expose the user config file to primerdesign.py

Author: Runsheng

bin/primerdesign.py

@@ -9,14 +9,16 @@
 """
 
 import argparse
-import os,sys
+import os
+import sys
+import json
 
 #currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
 #parentdir = os.path.dirname(os.path.dirname(currentdir))
 #sys.path.insert(0,parentdir)
 
 # self import
-from primerdiffer.walk_chr import flow_walk_chr
+from primerdiffer.walk_chr import flow_walk_chr, primer3_general_settings
 
 parser=argparse.ArgumentParser()
 parser.add_argument("-d", "--wkdir", default=None,
@@ -53,11 +55,25 @@
 parser.add_argument("--prefix", default="primers",
                     help="prefix of output file, default is primers")
 
+# add user settings
+parser.add_argument("--primer3config", default=None,
+                    help="the config file for the primer3 ")
 
 # default handler
 args = parser.parse_args(args=None if sys.argv[1:] else ['--help'])
 wkdir=os.getcwd() if args.wkdir is None else args.wkdir
 
+
+# deal with config
+primer3_setting = primer3_general_settings
+if args.primer3config is None:
+    pass
+else: # update the primer3 setting from the givien parameters
+    with open(args.primer3config, "r") as f:
+        primer3_user_setting = eval(f.read()) # read the config as a dict
+        primer3_setting.update(primer3_user_setting)
+
+
 flow_walk_chr(wkdir=wkdir,
               genome1=args.genome1,
               genome2=args.genome2,
@@ -69,4 +85,5 @@
               db2_maxhit=args.hit2,
               interval=args.interval,
               jump=args.jump,
-              out_prefix=args.prefix)
+              out_prefix=args.prefix,
+              primer3_settings=primer3_setting)

primerdiffer/__init__.py

@@ -1 +1 @@
-__version__= "0.1.2"
+__version__= "0.1.4"

primerdiffer/walk_chr.py

@@ -12,12 +12,15 @@
 
 from primerdiffer.primer_check import my_design_primer, primer_check
 from primerdiffer.utils import dic2dic, fasta2dic, chr_select, tuple_to_pos_str, pos_str_to_tuple, checkblastdb
+from primerdiffer.general_settings import primer3_general_settings
 
 
 def walk_chr_dense(genome, chro, start, end, db1, db2,
                    cutoff_alignlength=16, cutoff_free3=2, product_cutoff=2000,
                    db1_maxhit=1, db2_maxhit=0,
-                   interval=500000, jump=4000, out_prefix="primers", debugmod=False):
+                   interval=500000, jump=4000, out_prefix="primers", debugmod=False,
+                   primer3_settings=primer3_general_settings
+                   ):
     """
     :param genome: genome is a dict in name:seq,
     :param chro:
@@ -41,7 +44,7 @@ def walk_chr_dense(genome, chro, start, end, db1, db2,
             if "N" in seq.upper():
                 offset += 1
             else:
-                myprimer = my_design_primer(name=name, seq=seq)
+                myprimer = my_design_primer(name=name, seq=seq, primer3_settings=primer3_settings)
                 primer_used = primer_check(myprimer,db1,db2,
                                            cutoff_alignlength, cutoff_free3, product_cutoff,
                                            db1_maxhit, db2_maxhit,
@@ -67,7 +70,8 @@ def walk_chr_dense(genome, chro, start, end, db1, db2,
 def flow_walk_chr(wkdir, genome1, genome2, pos_str,
                   cutoff_alignlength=16, cutoff_free3=2, product_cutoff=2000,
                   db1_maxhit=1, db2_maxhit=0,
-                  interval=4000, jump=400, out_prefix="primers"):
+                  interval=4000, jump=400, out_prefix="primers",
+                  primer3_settings = primer3_general_settings):
     """
 
     genome1: the genome fasta file used to design primers
@@ -94,5 +98,6 @@ def flow_walk_chr(wkdir, genome1, genome2, pos_str,
                                product_cutoff=product_cutoff,
                                db1_maxhit=db1_maxhit,
                                db2_maxhit=db2_maxhit,
-                            interval=interval, jump=jump, out_prefix=out_prefix)
+                            interval=interval, jump=jump, out_prefix=out_prefix,
+                               primer3_settings=primer3_settings)
     print(primer_dict)

readme.md

@@ -18,7 +18,7 @@ pip install primerdiffer # will also install primer3-py and biopython
 conda install -c bioconda blast # install ncbi blast, which is not included in pip installation
 ```
 
-## Case example: primerdesign.py for primerdiffer
+## Case example: used primerdesign.py to design primers for two haplotypes 
 Design genome-wide specific primers for two species/sub-species/divergent sequences:
 - Greedy design primers for a region in genome1 and make a specificity check using genome2
 - The dis-similarity between genome1 and genome2 >= 5%. 
@@ -63,8 +63,8 @@ from [cb5.fa](https://github.com/Runsheng/cbgenome/releases/download/cb5pre_cn3p
 
 The _C. nigoni_ genome is cn3_new.fa and _C. briggsae_ genome is cb5.fa. To design _C. briggsae_ unique primer, 
 which would not amplify any region in _C. nigoni_, and amplify only one region in _C. briggsae_. 
-The targeted region for C. briggsae is ChrX:12881200-15106660 (-pos),
-one primer is designed for every 4kb interval (--interval).
+The targeted region for C. briggsae is ChrX:12881200-15106660 (-pos or --position),
+one primer is designed for every 4kb interval (-i or --interval).
 ```bash
 primerdesign.py -g1 cb5.fa -g2 cn3_new.fa -pos "ChrX:12881200-15106660" --interval 4000
 ```
@@ -119,9 +119,47 @@ head ispcr.fa
 #ATGATGATGATGATGGTGGGGTGAGAATAGAGT
 ```
 
+## Case example: Design general purpose primers with given parameters
+The default primer design parameter is as described in [general_setting.py](https://github.com/Runsheng/primerdiffer/blob/master/primerdiffer/general_settings.py):
+```python
+primer3_general_settings =  {
+        'PRIMER_OPT_SIZE': 20,
+        'PRIMER_PICK_LEFT_PRIMER':1,
+        'PRIMER_PICK_RIGHT_PRIMER':1,
+        'PRIMER_PICK_INTERNAL_OLIGO': 0,
+        'PRIMER_MIN_SIZE': 18,
+        'PRIMER_MAX_SIZE': 23,
+        'PRIMER_OPT_TM': 57.0,
+        'PRIMER_MIN_TM': 46.0,
+        'PRIMER_MAX_TM': 63.0,
+        'PRIMER_MIN_GC': 20.0,
+        'PRIMER_MAX_GC': 80.0,
+        'PRIMER_PRODUCT_SIZE_RANGE': [[250, 650]],
+        'PRIMER_NUM_RETURN':10,
+        'PRIMER_MIN_THREE_PRIME_DISTANCE':10,
+        'PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS':0
+}
+```
+The new parameter can be supplemnted as a file with the terms which need to be changed, for example, create a file with name of config.txt
+```python
+# content of config.txt
+# only changed the product size, the others are the same the default
+{'PRIMER_PRODUCT_SIZE_RANGE': [[100, 200]]}
+```
+Run primerdesign.py to design a qPCR primer(product size 100-20bp, use the config.txt for primer3config) for _C. briggsae_ mitochondrial DNA sequence
+[NC_009885.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_009885.1?report=fasta) in any region (use 0:-1 means from the first 
+nucleotide to the last); check the _C. briggsae_ genome cb5.fa for false priming, make sure the hit is 0.
+```bash
+primerdesign.py -g1 NC_009885.fa -g2 cb5.fa -pos "NC_009885.1:0:-1" \
+                --interval 1000 --hit1 1 --hit2 0 \
+                --primer3config config.txt
+```
+
+
+
+
 ## Roadmap for other functions:
-1. To use user-provided primer parameters.Primer design parameter now is fine-tuned for general purpose PCR, which can be found in "general_settings.py".This file may need be modified to generate primers for specific purpose PCR like real-time qPCR.
-2. To update the RFLP method for primer design to differ sequences with almost identical sequence.
-3. To update the primer design using VCF file for closely related haplotypes.
+1. To update the RFLP method for primer design to differ sequences with almost identical sequence.
+2. To update the primer design using VCF file for closely related haplotypes.
 
 

test/test_walk_chr.py

@@ -27,6 +27,12 @@ def setUp(self):
         self.cb4_genome = "/t1/ref_BN/cb5.fa"
         #self.name, self.seq = chr_select(self.cb4_genome, "ChrX", 19424476,19655212)
 
+    def test_config_dump_load(self):
+        import json
+        from primerdiffer.general_settings import primer3_general_settings
+        with open("./test/primer3config", "w") as fw:
+            json.dump(primer3_general_settings, )
+
 
     def test_walk_chr_dense(self):
         wkdir=os.getcwd()

test/user_settings.py

@@ -0,0 +1,19 @@
+# use the user setting
+# a minimal config can keep only the terms which need to be changed, like
+# {'PRIMER_PRODUCT_SIZE_RANGE': [[100,200]]}
+{ 'PRIMER_OPT_SIZE': 20,
+        'PRIMER_PICK_LEFT_PRIMER':1,
+        'PRIMER_PICK_RIGHT_PRIMER':1,
+        'PRIMER_PICK_INTERNAL_OLIGO': 0,
+        'PRIMER_MIN_SIZE': 18,
+        'PRIMER_MAX_SIZE': 23,
+        'PRIMER_OPT_TM': 57.0,
+        'PRIMER_MIN_TM': 46.0,
+        'PRIMER_MAX_TM': 63.0,
+        'PRIMER_MIN_GC': 20.0,
+        'PRIMER_MAX_GC': 80.0,
+        'PRIMER_PRODUCT_SIZE_RANGE': [[100,200]],
+        'PRIMER_NUM_RETURN':10,
+        'PRIMER_MIN_THREE_PRIME_DISTANCE':10,
+        'PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS':0
+}