Python Dictionary of Primer3-py Primer Designs

Question

[bhumm]

I am currently trying to create a primer designing program in python predicated on primer3-py.

I currently have a dictionary that contains all the primer designs and metadata as values and their arbitrary sequence name as the key. For example:

{'seq1': {'PRIMER_LEFT_EXPLAIN': 'considered 1483, GC content failed 178, low tm 998, high tm 125, high hairpin stability 2, ok 167',
  'PRIMER_RIGHT_EXPLAIN': 'considered 1493, GC content failed 141, low tm 1174, high tm 38, ok 128',
  'PRIMER_PAIR_EXPLAIN': 'considered 148, unacceptable product size 141, ok 7',
  'PRIMER_LEFT_NUM_RETURNED': 5,
  'PRIMER_RIGHT_NUM_RETURNED': 5,
  'PRIMER_INTERNAL_NUM_RETURNED': 0,
  'PRIMER_PAIR_NUM_RETURNED': 5,
…}
'seq2': {'PRIMER_LEFT_EXPLAIN': 'considered 1483, GC content failed 178, low tm 998, high tm 125, high hairpin stability 2, ok 167',
  'PRIMER_RIGHT_EXPLAIN': 'considered 1493, GC content failed 141, low tm 1174, high tm 38, ok 128',
  'PRIMER_PAIR_EXPLAIN': 'considered 148, unacceptable product size 141, ok 7',
  'PRIMER_LEFT_NUM_RETURNED': 5,
  'PRIMER_RIGHT_NUM_RETURNED': 5,
  'PRIMER_INTERNAL_NUM_RETURNED': 0,
  'PRIMER_PAIR_NUM_RETURNED': 5,
…}
}

(The above dict has been shortened for brevity’s sake)

Is it possible to ‘grep’ all values from the nested dictionary based on the pattern: 'PRIMER_LEFT_*_SEQUENCE', where the ‘*’ is a wildcard?

I can successfully extract some of the primer designs using bracket notation like so:

for i,j in design_output.items():
    print(i, j['PRIMER_LEFT_0_SEQUENCE'])

Primer3 will design multiple primers for you which I would like to capture. My goal is to create a loop which iterates through the dict and extracts out every instance of a novel primer design.

The output I am imagining might look something like this:

{'seq1': [‘atcgatcgta’,‘cgagcatct’,’cgcgcgaatgc’],
'seq2': [‘cgcgccagtcg’,’cgcgatatacgat’,taatcgatcg’]
}

Answer 1

[barslmn]

You're so close. You can simply loop over sequence dictionaries like you did with the design_output and check if the keys with startswith and endswith then append primers to a list.

[bhumm]

@barslmn, thank you so much! This was exactly what I was looking for!

For completeness (and for anyone else who may stumble across this post with the same problem) this is the code I used to address the problem above:

finaldesigns = {}
for key, value in design_output.items():
    primerdesignlist = []
    for i, j in value.items():
        if i.startswith('PRIMER_LEFT_') and i.endswith('_SEQUENCE'):
            primerdesignlist.append(j)
            finaldesigns.update({key: primerdesignlist})

With an output like so:

{'seq1': ['cgcgcgcatgcagcagc', 'gcgcgcgcatgcagcag', 'gcgcgcatgcagcagctac', 'cgcgcgcatgcagcagc', 'gcgcgcgcatgcagcag'], 'seq2': ['cgcgcgcatgcagcagc', 'gcgcgcgcatgcagcag', 'gcgcgcatgcagcagctac', 'cgcgcgcatgcagcagc', 'gcgcgcgcatgcagcag']}

(Please ignore the primer sequences as they are a contrived example)

[barslmn]

Looks great ^^. Here some slightly faster alternatives.

[bhumm]

Thank you again for your help!