Fix bug when removing primers.

Update dependencies.
cfe-lab · Jun 29, 2021 · 57f43bb · 57f43bb
1 parent db92888
commit 57f43bb
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Showing 4 changed files with 31 additions and 29 deletions.
diff --git a/Pipfile b/Pipfile
@@ -8,7 +8,7 @@ gotoh = {subdirectory = "micall/alignment", ref = "v7.7.0", git = "https://githu
 numpy = "==1.18.4"
 python-levenshtein = "==0.12.0"
 pandas = "==1.0.5"
-requests = "==2.24.0"
+requests = "==2.25.1"
 pyyaml = "*"
 
 [dev-packages]

diff --git a/Pipfile.lock b/Pipfile.lock
diff --git a/gene_splicer/primer_finder.py b/gene_splicer/primer_finder.py
@@ -385,8 +385,9 @@ def add_primers(row):
 
 def remove_primers(row):
     # Strip the primers out
-    newseq = row.sequence[int(row.fwd_sample_primer_size
-                              ):-int(row.rev_sample_primer_size)]
+    newseq = row.sequence[
+             row.fwd_sample_primer_size + row.fwd_sample_primer_start
+             :-(row.rev_sample_primer_size + row.rev_sample_primer_start)]
     row.sequence = newseq
     return row
 
@@ -395,7 +396,7 @@ def filter_df(df, nodups=True):
     filtered = df[(df['error'].isna()
                    & df['fwd_error'].isna()
                    & df['rev_error'].isna())]
-    filtered = filtered.apply(remove_primers, axis=1)
+    filtered = filtered.apply(remove_primers, axis=1, result_type='broadcast')
     if nodups:
         filtered = filtered.drop_duplicates(subset='sample', keep=False)
     if not filtered.empty:

diff --git a/setup.py b/setup.py
@@ -2,14 +2,14 @@
 
 setup(
     name='gene_splicer',
-    version='v2.3.1',
+    version='v2.3.9',
     packages=find_packages(),
     install_requires=[
         'gotoh @ git+https://github.com/cfe-lab/[email protected]#egg=gotoh&subdirectory=micall/alignment',
         'numpy==1.18.4',
         'python-Levenshtein==0.12.0',
         'pandas==1.0.5',
-        'requests==2.24.0',
+        'requests==2.25.1',
         'pyyaml'
     ],
     package_data={