Fix genes for copynumber track and improve support for mcool files

figeno/cli/cli.py

@@ -2,7 +2,7 @@
 
 from figeno.cli import gui, init,make
 
-__version__ = "1.4.0"
+__version__ = "1.4.1"
 
 def main():
     parser = ArgumentParser("figeno",formatter_class=ArgumentDefaultsHelpFormatter)

figeno/figeno.py

@@ -421,6 +421,7 @@ def draw_symmetrical(self,file,width=183,dpi=150,transparent=False,warnings=[]):
         self.update_total_width(width)
         self.update_regions_width_symmetrical()
         self.update_margins()
+        if len(self.regions)==1: warnings.append("The symmetrical layout is intended for displaying more than one region.")
 
         #for i in range(0,len(self.tracks_list)-1):
         #    if isinstance(self.tracks_list[i],sv_track) and isinstance(self.tracks_list[i+1],copynumber_track):

figeno/gui/package.json

@@ -1,6 +1,6 @@
 {
   "name": "figeno",
-  "version": "1.4.0",
+  "version": "1.4.1",
   "private": true,
   "homepage": "./",
   "dependencies": {

figeno/track_copynumber.py

@@ -48,7 +48,6 @@ def __init__(self,input_type=None,freec_ratios=None,freec_CNAs=None,CNAs=None,pu
         self.color_gain=color_gain
         self.color_cnloh=color_cnloh
         self.genes = genes
-        if "," in self.genes: self.genes = self.genes.split(",")
         self.reference=reference
         self.genes_file=genes_file
         self.chr_lengths=chr_lengths

figeno/track_hic.py

@@ -1,4 +1,5 @@
 import cooler
+import h5py
 import numpy as np
 import matplotlib.pyplot as plt
 import matplotlib.patches as patches
@@ -54,6 +55,14 @@ def draw(self, regions, box ,hmargin,warnings=[]):
         if self.file=="" or self.file is None:
             raise KnownException("Please provide a file for the hic track. This file must be in .cool format.")
         try:
+            if self.file.endswith(".mcool"):
+                f=h5py.File(self.file,'r')
+                resolutions=list(f["resolutions"].keys())
+                selected_resolution=resolutions[0]
+                warnings.append("You used a .mcool file without specifying the resolution ("+self.file+"), so the resolution was automatically set to "+str(selected_resolution)+". This .mcool file contains the following resolutions: "+\
+                                ", ".join([str(x) for x in resolutions])+". You can select the resolution by adding ::resolutions//"+str(selected_resolution)+" to the filename.")
+                self.file+="::resolutions//"+str(selected_resolution)
+
             c=cooler.Cooler(self.file)
         except: 
             raise KnownException("Failed to open file for the hic track: "+self.file+".\nThis file must be in .cool format.\nIf you have data in .hic format,"\

pyproject.toml

@@ -9,7 +9,7 @@ packages = ["figeno", "figeno.data", "figeno.cli", "figeno.gui"]
 
 [project]
 name = 'figeno'
-version = "1.4.0"
+version = "1.4.1"
 description = 'Package for generating genomics figures.'
 readme = 'README.md'
 authors = [