Merge pull request #246 from ENPICOM/amplicon-performance-and-features

Amplicon performance update and features

Author: HadrienG

Diff for: Pipfile

@@ -7,7 +7,6 @@ name = "pypi"
 numpy = "*"
 scipy = "*"
 biopython = "*"
-joblib = "*"
 pysam = "*"
 requests = "*"
 urllib3 = ">=1.26.5"

Diff for: Pipfile.lock

@@ -18,7 +18,6 @@ To install InSilicoSeq, type the following in your terminal:
 It will install InSilicoSeq as well as the following dependencies:
 
 * biopython
-* joblib
 * numpy
 * pysam
 * scipy

Diff for: doc/iss/install.rst

@@ -15,10 +15,12 @@ class BasicErrorModel(ErrorModel):
     equal between all nucleotides.
     """
 
-    def __init__(self):
+    def __init__(self, fragment_length=None, fragment_sd=None):
         super().__init__()
         self.read_length = 125
         self.insert_size = 200
+        self.fragment_length = fragment_length
+        self.fragment_sd = fragment_sd
         self.quality_forward = self.quality_reverse = 30
         self.subst_choices_for = self.subst_choices_rev = [
             {

Diff for: iss/app.py

@@ -21,14 +21,17 @@ class KDErrorModel(ErrorModel):
     - the insertion and deletion rates for each position (for R1 and R2)
     """
 
-    def __init__(self, npz_path):
+    def __init__(self, npz_path, fragment_length=None, fragment_sd=None):
         super().__init__()
         self.npz_path = npz_path
         self.error_profile = self.load_npz(npz_path, "kde")
 
         self.read_length = self.error_profile["read_length"]
         self.i_size_cdf = self.error_profile["insert_size"]
 
+        self.fragment_length = fragment_length
+        self.fragment_sd = fragment_sd
+
         self.mean_forward = self.error_profile["mean_count_forward"]
         self.mean_reverse = self.error_profile["mean_count_reverse"]
 

Diff for: iss/error_models/basic.py

@@ -11,10 +11,12 @@ class PerfectErrorModel(ErrorModel):
     All Phred score are 40. No errors are introduced at all.
     """
 
-    def __init__(self):
+    def __init__(self, fragment_length=None, fragment_sd=None):
         super().__init__()
         self.read_length = 125
         self.insert_size = 200
+        self.fragment_length = fragment_length
+        self.fragment_sd = fragment_sd
         self.quality_forward = self.quality_reverse = 40
 
         self.subst_choices_for = self.subst_choices_rev = [