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Simple in silico PCR

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PyPI PyPI - Python Version PyPI - License Coookiecutter - Wolt


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A simple, light-weight package written in base Python to perform in silico PCR to determine primer performance.

Currently in development


pip install ispcr


File-based in silico PCR

The main function to use in this package is get_pcr_products, which performs in silico PCR using two files:

  • primer_file - the path to fasta file containing your primers
    • This is currently limited to a fasta file containing two sequences, with the forward primer coming first and the reverse primer coming second
  • sequence_file the path to the fasta file containing the sequences to test your primers against

get_pcr_products will then iterate through the sequences in sequence_file and find all products amplified by the forward and reverse primer.

Refining results

You can also refine your results by using the min_product_length and max_product_length arguments, and only print out the columns you are interested in by using the cols argument. For example, if we're only interested in products between 100 and 250 bp and we only want the name of the sequence the product was amplified from, the length of the product, and the start and end position of the product in the sequence:

Writing out isPCR results to a file

get_pcr_products also takes an output_file argument. If provided, the results of the in silico PCR (including any product length restrictions or column selections) to that file. This will overwrite the file.

Sequence-based in silico PCR

The get_pcr_products function is a wrapper around calculate_pcr_product. The following arguments are required to run calculate_pcr_product:

  • sequence: the target sequence to test the primers against
  • forward_primer: the forward primer used to amplify the sequence
  • reverse_primer: the reverse primer (5'-3') used to amplify the sequence

sequence, forward_primer, and reverse_primer should be entered as FastaSequence objects. A FastaSequence is just a small convenience class to package a sequence with its header. An example run of calculate_pcr_products might look like:

calculate_pcr_product uses all of the same arguments as get_pcr_products, so you can filter results and select columns just as before:

This will also work with the output_file argument.

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