updated recipe

Author: Tobias Andermann

build/lib/secapr/_version.py

@@ -8,11 +8,11 @@
 
 version_json = '''
 {
- "date": "2022-03-31T19:57:19+0200",
- "dirty": true,
+ "date": "2022-04-11T12:12:59+0200",
+ "dirty": false,
  "error": null,
- "full-revisionid": "1dd1190c2db1975140823836653618bcbfc812e8",
- "version": "2.2.3+13.g1dd1190.dirty"
+ "full-revisionid": "d729f215e555404d7c7213d5c172677002ebdafb",
+ "version": "2.2.3+15.gd729f21"
 }
 '''  # END VERSION_JSON
 

build/lib/secapr/clean_reads.py

@@ -124,18 +124,27 @@ def add_arguments(parser):
 
 
 def longest_common_substring(s1, s2):
-    m = [[0] * (1 + len(s2)) for i in range(1 + len(s1))]
-    longest, x_longest = 0, 0
-    for x in range(1, 1 + len(s1)):
-        for y in range(1, 1 + len(s2)):
-            if s1[x - 1] == s2[y - 1]:
-                m[x][y] = m[x - 1][y - 1] + 1
-                if m[x][y] > longest:
-                    longest = m[x][y]
-                    x_longest = x
-            else:
-                m[x][y] = 0
-    return s1[x_longest - longest: x_longest]
+    m = []
+    for i, letter in enumerate(list(s1)):
+        if letter == list(s2)[i]:
+            m.append(letter)
+        else:
+            break
+    return ''.join(m)
+
+# def longest_common_substring(s1, s2):
+#     m = [[0] * (1 + len(s2)) for i in range(1 + len(s1))]
+#     longest, x_longest = 0, 0
+#     for x in range(1, 1 + len(s1)):
+#         for y in range(1, 1 + len(s2)):
+#             if s1[x - 1] == s2[y - 1]:
+#                 m[x][y] = m[x - 1][y - 1] + 1
+#                 if m[x][y] > longest:
+#                     longest = m[x][y]
+#                     x_longest = x
+#             else:
+#                 m[x][y] = 0
+#     return s1[x_longest - longest: x_longest]
 
 def read_count(input):
     # Use bash command to count the read number

recipe/meta.yaml

@@ -1,12 +1,12 @@
-{% set version = "2.1.0" %}
+{% set version = "2.2.6" %}
 
 package:
   name: secapr
   version: {{ version }}
 
 source:
   url: https://github.com/AntonelliLab/seqcap_processor/archive/v{{ version }}.tar.gz
-  sha256: bc69147dbc452acf56dc75452c5cadcdaeeeda1d0a3a81c5c3667e0018924031
+  sha256: 63a67d6bc5d139b2910e562dc7969e7c8374c01720af5319a0f7a9d06c5983c0
 
 build:
   noarch: generic
@@ -17,24 +17,24 @@ build:
 
 requirements:
   host:
-    - python 3.7
+    - python
     - pip
 
   run:
-    - python
+    - python=3.8
     - pandas
     - matplotlib-base
-    - biopython=1.76
+    - biopython
     - trimmomatic
     - fastqc
-    - abyss
-    - spades
+    - fastp=0.23
+    - spades=3.15.2
     - blast
     - mafft
     - muscle
     - emboss
     - bwa
-    - samtools=1.9
+    - samtools==1.3.1
     - trimal
 
 test:

secapr.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: secapr
-Version: 2.2.3+13.g1dd1190.dirty
+Version: 2.2.3+15.gd729f21
 Summary: Process sequence-capture fastq files into alignments for phylogenetic analyses
 Home-page: https://github.com/AntonelliLab/seqcap_processor
 Author: Tobias Andermann