Check for identical sequences and names

seqreport/SeqCollection.py

@@ -46,8 +46,8 @@ def __init__(
         currency_symbol="£",
         projectname="",
         comments="",
-        min_length=0,
-        max_length=0,
+        min_length=100,  # a good cutoff for min DNA synthesis length
+        max_length=3000,  # a good cutoff for max DNA synthesis length
         name_length=15,  # max seq record name length. Genbank character limit.
     ):
         self.sequences = records
@@ -66,24 +66,65 @@ def calculate_values(self):
         self.cost_per_seq = float(self.cost_per_seq)
         self.n_seq = len(self.sequences)
 
+        # Numbers section
         n_bp = 0
         for part in self.sequences:
             n_bp += len(part.seq)
         self.n_bp = n_bp
         self.cost = self.n_seq * self.cost_per_seq + self.n_bp * self.cost_per_base
 
+        # Lengths section
         self.too_short = []
         self.too_long = []
         self.long_names = []
         for record in self.sequences:
             if len(record) < self.min_length:
                 self.too_short += [record.id]
-            if self.max_length > 0:  # otherwise skip if default
-                if len(record) > self.max_length:
-                    self.too_long += [record.id]
+            if len(record) > self.max_length:
+                self.too_long += [record.id]
             if len(record.id) > self.name_length:
                 self.long_names += [record.id]
 
+        self.too_short = list(set(self.too_short))
+        self.too_long = list(set(self.too_long))
+        self.long_names = list(set(self.long_names))
+        # Repeats will be checked further below.
+
+        # For the PDF report:
+        self.too_short_text = " ; ".join(self.too_short)
+        self.too_long_text = " ; ".join(self.too_long)
+        self.long_names_text = " ; ".join(self.long_names)
+
+        # Repeats section
+        self.repeat_names = []
+        self.repeat_seq = []
+        self.reverse_complement_seq = []
+        for index, record in enumerate(self.sequences[:-1]):
+            for other_record in self.sequences[index+1:]:
+                if record.id == other_record.id:
+                    self.repeat_names += [record.id]
+                if record.seq == other_record.seq:
+                    self.repeat_seq += [(record.id, other_record.id)]
+                if record.seq == other_record.seq.reverse_complement():
+                    self.reverse_complement_seq += [(record.id, other_record.id)]
+
+        self.repeat_names = list(set(self.repeat_names))
+
+        # For the PDF report:
+        self.repeat_names_text = " ; ".join(self.repeat_names)
+
+        repeat_seq_text_list = []
+        for identifier in self.repeat_seq:
+            combined = " = ".join(identifier)
+            repeat_seq_text_list += [combined]
+        self.repeat_seq_text = " ; ".join(repeat_seq_text_list)
+
+        reverse_complement_seq_text_list = []
+        for identifier in self.reverse_complement_seq:
+            combined = " = ".join(identifier)
+            reverse_complement_seq_text_list += [combined]
+        self.reverse_complement_seq_text = " ; ".join(reverse_complement_seq_text_list)
+
 
 def read_fasta(fasta):
     """Read a FASTA sequence file into a list of records.

seqreport/report_assets/seq_report.pug

@@ -21,27 +21,48 @@ p.
 p.
   Estimated cost: <b>{{ seqcollection.currency_symbol }} {{ seqcollection.cost }}</b>
 
-if seqcollection.too_short
+if seqcollection.too_short_text
   p.
-    #[span.red ☒] Sequences shorter than <b>{{ seqcollection.min_length }}</b> bp: {{ seqcollection.too_short }}
+    #[span.red ☒] Sequences shorter than <b>{{ seqcollection.min_length }}</b> bp: {{ seqcollection.too_short_text }}
 else
   p.
     #[span.green ☑] None of the sequences are shorter than <b>{{ seqcollection.min_length }}</b> bp.
 
-if seqcollection.too_long
+if seqcollection.too_long_text
   p.
-    #[span.red ☒] Sequences longer than <b>{{ seqcollection.max_length }}</b> bp: {{ seqcollection.too_long }}
+    #[span.red ☒] Sequences longer than <b>{{ seqcollection.max_length }}</b> bp: {{ seqcollection.too_long_text }}
 else
   p.
     #[span.green ☑] None of the sequences are longer than <b>{{ seqcollection.max_length }}</b> bp.
 
-if seqcollection.long_names
+if seqcollection.long_names_text
   p.
-    #[span.red ☒] Sequence IDs longer than <b>{{ seqcollection.name_length }}</b> characters: {{ seqcollection.long_names }}
+    #[span.red ☒] Sequence IDs longer than <b>{{ seqcollection.name_length }}</b> characters: {{ seqcollection.long_names_text }}
 else
   p.
     #[span.green ☑] None of the IDs are longer than <b>{{ seqcollection.name_length }}</b> characters.
 
+if seqcollection.repeat_names_text
+  p.
+    #[span.red ☒] Sequence IDs appearing more than once: {{ seqcollection.repeat_names_text }}
+else
+  p.
+    #[span.green ☑] None of the IDs are duplicated.
+
+if seqcollection.repeat_seq_text
+  p.
+    #[span.red ☒] Identical sequence-pairs: {{ seqcollection.repeat_seq_text }}
+else
+  p.
+    #[span.green ☑] None of the sequences are identical.
+
+if seqcollection.reverse_complement_seq_text
+  p.
+    #[span.red ☒] Sequence-pairs with identical reverse complements: {{ seqcollection.reverse_complement_seq_text }}
+else
+  p.
+    #[span.green ☑] None of the sequences are reverse complements.
+
 if seqcollection.comments
   p.
     Comments: <i>{{ seqcollection.comments }}</i>

tests/data/test.fa

@@ -4,3 +4,9 @@ ACGGCCAATT
 CTCAATCAGATCGATTGCAATGCACCATCGGG
 >sequence3
 TGATGATGAAAGACAGCCGATGACATGGCGTACTACAGACGC
+>seq2
+TGATGATGAAAGACAGCCGATGACCGT
+>duplicate
+CTCAATCAGATCGATTGCAATGCACCATCGGG
+>reverse_complement
+CCCGATGGTGCATTGCAATCGATCTGATTGAG

tests/test_SeqCollection.py

@@ -14,20 +14,23 @@ def test_SeqCollection():
         comments="This is a test sequence set.",
         min_length=20,
         max_length=40,
-        name_length=5,
+        name_length=10,
     )
-    assert seq_coll.n_seq == 3
-    assert seq_coll.n_bp == 84
+    assert seq_coll.n_seq == 6
+    assert seq_coll.n_bp == 175
     assert seq_coll.projectname == "EGF24"
     assert seq_coll.comments != ""
     assert len(seq_coll.too_short) == 1
     assert len(seq_coll.too_long) == 1
     assert len(seq_coll.long_names) == 1
+    assert len(seq_coll.repeat_names) == 1
+    assert len(seq_coll.repeat_seq) == 1
+    assert len(seq_coll.reverse_complement_seq) == 2
 
 
 def test_read_fasta():
     seq_records = seqreport.read_fasta(seq_fasta)
-    assert len(seq_records) == 3
+    assert len(seq_records) == 6
 
 
 def test_seqcollection_from_csv():