fix read mode on region reeader.

README.md

@@ -14,7 +14,6 @@ Furthermore, the following python packages are required:
 * biopython >= 1.66
 * lxml >= 3.4.4
 * pyfaidx >= 0.4.4
-* fastools >= 0.12.0
 * pyvcf >= 0.6.7 
 
 

prinia/design.py

@@ -278,12 +278,17 @@ def find_snps(primer, db_snp=None, field="AF"):
     except:
         return None
 
+    if db_snp is None:
+        return None
+
     reader = vcf.Reader(filename=db_snp)
 
     left_end = int(primer.left_pos) + len(primer.left)
     right_end = int(primer.right_pos) + len(primer.right)
 
     contigs = list(reader.contigs.keys())
+    if len(contigs) == 0:
+        raise ValueError("The VCF file does not contain contigs in the header.")
     if "chr" in contigs[0] and not "chr" in primer.chromosome:
         chrom = "chr" + primer.chromosome
     elif "chr" in primer.chromosome and not "chr" in contigs[0]:

prinia/primerdesign.py

@@ -56,7 +56,7 @@ def primers_from_region(bed_path, padding, product_size, n_prims, reference,
     """**prim_args will be passed on to primer3"""
     regions = []
     primers = []
-    with open(bed_path, "rb") as bed:
+    with open(bed_path, "r") as bed:
         for line in bed:
             if line.startswith("track"):  # ignore tracklines
                 continue
@@ -273,6 +273,3 @@ def main():
 
 if __name__ == '__main__':
     main()
-
-
-