optimisation for #237

example.py

@@ -0,0 +1,69 @@
+# -*- coding: utf-8 -*-
+import requests
+from pydna.design import primer_design
+from pydna.dseqrecord import Dseqrecord
+from pydna.tm import tm_default
+import time
+
+
+def primer_tm_neb(primer, conc=0.5, prodcode="q5-0"):
+    """Calculates a single primers melting temp from NEB.
+
+    Parameters
+    ----------
+    primer1 : str
+    conc : float
+    prodcode : str
+        find product codes on nebswebsite: https://tmapi.neb.com/docs/productcodes
+
+    Returns
+    -------
+    tm : int
+        primer melting temperature
+
+    """
+
+    url = "https://tmapi.neb.com/tm"
+
+    params = {"seq1": primer, "conc": conc, "prodcode": prodcode}
+
+    # Mimic a browser request with this headers
+    headers = {
+        "User-Agent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/91.0.4472.124 Safari/537.36",
+        "Accept": "text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8",
+        "Accept-Encoding": "gzip, deflate, br",
+        "Accept-Language": "en-US,en;q=0.5",
+        "Connection": "keep-alive",
+        "Referer": "https://example.com",
+    }
+    res = requests.get(url, params=params, headers=headers)
+    r = res.json()
+    print("making a request")
+    if r["success"]:
+        return r["data"]["tm1"]
+    else:
+        print("request failed")
+        print(r["error"][0])
+
+
+start_time = time.time()
+result = primer_design(
+    Dseqrecord("atgtcgtATGaaaccgttatcgatcatatgtGcgaaatgtcgcgcgtcatctacgtatcatcgatctactTAAacgtgta"),
+    limit=8,
+    target_tm=60,
+    estimate_function=tm_default,
+    tm_func=primer_tm_neb,
+)
+print("result", result.seq)
+print("--- %s seconds ---" % (time.time() - start_time))
+
+
+start_time = time.time()
+result = primer_design(
+    Dseqrecord("atgtcgtATGaaaccgttatcgatcatatgtGcgaaatgtcgcgcgtcatctacgtatcatcgatctactTAAacgtgta"),
+    limit=8,
+    target_tm=60,
+    tm_func=primer_tm_neb,
+)
+print("result", result.seq)
+print("--- %s seconds ---" % (time.time() - start_time))

src/pydna/design.py

@@ -24,11 +24,44 @@
 from pydna.dseqrecord import Dseqrecord as _Dseqrecord
 from pydna.primer import Primer as _Primer
 import logging as _logging
+import operator as _operator
 
 _module_logger = _logging.getLogger("pydna." + __name__)
 
 
-def primer_design(template, fp=None, rp=None, limit=13, target_tm=55.0, tm_func=_tm_default, **kwargs):
+def get_tm_and_primer(target_tm, template, limit, tm_func, starting_temp=0) -> tuple[float, str]:
+    """returns a string"""
+    tmp = starting_temp
+    length = limit
+    tlen = len(template)
+    p = str(template.seq[:length])
+
+    if starting_temp < target_tm:
+        condition = _operator.le
+        increment = 1
+    else:
+        condition = _operator.ge
+        increment = -1
+    while condition(tmp, target_tm):
+        length += increment
+        p = str(template.seq[:length])
+        tmp = tm_func(p)
+        if length >= tlen or length == 0:
+            break
+    ps = p[:-1]
+    tmps = tm_func(str(ps))
+    _module_logger.debug(((p, tmp), (ps, tmps)))
+    return min((abs(target_tm - tmp), p), (abs(target_tm - tmps), ps))
+
+
+def get_tm_and_primer_with_estimate(target_tm, template, limit, tm_func, estimate_function):
+    first_temp, first_guess = get_tm_and_primer(target_tm, template, limit, estimate_function)
+    return get_tm_and_primer(target_tm, template, len(first_guess), tm_func, first_temp)
+
+
+def primer_design(
+    template, fp=None, rp=None, limit=13, target_tm=55.0, tm_func=_tm_default, estimate_function=None, **kwargs
+):
     """This function designs a forward primer and a reverse primer for PCR amplification
     of a given template sequence.
 
@@ -118,21 +151,10 @@ def primer_design(template, fp=None, rp=None, limit=13, target_tm=55.0, tm_func=
     """
 
     def design(target_tm, template):
-        """returns a string"""
-        tmp = 0
-        length = limit
-        tlen = len(template)
-        p = str(template.seq[:length])
-        while tmp < target_tm:
-            length += 1
-            p = str(template.seq[:length])
-            tmp = tm_func(p)
-            if length >= tlen:
-                break
-        ps = p[:-1]
-        tmps = tm_func(str(ps))
-        _module_logger.debug(((p, tmp), (ps, tmps)))
-        return min((abs(target_tm - tmp), p), (abs(target_tm - tmps), ps))[1]
+        if estimate_function:
+            return get_tm_and_primer_with_estimate(target_tm, template, limit, tm_func, estimate_function)[1]
+        else:
+            return get_tm_and_primer(target_tm, template, limit, tm_func)[1]
 
     if not fp and not rp:
         _module_logger.debug("no primer given, design forward primer:")