<div dir="ltr"><div><div><div><div>Good point!<br></div>The InsdcParser class is responsible of parsing locations and nested locations with splits. It reads and records the numbers in the location string as they are in genbank file. So it is 1 based.<br><br>Andreas, does biojava has to be considered 0 based or 1 based for sequence coordinates? Or it is an uncoded behaviour? <br></div>Said so, no tests have actually failed, so I tought that sequence coordinates are 1 based as in other bio projects. <br><br></div>Also, in my last before-send-this-email check, AbstractSequence.getSubSequence() (and ProxyView) does not apply any transformation so I can conclude that biojava is 1 based.<br><br></div>Paolo<br></div><div class="gmail_extra"><br><div class="gmail_quote">2015-02-13 13:42 GMT+01:00 Peter Cock <span dir="ltr"><<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">On Fri, Feb 13, 2015 at 9:53 AM, stefan harjes <<a href="mailto:stefanharjes@yahoo.de">stefanharjes@yahoo.de</a>> wrote:<br>
> Hi Erik,<br>
><br>
> thanks for the offer, but the little mistake with the enumeration was very<br>
> quick to find. There is an increment of one added to the start position of<br>
> each location for some reason. If you change it from 1 to 0, the sequence<br>
> location start positions are no longer incremented.<br>
><br>
> you can find it in line 284 of GenericInsdcHeaderFormat.java<br>
><br>
> Cheers<br>
> Stefan<br>
<br>
</span>Erik said the code was copied and translated from Biopython,<br>
in which case we deliberately adjust the start position on parsing<br>
*and* writing to use Python style slice counting, rather than the<br>
INSDC feature table one-based counting.<br>
<br>
I would first check the BioJava policy on feature coordinates,<br>
it may be the bug is actually in the BioJava GenBank parser?<br>
<br>
Regards,<br>
<br>
Peter<br>
</blockquote></div><br></div>