removed bioalphabet

jhawkey · Jul 13, 2021 · 5c865ce · 5c865ce
1 parent 9e5a3e7
commit 5c865ce
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Showing 2 changed files with 3 additions and 5 deletions.
diff --git a/scripts/create_output.py b/scripts/create_output.py
@@ -3,7 +3,6 @@
 from Bio import SeqIO
 from Bio.SeqRecord import SeqRecord
 from Bio.Seq import Seq
-from Bio.Alphabet import generic_dna
 from run_commands import run_command
 
 class RemovedHit(object):
@@ -336,7 +335,7 @@ def check_seq_between(genbank_seq, insertion, start, end, name, temp):
     # Get sequence between left and right ends
     seq_between = genbank_seq[start:end]
     # Turn the sequence into a fasta file
-    seq_between = SeqRecord(Seq(str(seq_between), generic_dna), id=name)
+    seq_between = SeqRecord(Seq(str(seq_between)), id=name)
     out_seq_between = os.path.join(temp, name + '.fasta')
     out_insertion = os.path.join(temp, name + 'ISseq.fasta')
     SeqIO.write(seq_between, out_seq_between, 'fasta')

diff --git a/scripts/mapping_to_query.py b/scripts/mapping_to_query.py
@@ -3,7 +3,6 @@
 import shlex
 from Bio import SeqIO
 from Bio.Seq import Seq
-from Bio.Alphabet import generic_dna
 import logging
 from subprocess import Popen, PIPE
 from run_commands import run_command, CommandError, make_directories
@@ -141,7 +140,7 @@ def extract_clipped_reads(sam_file, min_size, max_size, out_left_file, out_right
             if map_regions[0][-1] == 'S':
                 num_soft_clipped = int(map_regions[0][:-1])
                 if min_size <= num_soft_clipped <= max_size:
-                    soft_clipped_seq = Seq(entries[9][:num_soft_clipped], generic_dna)
+                    soft_clipped_seq = Seq(entries[9][:num_soft_clipped])
                     qual_scores = entries[10][:num_soft_clipped]
                     if reverse_complement:
                         out_left.write('@' + read_name + '\n' + str(soft_clipped_seq.reverse_complement()) + '\n+\n' + qual_scores[::-1] + '\n')
@@ -150,7 +149,7 @@ def extract_clipped_reads(sam_file, min_size, max_size, out_left_file, out_right
             if map_regions[-1][-1] == 'S':
                 num_soft_clipped = int(map_regions[-1][:-1])
                 if min_size <= num_soft_clipped <= max_size:
-                    soft_clipped_seq = Seq(entries[9][-num_soft_clipped:], generic_dna)
+                    soft_clipped_seq = Seq(entries[9][-num_soft_clipped:])
                     qual_scores = entries[10][-num_soft_clipped:]
                     if reverse_complement:
                         out_right.write('@' + read_name + '\n' + str(soft_clipped_seq.reverse_complement()) + '\n+\n' + qual_scores[::-1] + '\n')