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PyCogent full changelog

PyCogent full changelog

PyCogent 1.5.3 released Nov 9, 2012 (New Release)
New Features:
· Added a withoutLostSpans() method to Feature objects in cogent.core.annotation. Useful after projecting features from one aligned sequence across to another. Implemented for ordinary Features and SimpleVariables but not xxy_list Variables.

Changes:
· Make Span.remapWith() a little clearer in cogent.core.location.
· Tidy annotation remapping code in cogent.core.annotation and cogent.core.sequence so that new positions are only calculated once when slicing, projecting, or otherwise remapping parts of sequences. The old code was needlessly doing it twice.

Bug Fixes:
· Fixed bug in BLAT application controller (cogent.app.blat) which would drop some input sequences when running assign_dna_reads_to_protein_database.
· Prevent negative widths from arising in cogent.draw.compatibility when alignment is too wide.

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Full PyCogent 1.5.3 details

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