Merge pull request #150 from Fxe/dev

genome IO

Author: Fxe

modelseedpy/core/msgenome.py

@@ -8,18 +8,21 @@
 DEFAULT_SPLIT = " "
 
 
-def to_fasta(features, filename, l=80, fn_header=None):
+def to_fasta(features, filename, line_size=80, fn_header=None):
     with open(filename, "w") as fh:
         for feature in features:
-            h = f">{feature.id}\n"
-            if fn_header:
-                h = fn_header(feature)
-            fh.write(h)
-            lines = [
-                feature.seq[i : i + l] + "\n" for i in range(0, len(feature.seq), l)
-            ]
-            for line in lines:
-                fh.write(line)
+            if feature.seq:
+                h = f">{feature.id}\n"
+                if fn_header:
+                    h = fn_header(feature)
+                fh.write(h)
+                _seq = feature.seq
+                lines = [
+                    _seq[i : i + line_size] + "\n"
+                    for i in range(0, len(_seq), line_size)
+                ]
+                for line in lines:
+                    fh.write(line)
     return filename
 
 
@@ -188,3 +191,15 @@ def search_for_gene(self, query):
             return self.features.get_by_id(query)
         aliases = self.alias_hash()
         return aliases[query] if query in aliases else None
+
+    def _repr_html_(self):
+        return f"""
+        <table>
+            <tr>
+                <td><strong>Memory address</strong></td>
+                <td>{f"{id(self):x}"}</td>
+            </tr><tr>
+                <td><strong>Features</strong></td>
+                <td>{len(self.features)}</td>
+            </tr>
+        </table>"""

modelseedpy/core/mstemplate.py

@@ -520,23 +520,23 @@ def get_data(self):
 class MSTemplateBiomass:
     def __init__(
         self,
-        bio_id,
-        name,
-        type,
-        dna,
-        rna,
-        protein,
-        lipid,
-        cellwall,
-        cofactor,
-        pigment,
-        carbohydrate,
-        energy,
-        other,
+        biomass_id: str,
+        name: str,
+        type: str,
+        dna: float,
+        rna: float,
+        protein: float,
+        lipid: float,
+        cellwall: float,
+        cofactor: float,
+        pigment: float,
+        carbohydrate: float,
+        energy: float,
+        other: float,
     ):
         """
 
-        :param bio_id:string
+        :param biomass_id:string
         :param name:string
         :param type:string
         :param dna:float
@@ -550,7 +550,7 @@ def __init__(
         :param energy:float
         :param other:float
         """
-        self.id = bio_id
+        self.id = biomass_id
         self.name = name
         self.type = type
         self.dna = dna