0.0.16

seqyuan · Mar 2, 2024 · 9308e69 · 9308e69
1 parent 9c2c11e
commit 9308e69
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diff --git a/README.rst b/README.rst
@@ -1,7 +1,3 @@
-.. image:: https://zenodo.org/badge/572302042.svg
-   :target: https://zenodo.org/badge/latestdoi/572302042
-
-
 =======
 trackc
 =======
@@ -100,7 +96,7 @@ trackc support both api and cli. Here is a cli example:
 
 .. image:: neo-domain.png
 
-conf.yml content
+**conf.yml** content
 
 .. code-block:: yaml
 
@@ -116,7 +112,7 @@ conf.yml content
             row_regions:
               - 18:47400000-48280000
               - 18:75280000-74030000
-        mapC:
+          mapC:
             map_type: tri
             label: neo tad
             cmap: PuBu

diff --git a/docs/gallery/genome_denovo_scaffolding.ipynb b/docs/gallery/genome_denovo_scaffolding.ipynb
diff --git a/docs/gallery/index.rst b/docs/gallery/index.rst
@@ -20,11 +20,20 @@ Here are some flexible practical examples of trackc
     :glob:
 
     rearranged_interactions
+    neo_domain
 
 
 .. nbgallery::
     :caption: AML 3DGenome
     :name: rst-gallery3
     :glob:
 
-    ../track_types/Virtual4C
+    ../track_types/Virtual4C
+
+.. nbgallery::
+    :caption: 
+    :name: rst-gallery4
+    :glob 
+
+    scaffold_contig_reorder
+    genome_denovo_scaffolding
diff --git a/docs/gallery/neo_domain.ipynb b/docs/gallery/neo_domain.ipynb
diff --git a/docs/gallery/rearranged_interactions.ipynb b/docs/gallery/rearranged_interactions.ipynb
diff --git a/docs/gallery/scaffold_contig_reorder.ipynb b/docs/gallery/scaffold_contig_reorder.ipynb
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "trackc"
-version = "v0.0.15"
+version = "v0.0.16"
 description = ""
 authors = ["seqyuan <[email protected]>", "Minghong Li <[email protected]>"]
 readme = "README.rst"

diff --git a/trackc/pl/zoomin.py b/trackc/pl/zoomin.py
@@ -80,6 +80,10 @@ def zoomin(
     if colors == None:
         colors = trackcl_11
 
+
+    if len(colors) < zoomin_GRs.shape[0]:
+    	colors = colors * (int(zoomin_GRs.shape[0]/len(colors)) + 1)
+    	print(len(colors))
     for i, row in zoomin_GRs.iterrows():
         x = row[["ps", "pe", "ore", "ors"]]
         y = [0, 0, 1, 1]

diff --git a/trackc/scripts/gtf2bed12.py b/trackc/scripts/gtf2bed12.py
@@ -39,7 +39,7 @@ def tostr(self, biotype2bed13):
                 blockStarts = blockStarts + "," + tmp[0]
 
         obj_str = (
-            "{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}\t{11}\t{12}".format(
+            "{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}\t{11}".format(
                 self.chrom,
                 self.start,
                 self.end,
@@ -55,9 +55,9 @@ def tostr(self, biotype2bed13):
                 self.gene_biotype,
             )
         )
-        if biotype2bed13 == False:
+        if biotype2bed13 == True:
             obj_str = (
-                "{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}\t{11}".format(
+                "{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}\t{11}\t{12}".format(
                     self.chrom,
                     self.start,
                     self.end,

diff --git a/trackc/scripts/trackc_cli.py b/trackc/scripts/trackc_cli.py
@@ -73,7 +73,7 @@ def hicContactMap(Paras, ax):
     if "mat2" in Paras.keys():
         if Paras["mat2"]["method"] == "extractCisContact":
             del Paras["mat2"]["method"]
-            mat = tc.tl.extractCisContact(**Paras["mat2"])
+            mat2 = tc.tl.extractCisContact(**Paras["mat2"])
 
         elif Paras["mat2"]["method"] == "extractContactRegions":
             if (
@@ -84,7 +84,7 @@ def hicContactMap(Paras, ax):
                 mat_obj = tc.tl.extractContactRegions(
                     clr=Paras["mat2"]["clr"], row_regions=region
                 )
-                mat = mat_obj.cmat
+                mat2 = mat_obj.cmat
         else:
             pass
 
@@ -150,6 +150,9 @@ def cli(config, regions, outfile, basefigsize):
             ax = ten.axs(axs_pre.loc[tt["ax"], "rank_u"])
             ax.set_axis_off()
             continue
+
+        print('ax: ', tt["ax"])
+
         paras = tt["track_para"]
         if track_type in regions_type:
             if "regions" not in paras.keys():