iCLIP.utils.TranscriptCoordInterconverter.genome_interval2transcript

TranscriptCoordInterconverter.genome_interval2transcript(interval)

Convert an interval in genomic coordinates into an interval in transcript-coordinates.

Parameters:

• interval (tuple of int) – Tuple with zero-based half open interval of form
• end) in the genome domain. start < end ((start,) –

Returns:

Half open (start, end) tuple starts and ends at the same bases as the interval described in interval, but in transcript domain coordinates.

Return type:

tuple of int

Raises:

ValueError – If the supplied strart or end is not in the transcript.

See also

genome2transcript()

Does the actaul conversion

genome_interval2transcript()

Almost the inverse of this

Notes

This is not quite the inverse of :method:`transcript_interval2genome_intervals`, because of how intervals that split across introns are handled. See :method:`transcript_interval2genome_intervals` for details of the difference.

Warning

This method current has a known issue where if the interval includes the last base of the transcripts (one the +ve strand) or the first base (on the -ve strand), an error will occur. I aim to fix this before release.