Generate cDNAs

Generate cDNA copies of transcripts, allowing for the priming of DNA synthesis at transcript-internal sites.

Input:

1. fasta-formatted file of transcript sequences
2. gtf-formatted file with potential priming sites for individual transcripts, with associated probabilities
3. file with the copy number of each unique transcript subjected to the cDNA synthesis

Output:

1. fasta-formatted file with DNA copies of the transcripts, ending at the one of the possible priming sites for each transcript. Priming sites are sampled in proportion to their probability of being used within a transcript. Each copy of a unique transcript is independently sampled, but only unique DNA sequences are saved to the output file.
2. Csv-formatted file with the copy number of each unique DNA copy.