fix bugs

pyrcos/__init__.py

@@ -1 +1,3 @@
-__version__ = "0.0.1"
+from pyrcos import objects,utils
+__version__ = "0.0.1"
+

pyrcos/objects.py

@@ -115,6 +115,10 @@ def from_file(self, path):
                     rows.append(KaryotypeChromosome.parse(line))
                 else:
                     rows.append(KaryotypeBand.parse(line))
+        if hasattr(self,'rows') and type(self.rows) is list:
+            self.rows.extend(rows)
+        else:
+            self.rows=rows
 
 
 class Circos(CircosObject):
@@ -218,13 +222,20 @@ def __init__(self, file=None, color=None, radius=None, bezier_radius=0.1, bezier
 
 class Rules(object):
     def __init__(self, rules=None):
-        if isinstance(rules, Rules):
+        if rules is None:
+           rules=[]
+        elif isinstance(rules, Rules):
             rules = rules.rules
-        self.rules = [] if rules is None else rules
+        elif isinstance(rules, Rule):
+            rules = [ rules ]
+        self.rules = rules
 
     def __len__(self):
         return len(self.rules)
 
+    def __getitem__(self, item):
+        return self.rules[item]
+
 
 class Rule(CircosObject):
     __template__ = "rule.config.template"
@@ -468,7 +479,7 @@ def thickness(self, thickness):
 
 class Scatter(Plot):
     def __init__(self, file, r0, r1, backgrounds=None, axes=None, rules=None, color=None,
-                 glyph=None, glyph_size=None, stroke_color=None, stroke_thickness=None, orientation=None):
+                 glyph=None, glyph_size=None, stroke_color=None, stroke_thickness=None, orientation=None, **kwds):
         super(Scatter, self).__init__("scatter", file, r0, r1,
                                       backgrounds=backgrounds,
                                       axes=axes,
@@ -478,7 +489,7 @@ def __init__(self, file, r0, r1, backgrounds=None, axes=None, rules=None, color=
                                       glyph_size=glyph_size,
                                       stroke_color=stroke_color,
                                       stroke_thickness=stroke_thickness,
-                                      orientation=orientation)
+                                      orientation=orientation, **kwds)
 
     @property
     def glyph(self):
@@ -628,9 +639,9 @@ def __init__(self, ticks, show_label=True):
             ticks = ticks.ticks
         elif isinstance(ticks, Tick):
             ticks = [ticks]
-        self.ticks = ticks
+        self.ticks      = ticks
         self.show_label = show_label
-
+        self.thickness  = '3p'
     def __len__(self):
         return len(self.ticks)
 
@@ -642,23 +653,25 @@ class Tick(CircosObject):
     __template__ = "tick.config.template"
 
     def __init__(self, size=None, spacing=None, color=None, show_label=True, label_size=None,
-                 format=None, grid=False, grid_color=None, grid_thickness=None, radii=None, radius=None):
+                 format=None, grid=False, grid_color=None, grid_thickness=None, radii=None, radius=None, **kwds):
         super(Tick, self).__init__()
 
-        self.size = size
-        self.spacing = spacing
-        self.color = color
-        self.show_label = show_label
-        self.label_size = label_size
-        self.format = format
-        self.grid = grid
-        self.grid_color = grid_color
+        self.size           = size
+        self.spacing        = spacing
+        self.color          = color
+        self.show_label     = show_label
+        self.label_size     = label_size
+        self.format         = format
+        self.grid           = grid
+        self.grid_color     = grid_color
         self.grid_thickness = grid_thickness
-        self.radii = radii if radii is not None else []
+        self.attributes     = kwds
+        self.radii          = radii if radii is not None else []
         if radii is None and radius is not None:
             self.radii.append(radius)
 
 
+
 class Highlights(object):
     def __init__(self, highlights=None):
         if highlights is None:
@@ -684,4 +697,4 @@ def __init__(self, file, r0, r1, color=None, init_counter=None, **kwargs):
         CircosObjectWithinRadius.__init__(self, r0, r1)
         self.attributes = kwargs
         self.attributes['fill_color'] = color
-        self.attributes['init_counter'] = init_counter
+        self.attributes['init_counter'] = init_counter

pyrcos/templates/axis.config.template

@@ -3,17 +3,17 @@ y0 = {{ y0 }}
 y1 = {{ y1 }}
 {% if spacing is not none %}
 spacing = {{ spacing }}
-{ %endif} %}
+{% endif %}
 {% if position is not none %}
 position = {{ position }}
-{ %endif} %}
+{% endif %}
 {% if position_skip is not none %}
 position_skip = {{ position_skip }}
-{ %endif} %}
+{% endif %}
 {% if color is not none %}
 color = {{ color }}
-{ %endif} %}
+{% endif %}
 {% if thickness is not none %}
 thickness = {{ thickness }}
-{ %endif} %}
-</axis>
+{% endif %}
+</axis>

pyrcos/templates/circos.conf.template

@@ -14,9 +14,13 @@ karyotype = {{ karyotypes|join(',', attribute='filename')}}
 {% endif %}
 
 {% if ticks|length > 0 %}
-<ticks>
 show_ticks = True
 show_tick_labels = {{ ticks.show_label }}
+<ticks>
+multiplier       = 1/1u
+thickness        = {{ ticks.thickness }}
+tick_separation  = 2p
+label_separation = 5p
 {% for tick in ticks %}
 {{ tick.configuration }}
 {% endfor %}
@@ -46,4 +50,4 @@ radius* = {{ radius }}p
 
 {% for k, v in attributes.iteritems() %}
 {{ k }} = {{ v }}
-{% endfor %}
+{% endfor %}

pyrcos/templates/rule.config.template

@@ -4,9 +4,9 @@ color     = {{ color }}
 show      = {{ "yes" if show else "no" }}
 flow      = {{ flow }}
 {% if radius1 is not none %}
-radius1   = radius1
+radius1   = {{ radius1 }} #check?
 {% endif %}
 {% if radius2 is not none %}
-radius2   = radius2
+radius2   = {{ radius2 }}
 {% endif %}
-</rule>
+</rule>

pyrcos/templates/tick.config.template

@@ -9,6 +9,12 @@ grid           = {{ "yes" if grid else "no" }}
 grid_color     = {{ grid_color }}
 grid_thickness = {{ grid_thickness }}
 
+#other attributes
+{% for k, v in attributes.iteritems() %}
+{{ k }} = {{ v }}
+{% endfor %}
+
+
 {% for radius in radii %}
-radius = {{ radius }}r {% endif %}
-</tick>
+radius = {{ radius }} {% endfor %}
+</tick>

pyrcos/utils.py

@@ -6,6 +6,7 @@
 
 
 def seq_records_to_karyotype(records, color_map={}):
+    records=list(records)
     assert all([isinstance(r, SeqRecord) for r in records])
     chrs = []
     for i, record in enumerate(records):
@@ -29,4 +30,21 @@ def seq_record_to_tiles(records, feature_types=["gene"]):
         track["start"] = np.array(track["start"], dtype=int)
         track["end"] = np.array(track["end"], dtype=int)
 
+        yield track
+
+def seq_record_to_texts(records, feature_types=["gene"]):
+    for record in records:
+        track = DataFrame(columns=["chromosome", "start", "end", "value", "options"])
+        i = 0
+        for feature in record.features:
+            if feature.type in feature_types:
+                track.loc[i] = (record.id, int(feature.location.start+1),
+                                           int(feature.location.end),
+                                           feature.qualifiers.get(feature.qualifiers.keys()[0], ['unidentified'] )[0], "")
+                i += 1
+
+        track["start"] = np.array(track["start"], dtype=int)
+        track["end"] = np.array(track["end"], dtype=int)
+        track['value']=track['value'].str.replace(' ','_')
+        track['value']=np.where(track['value'].str.len()>8, track['value'].str[:8]+'...', track['value'] )
         yield track