pip install strawC")
+            slist = self.__fetch_straw_list_straw(genome_range1, genome_range2, binsize)
+            siter = ((r[0] * binsize, r[1] * binsize, r[2]) for r in zip(*slist))
+        return siter
+
+    def __fetch_straw_list_straw(self, genome_range1, genome_range2, binsize):
         from coolbox.utilities.hic.straw import straw
+        s1, e1 = genome_range1.start//binsize, genome_range1.end//binsize
+        s2, e2 = genome_range2.start//binsize, genome_range2.end//binsize
+        straw_obj = straw(self.hic_file)
+        matrix_obj = straw_obj.getNormalizedMatrix(genome_range1.chrom, genome_range2.chrom, self.normalization, 'BP', binsize)
+        if matrix_obj is None:
+            log.warning("Try to read unbalanced matrix.")
+            self.normalization = "NONE"
+            matrix_obj = straw_obj.getNormalizedMatrix(genome_range1.chrom, genome_range2.chrom, self.normalization, 'BP', binsize)
+        slist = matrix_obj.getDataFromBinRegion(s1, e1, s2, e2)
+        return slist
+
+    def __fetch_straw_list_strawc(self, genome_range1, genome_range2, binsize):
+        import strawC
         chr1loc = str(genome_range1).replace('-', ':')
         chr2loc = str(genome_range2).replace('-', ':')
         slist = []
         try:
-            slist = straw(self.normalization, self.hic_file, chr1loc, chr2loc, 'BP', binsize)
+            slist = strawC.strawC(self.normalization, self.hic_file, chr1loc, chr2loc, 'BP', binsize)
         except Exception as e:
             log.warning("Error occurred when reading the dothic file with straw:")
             log.warning(str(e))
@@ -85,7 +116,7 @@ class StrawWrap(object):
                 log.warning("Try to read unbalanced matrix.")
                 self.normalization = "NONE"
                 try:
-                    slist = straw(self.normalization, self.hic_file, chr1loc, chr2loc, 'BP', binsize)
+                    slist = strawC.strawC(self.normalization, self.hic_file, chr1loc, chr2loc, 'BP', binsize)
                 except Exception as e:
                     log.warning("Failed.")
                     log.warning(str(e))
@@ -101,9 +132,9 @@ class StrawWrap(object):
         if genome_range2.chrom.startswith("chr"):
             genome_range2.change_chrom_names()
         binsize = self.infer_binsize(genome_range1)
-        slist = self.__fetch_straw_list(genome_range1, genome_range2, binsize)
-        pixels = DataFrame(slist)
-        pixels = pixels.T
+        siter = self.__fetch_straw_iter(genome_range1, genome_range2, binsize)
+        rows = [[i[0], i[1], i[2]] for i in siter]
+        pixels = DataFrame(rows)
         pixels.columns = ['start1', 'start2', 'value']
         pixels['start1'] = pixels['start1'].astype('int32')
         pixels['start2'] = pixels['start2'].astype('int32')
@@ -114,13 +145,13 @@ class StrawWrap(object):
         pixels = pixels[['chrom1', 'start1', 'end1', 'chrom2', 'start2', 'end2', 'value']]
         return pixels
 
-    def __list_to_matrix(self, straw_list, genome_range1, genome_range2, binsize):
+    def __straw_to_matrix(self, straw_iter, genome_range1, genome_range2, binsize):
         import numpy as np
         binlen1 = (genome_range1.length // binsize) + 1
         binlen2 = (genome_range2.length // binsize) + 1
         mat = np.zeros((binlen1, binlen2), dtype=np.float64)
         is_cis = (genome_range1 == genome_range2)
-        for rec in zip(*straw_list):
+        for rec in straw_iter:
             loc1, loc2, c = rec[0], rec[1], rec[2]
             bin1id = (loc1 - genome_range1.start) // binsize
             bin2id = (loc2 - genome_range2.start) // binsize

{coolbox-0.3.7.dist-info → coolbox-0.3.9.dist-info}/METADATA

@@ -1,13 +1,12 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: coolbox
-Version: 0.3.7
+Version: 0.3.9
 Summary: Jupyter notebook based genomic data visulization toolkit.
 Home-page: https://github.com/GangCaoLab/CoolBox
 Author: Weize Xu
 Author-email: vet.xwz@gmail.com
 License: GPLv3
 Keywords: genomics,bioinformatics,visualization,Jupyter
-Platform: UNKNOWN
 Classifier: Development Status :: 3 - Alpha
 Classifier: Operating System :: POSIX
 Classifier: Programming Language :: Python
@@ -20,25 +19,35 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Visualization
 Requires-Python: >=3.7, <4
-Requires-Dist: scipy (>=1.0.0)
+License-File: LICENSE
+Requires-Dist: scipy>=1.0.0
 Requires-Dist: numpy
-Requires-Dist: pandas (>=1.0.0)
+Requires-Dist: pandas>=1.0.0
 Requires-Dist: statsmodels
-Requires-Dist: matplotlib (>=3.1.1)
-Requires-Dist: jupyter (>=1.0.0)
-Requires-Dist: ipywidgets (>=7.5.1)
+Requires-Dist: matplotlib>=3.8.4
+Requires-Dist: jupyter>=1.0.0
+Requires-Dist: ipywidgets>=7.5.1
 Requires-Dist: nbformat
 Requires-Dist: voila
 Requires-Dist: svgutils
 Requires-Dist: intervaltree
-Requires-Dist: dna-features-viewer
+Requires-Dist: dna_features_viewer
 Requires-Dist: h5py
 Requires-Dist: cooler
 Requires-Dist: pybbi
 Requires-Dist: numpydoc
 Requires-Dist: fire
 Requires-Dist: pytest
+Requires-Dist: strawC
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 See https://github.com/GangCaoLab/CoolBox
-
-

{coolbox-0.3.7.dist-info → coolbox-0.3.9.dist-info}/RECORD

@@ -1,62 +1,62 @@
-coolbox/__init__.py,sha256=MZROqMwVP4JA-LXfTOR7mgacQSXDOlHt1eBZRUHPRnc,22
+coolbox/__init__.py,sha256=gbDwVXQgqJCrp_LBD8s-Ao23kHOWEZvGI_dULd1w5y8,22
 coolbox/api.py,sha256=kFF91EQBjVhJt0_TWzOea9_K15lORsqpwS6lB33hMec,1371
-coolbox/cli.py,sha256=Q4JpKmWqV-XzwEgjKpbPS3s7htxzf3udxMSiL4g7nZ8,13072
+coolbox/cli.py,sha256=ZnnuBlLQIn-SfSnpO8s5XKwEbNBv1fGfLx7F1seyfwU,13032
 coolbox/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 coolbox/core/feature.py,sha256=uS_lxkSY5XiEDV3Sy7kvSptZSLKjUXyGYdqU0jItK1Y,4783
 coolbox/core/browser/__init__.py,sha256=sSnKCwXPqLX8Lj349CWohF6zt6ORYjl68EtXNPev85c,1188
-coolbox/core/browser/base.py,sha256=xxMpnpyODBku63mR1ge9ulW_ocmBMRt4uyu-bhwNT54,9049
+coolbox/core/browser/base.py,sha256=5uVfulYpOh64Ln0ByeRmspliJNMqaQrM310PQ42ZOHE,9257
 coolbox/core/browser/widgets/__init__.py,sha256=_nTbIanG1hHuAtXRXj_hQ_jzx8jqTINKFGWVUYVF6ck,64
 coolbox/core/browser/widgets/base.py,sha256=7JqUcbm6JiEKGAV7tTgS9dxdv5iLy5VTNkfgEp7jgVk,772
 coolbox/core/browser/widgets/full.py,sha256=tTzIpGqi3zDdkHkDk8T7V03HO8q1wsr_iURZn271ZBc,1380
 coolbox/core/browser/widgets/navigation.py,sha256=uZaspuG_ihYo1fijUE9GT1qxUlQTbf14F_NO11XaqzY,10329
 coolbox/core/browser/widgets/simple.py,sha256=edMR5ATFyNfeZ9vF0WgfdbkfV1cOivQ7vdhsCqJslko,858
-coolbox/core/coverage/__init__.py,sha256=S3NkyPxwWy-ut2Gi-MR3XsRTrWXUzBE64N0HPO8Oou4,629
+coolbox/core/coverage/__init__.py,sha256=kbnMBT9CmUnHCNLxE4avQSkPHoQ-HYUooRs5YZzlSBo,629
 coolbox/core/coverage/base.py,sha256=hybOLXk0H0Btz7zJ308i0mrx7YaG8lFA4INp8KNVQdc,6075
-coolbox/core/coverage/highlights.py,sha256=3buduSzFNDTmKq_amS7Bnjl_Z0uWWzOyo3nTRs_qHvQ,6292
+coolbox/core/coverage/highlights.py,sha256=elXU0In66521Cg2hM-TvbxhtuCqtFfcccdlxoyW5OSI,6294
 coolbox/core/coverage/hlines.py,sha256=f-v54Mgz82peaJAZ3qsrqASo_0PiUzSNI9CvHCEfoaY,1744
 coolbox/core/coverage/vlines.py,sha256=6JPrFdkyHgmiGFMHLTJCAfpXGtJHv09pwJo-1Rt28xQ,3798
 coolbox/core/frame/__init__.py,sha256=uNle3cyOXuSsoneUzr0Zu8v6YNVSaKLRkR1D6Xic1Ts,59
 coolbox/core/frame/base.py,sha256=TOd-X_Cs6zQbC-xgGXMmqGjx6Vh2F9pIxdLHDwJyJpg,10645
-coolbox/core/frame/frame.py,sha256=KjSjtz_M-LbURNZ0geDC0kHehXkdSbz448pKuEfTh-0,7305
+coolbox/core/frame/frame.py,sha256=Ltrsty0xj_iSMDkNqVEZL8dCT6Trrol3P7VvpfTLkFw,7823
 coolbox/core/frame/superframe/__init__.py,sha256=GmuujYuf1O9Dy9LcU_Q774cCK_GV1R9R9rGIY82qYQk,33
 coolbox/core/frame/superframe/base.py,sha256=eX-Vx6_bjREyFJzlx7wcIxH64c2PF8hebiX5k1bvIYc,2270
 coolbox/core/frame/superframe/jointview.py,sha256=lTD20hOgl_bCo8H6Jlzm9OAFtXtBKMv0AXGJO7cRYec,9474
-coolbox/core/track/__init__.py,sha256=sKAkB6LJCw_jJft_DA9Wv25GsqQV6GPVUbM4I9cGVCs,449
+coolbox/core/track/__init__.py,sha256=GNsVAhhq3kcJtWdanlJo1IQaI4JkMQo8tO3FnVKtU4s,465
 coolbox/core/track/bam.py,sha256=eLFpbIjNXql81GBJDI8KW-ZoeRmoW5RKOwMKzEJMeiY,3297
 coolbox/core/track/base.py,sha256=UA21GuqrbWGIO4LxvGbrMViMlSzAHrWevHysLtrF0k8,8027
-coolbox/core/track/gtf.py,sha256=WNyF25pc-BF36zkuC2P8JqTAgVeRzdXo7HPvEveNjcE,5395
-coolbox/core/track/ideogram.py,sha256=hSG_W96ZKtU9oo-X4odvCSCjWrt8flANBiTHqh4_vgY,4250
-coolbox/core/track/pseudo.py,sha256=LGH9vsIHcBmlcGTzjKKj_3edFRTkJBUsBwmN4t8eyss,4813
+coolbox/core/track/gtf.py,sha256=ZgmL_Pjvb2FuznGikbRJJ9_X8MI1voFrDZvkj70mlUk,5341
+coolbox/core/track/ideogram.py,sha256=vbdIi3_Yp6kP-uwAR7HQ1KxZnJLB0cw_nMfv_orva5M,4522
+coolbox/core/track/pseudo.py,sha256=qyBpD2PqEKJoQivZ2QaKN5XJJpzLvH_cOXc_Iuzmls0,4969
+coolbox/core/track/tad.py,sha256=P7hhqWjACW47qszDzjnA4TuBJU-79lY7rIotp_qYdyo,7791
 coolbox/core/track/arcs/__init__.py,sha256=rdZHnRJ11jC2Sp1fwx29gNMteUoqkeNvS7MsN0hWIIw,553
 coolbox/core/track/arcs/base.py,sha256=kIZR-vEPGZ7ygUHDA2HGqdWVK0-2lL-sa_QzKrsPuSU,3147
 coolbox/core/track/arcs/bedpe.py,sha256=bxyXjD3a6lui4y-5lkPzjPtqF_pp1VR7gFLnuGF1wfs,2628
 coolbox/core/track/arcs/fetch.py,sha256=_VE_Aixx9Kx0s0mP50stika0d5yx7UKYBxBG_dCsvIc,660
 coolbox/core/track/arcs/hicpeaks.py,sha256=XZWU9L1MM36EN2Zvg5dWZGcxoLgChMMae-Im4y6bZTY,540
 coolbox/core/track/arcs/pairs.py,sha256=j8xNMBBGbLzEfuQMVBDeBWCKprJ6ALLhiDRtLN7TmpE,1316
-coolbox/core/track/arcs/plot.py,sha256=cIiWGAsVlax1xArmqAmYhnlEErqF35GWhMbnTNklIRo,8298
-coolbox/core/track/bed/__init__.py,sha256=Z-4E2W5utvF_aw9Ecn078dOhGzE4CygWVVJjRWkZGFQ,67
-coolbox/core/track/bed/base.py,sha256=0m8Eh7p3FzQfjn9laTg_YzdaHbdLJjdgx8VmevAfLNY,3898
-coolbox/core/track/bed/bed.py,sha256=UlICZQHVqWfj9qFKIcsiM58RdUgSfzKHxAHWQEoFZUs,929
-coolbox/core/track/bed/fetch.py,sha256=SRVJjkWEybI6uTuo1VOrCVufHPaYzAeqdzLTIqVEvIY,2018
-coolbox/core/track/bed/plot.py,sha256=z2-0WStFOkQ5L0TUMV-BMcqBvKIX2qRM9pWzbsMs0dU,23523
-coolbox/core/track/bed/tad.py,sha256=RUK371ljvanrktc1tY9PLwDyqEFlrYd7185j8Mx7DTI,371
+coolbox/core/track/arcs/plot.py,sha256=nJk9OM3QmScA2kKpNQgooBzZW37cZmerMN8td1eox08,8402
+coolbox/core/track/bed/__init__.py,sha256=Jfr1EhUYCTpJdepIFq-89bk83Fr8LDaP1twiUWrFCQI,46
+coolbox/core/track/bed/base.py,sha256=dNioGhgFCOLeoiu3mhv8ExokonHGL6CrkNzf6KLKpro,5486
+coolbox/core/track/bed/bed.py,sha256=7tSL25mU3_1heg1ftdXs-3kn79trv7faQbR3t1t4KIw,1739
+coolbox/core/track/bed/fetch.py,sha256=IR2wAeCUS1YS0qEkelkwhZNI33fjKR4e9IepAGcyK9Q,2019
+coolbox/core/track/bed/plot.py,sha256=07lnIh0-xclFbBVMyDeUmCtfSIUDveGCnWv436KDS0s,17190
 coolbox/core/track/hicmat/__init__.py,sha256=JHuqWKQ3icSRvN1DUiROizvGrGHdEfHZlokQoQRCWc0,146
-coolbox/core/track/hicmat/base.py,sha256=a9Kya9Yff3DLSH9jdSxb351MMjA2ybb39CtK6zxpyKc,5416
-coolbox/core/track/hicmat/cool.py,sha256=UB8y1dVoLfBaxROD5Al6c43Ib8p2oGxkelN8EYa_k7M,2615
-coolbox/core/track/hicmat/dothic.py,sha256=fshXJFrd4qacA9jwS4B62fMDJc90J7cl5SzXRdDoLb8,2720
-coolbox/core/track/hicmat/hicmat.py,sha256=WZ8gZTjhCoyLUAWSYPgv8q889L13WImFANTpOi7xpsU,891
-coolbox/core/track/hicmat/plot.py,sha256=Vm7zjG2He75Zpcl08r1DD1PY3Lxoxu2Co1tV4KBxeME,9226
+coolbox/core/track/hicmat/base.py,sha256=vIoTfqXneugynhw0wkNCqob6Ptt4IVTkPdSWUQiUhJk,5693
+coolbox/core/track/hicmat/cool.py,sha256=FGs6JsHjG2Iy4vDjETzfhticctEaOuprzgHTyk4OBcg,2668
+coolbox/core/track/hicmat/dothic.py,sha256=M7gD85juT1vQOmbkFuoCXGF9RWI_iFyo6cfYsG7yO-0,2741
+coolbox/core/track/hicmat/hicmat.py,sha256=ZOnCN3sFJxILW11Qcw2JIU7phIjOhsbvWd9Trq7unSI,814
+coolbox/core/track/hicmat/plot.py,sha256=STFiEJEo8scg9GcJiVr4fgrt8DbDY0hUlyDvHl4t4OM,9411
 coolbox/core/track/hicmat/process.py,sha256=ETl2dufEVyrejcsSjyyqMvhhMLh28eV_fSMGaEY_J4g,5672
 coolbox/core/track/hicmat/hicdiff/__init__.py,sha256=7Ce79XaFBTrpG9isJykt3e7dM5p5IXJgGe1OeJKAAn0,55
 coolbox/core/track/hicmat/hicdiff/diff.py,sha256=Xu6kON7rhTurmhn7hUgnmSaEjQT-OOWWzrZyfigL1Ys,2818
 coolbox/core/track/hicmat/hicdiff/selfish.py,sha256=HRaeemZwO4MyBZAx4R4Z_NaNlwmZ1qhZwD5dlmD8USY,5184
-coolbox/core/track/hist/__init__.py,sha256=uasp1W_Hr3VhTlF6rw16jFpFpBdd8KNryhYFxhRDZR8,889
+coolbox/core/track/hist/__init__.py,sha256=GzKbiXG9kR7dfr_NZlM2EmWXl5GzzKPEcNZlzrii7FE,1090
 coolbox/core/track/hist/bam.py,sha256=tskPKPX2LdrNuuNcbxw4qcKAQJF6V3sOGNtQarNpN_E,1111
 coolbox/core/track/hist/base.py,sha256=3l34G8pGtVDHJEf_gGCQpYz75-25emUV_c3uSzYq6UY,4408
 coolbox/core/track/hist/bedgraph.py,sha256=5JCXE3pjgv_Pu4HFhaAY3Q01-nmOFZxKP_cWjbLbJCc,1609
-coolbox/core/track/hist/bigwig.py,sha256=yFU99oKJKH8d4IAJw7htqIRpQSO3rN6VFoBd8hUlfE8,3728
+coolbox/core/track/hist/bigwig.py,sha256=ZwFJAUrB9w4mTpPB3LZadtfFzGo6aGUOPi2Fp6RZjJI,3343
 coolbox/core/track/hist/hicfeature.py,sha256=d9EyUU3GNvsjzyf9hS3J-22qtdc5hfu6fbu2Q7O3-mw,9371
-coolbox/core/track/hist/plot.py,sha256=iVUWqGEAnT4vmjKbdJQObW6fovItBFy19JlQBEj8D3I,7879
+coolbox/core/track/hist/plot.py,sha256=RkN2lzhV-z6cQYIezBLUUF_KXzKCF2Zjk21vFAR4XaU,8199
 coolbox/core/track/hist/snp.py,sha256=iSn7r4CowSZMDkJ2zfRwavfQYDJhRinP5cwZVnoNLZY,3354
 coolbox/genome/hg19.txt,sha256=IdcU4R0MhT9t4wC0GyvXMiJmZAHizjPpHOzdPzyjy70,423
 coolbox/genome/hg38.txt,sha256=8LUJl2Mc9PDszabammK1DRV7Wpf7PDBvMiRjBdOHJtg,423
@@ -64,7 +64,7 @@ coolbox/genome/mm10.txt,sha256=vzWeqUgcJwoWaKFMO-p2vEQJi-Sp1C5CWhquvpu6H44,372
 coolbox/genome/mm9.txt,sha256=Hdpx0s3MmDbahX1lIuO8FEMZ5BlnrgpGZ9IG6RDT8Ho,372
 coolbox/utilities/__init__.py,sha256=yH4OKxaB2CC2KMMESC_8VswEPa60jb-QBSOLp_d2FFg,2411
 coolbox/utilities/bam.py,sha256=qR9Gey4sk2m8KjYw4jFlTKn_hYKIjyaRwE4EkehoDH4,2338
-coolbox/utilities/bed.py,sha256=j2XVZ6EteycjNZmMFsuq0UMsokFrD8kYU9ltrTOYkkY,17800
+coolbox/utilities/bed.py,sha256=s0KSgC2vXjKTzFPI3klGiyigcF14d0PGshEZH46SEz0,17804
 coolbox/utilities/doctool.py,sha256=ZfC6jLBhkATJR6iO8ghpdW3C8th7Gv7QNokfh5mo5FQ,4413
 coolbox/utilities/figtools.py,sha256=3SmHIyP8hQBHaBSVt2jgTAEtBwY9JptR6D4Z8utPcQU,4664
 coolbox/utilities/filetool.py,sha256=aEqqa7VBMZyqHtct48Qn8WizGmU65EIVi-zv9k4M9gY,2378
@@ -72,12 +72,12 @@ coolbox/utilities/fmtconvert.py,sha256=dK5X39ArYqaD31DDZPPT1BwrTCYZynPc6BP6GH7G2
 coolbox/utilities/genome.py,sha256=s3d8CH1xKJ8LhlBGjLvXxCK62CRI2P2b-TIyjlNWtj4,7743
 coolbox/utilities/logtools.py,sha256=-AY2Hb_RPv7Qydlb6ShwAknDqDPFKwXKq867AF8E99A,516
 coolbox/utilities/hic/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-coolbox/utilities/hic/straw.py,sha256=SF6x-5_9GThQVk3wk6SVcg1fHxQ6E7spvDkrpzxH2k8,23788
+coolbox/utilities/hic/straw.py,sha256=OccMxjTnvR6_tmdQajRzDSWhubdKUka_mbMA-YH0AYk,30655
 coolbox/utilities/hic/tools.py,sha256=d2jYcrMVSVp7Ft7MholvFmdMlFzPJYagI_Od5ewH4Tk,1818
-coolbox/utilities/hic/wrap.py,sha256=EYoF8Xcfxy7Dk9nlSocS6OkIEh5nGJ7E-UUYlFjhDoY,11174
-coolbox-0.3.7.data/scripts/coolbox,sha256=82rDcSSoAUZ8YUiahT-lSv77QZho8FCr1xPpbN_dK_c,67
-coolbox-0.3.7.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-coolbox-0.3.7.dist-info/METADATA,sha256=eCuwWsTIOCiJ2gciYplaO5zLvv0UKetqG6xag9d4VHg,1428
-coolbox-0.3.7.dist-info/WHEEL,sha256=OqRkF0eY5GHssMorFjlbTIq072vpHpF60fIQA6lS9xA,92
-coolbox-0.3.7.dist-info/top_level.txt,sha256=0n3TkrhoWU8tLVxqBDHrQNeqiV2IelFbwI4UIZC7R14,8
-coolbox-0.3.7.dist-info/RECORD,,
+coolbox/utilities/hic/wrap.py,sha256=Kq_EsP78gt3sT7oFqgzb7j19G395geMoXOAu87CtUFQ,12492
+coolbox-0.3.9.data/scripts/coolbox,sha256=82rDcSSoAUZ8YUiahT-lSv77QZho8FCr1xPpbN_dK_c,67
+coolbox-0.3.9.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+coolbox-0.3.9.dist-info/METADATA,sha256=FAMWtEhJF3eJN11hbMbV-HbwieoB4dkELvoOMKCdA_A,1635
+coolbox-0.3.9.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
+coolbox-0.3.9.dist-info/top_level.txt,sha256=0n3TkrhoWU8tLVxqBDHrQNeqiV2IelFbwI4UIZC7R14,8
+coolbox-0.3.9.dist-info/RECORD,,

{coolbox-0.3.7.dist-info → coolbox-0.3.9.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.36.2)
+Generator: setuptools (75.8.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

coolbox/core/track/bed/tad.py

@@ -1,18 +0,0 @@
-from .bed import BED
-from .base import BedBase
-
-
-class TAD(BED):
-    """
-    Tad tack from bed file
-    """
-
-    DEFAULT_PROPERTIES = {
-        'style': BedBase.STYLE_TAD,
-        'alpha': 0.3,
-    }
-
-    def __init__(self, file, **kwargs):
-        properties = TAD.DEFAULT_PROPERTIES.copy()
-        properties.update(kwargs)
-        super().__init__(file, **properties)