Given a GTF annotation and a corresponding fasta file, prints out a file containing the processed transcripts, and another file containing a window of size 2L-2 around each splice junction of each transcript.

./isolate_transcripts.py annotation.gtf scaffolds.fasta output_directory [-L LENGTH]

• annotation.gtf Contains annotations for exons, transcripts, and genes
• scaffolds.fasta Fasta file that corresponds to annotation.gtf
• output_directory The directory in which the results are to be written.
• [-L LENGTH], where LENGTH is the read length (default 98)

In order to generate a list of transcripts to capture using bustools capture, you can use the following sed command on the fasta files generated by isolate_transcripts.py:

sed -n 's/^>//p' foo.fasta > foo.to_capture.fasta