Thread: [Treesoft-treefam] Invalid NHX format in TF102048 from API
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From: Sebastien M. <Seb...@un...> - 2008-09-05 09:18:58
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Hi, It seems that API produces an invalid HNX tree for TF102048 family. From the database (TreeFam6), the tree looks proper. Here is a view: ... T=8090:G=ENSORLG00000004203]):1.7):0.070715[&&NHX:S=Percomorpha:D=N:B=23]):0.104119[&&NHX ... There is no NHX information for the 1.7 branch long. Nevertheless, the API returns this: ... T=8090:G=ENSORLG00000004203]):1.7[&&NHX]):0.070715[&&NHX:S=Percomorpha:D=N:B=23]):0.104119[&&NHX ... 1.7[&&NHX] instead of 1.7 How to fix this ? Thanks -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 |
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From: Jean-Karim H. <jk...@sa...> - 2008-09-05 12:16:03
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Hi Sebastien, Is the API not working because of this ? I believe that the API produces a correct tree and that the database is possibly wrong: the database tree should have an empty [&&NHX] (this was the case in previous versions of Treefam). Having [&&NHX] makes the nodes consistent and I think this doesn't violate the specifications of the format. This is down to the interpretation of the format: Should a node with no information get an empty [&&NHX] or nothing ? What do other treefamers think ? J-K On Fri, 2008-09-05 at 11:18 +0200, Sebastien Moretti wrote: > Hi, > It seems that API produces an invalid HNX tree for TF102048 family. > > From the database (TreeFam6), the tree looks proper. > Here is a view: > ... > T=8090:G=ENSORLG00000004203]):1.7):0.070715[&&NHX:S=Percomorpha:D=N:B=23]):0.104119[&&NHX > ... > > There is no NHX information for the 1.7 branch long. > Nevertheless, the API returns this: > ... > T=8090:G=ENSORLG00000004203]):1.7[&&NHX]):0.070715[&&NHX:S=Percomorpha:D=N:B=23]):0.104119[&&NHX > ... > > > 1.7[&&NHX] instead of 1.7 > > How to fix this ? > Thanks > |
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From: Sebastien M. <Seb...@un...> - 2008-09-05 13:49:55
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> Hi Sebastien, > > Is the API not working because of this ? The API works for this family. But it should cause some problems with some tree viewers. > I believe that the API produces a correct tree and that the database is > possibly wrong: the database tree should have an empty [&&NHX] (this was > the case in previous versions of Treefam). Having [&&NHX] makes the > nodes consistent and I think this doesn't violate the specifications of > the format. > > This is down to the interpretation of the format: Should a node with no > information get an empty [&&NHX] or nothing ? > What do other treefamers think ? > > J-K > > > On Fri, 2008-09-05 at 11:18 +0200, Sebastien Moretti wrote: >> Hi, >> It seems that API produces an invalid HNX tree for TF102048 family. >> >> From the database (TreeFam6), the tree looks proper. >> Here is a view: >> ... >> T=8090:G=ENSORLG00000004203]):1.7):0.070715[&&NHX:S=Percomorpha:D=N:B=23]):0.104119[&&NHX >> ... >> >> There is no NHX information for the 1.7 branch long. >> Nevertheless, the API returns this: >> ... >> T=8090:G=ENSORLG00000004203]):1.7[&&NHX]):0.070715[&&NHX:S=Percomorpha:D=N:B=23]):0.104119[&&NHX >> ... >> >> >> 1.7[&&NHX] instead of 1.7 >> >> How to fix this ? >> Thanks -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 |
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From: Sebastien M. <Seb...@un...> - 2008-09-05 14:39:03
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The same kind of thing for family TF105088 with 1.3 distance >> Hi Sebastien, >> >> Is the API not working because of this ? > > The API works for this family. > But it should cause some problems with some tree viewers. > >> I believe that the API produces a correct tree and that the database is >> possibly wrong: the database tree should have an empty [&&NHX] (this was >> the case in previous versions of Treefam). Having [&&NHX] makes the >> nodes consistent and I think this doesn't violate the specifications of >> the format. >> >> This is down to the interpretation of the format: Should a node with no >> information get an empty [&&NHX] or nothing ? >> What do other treefamers think ? >> >> J-K >> >> >> On Fri, 2008-09-05 at 11:18 +0200, Sebastien Moretti wrote: >>> Hi, >>> It seems that API produces an invalid HNX tree for TF102048 family. >>> >>> From the database (TreeFam6), the tree looks proper. >>> Here is a view: >>> ... >>> T=8090:G=ENSORLG00000004203]):1.7):0.070715[&&NHX:S=Percomorpha:D=N:B=23]):0.104119[&&NHX >>> ... >>> >>> There is no NHX information for the 1.7 branch long. >>> Nevertheless, the API returns this: >>> ... >>> T=8090:G=ENSORLG00000004203]):1.7[&&NHX]):0.070715[&&NHX:S=Percomorpha:D=N:B=23]):0.104119[&&NHX >>> ... >>> >>> >>> 1.7[&&NHX] instead of 1.7 >>> >>> How to fix this ? >>> Thanks -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 |
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