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jiajiexiao / SeqInfer

A Python library to infer from sequences
https://pypi.org/project/seqinfer/
MIT License
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Seqinfer for generating simulated sequences that follow a particular pattern? #1

Open panosioannidis opened 4 months ago

panosioannidis commented 4 months ago

Hello,

I'm interested in generating simulated DNA sequences that follow a particular pattern (e.g. a particular dinucleotide composition). Can I use seqinfer for this? From the available documentation it seems to be the case, but it's not clear to me how I can do it.

More specifically, I have a set of "positive" sequences (fasta file) which I use in order to calculate a transition matrix and use it for generating a simulated DNA sequence. But I was wondering if there's another way of doing this. Seqinfer seems to be able to do it (as I understand by reading the available documentation), but I don't see exactly how. Could you please give me a short example that starts with a fasta file (or maybe two, if I have to have a "negative" set as well)?

Thank you, Panos

jiajiexiao commented 1 month ago

Hi Panos, thx for your interest in SeqInfer, and my apologies for the late reply. Here is an example how we can use PWMInserter and RandomSequenceGenerator to simulate positive and negative sequences. Please take a look and let me know if this meets your needs.