BiomTable.iterObservations not working in biom2

[george-weingart]

Hello,

I have code that was working in biom1 and now have to modify to work in biom2.
It was using BiomTable.iterObservations as follows but now in biom2 iterObservations is not working.

What is the easiest way to do it in biom2?

Thanks!

George Weingart

BiomObservations = BiomTable.iterObservations(conv_to_np=True)
for BiomObservationData in BiomObservations:
sBugName = str( BiomObservationData[1])
BiomTaxDataEntry = list()
BiomTaxDataEntry.append(sBugName)
BiomObservationsValues = BiomObservationData[0]
for BiomDataValue in BiomObservationsValues:
BiomTaxDataEntry.append(BiomDataValue)
BiomTaxDataWork.append(tuple(BiomTaxDataEntry))

[adamrp]

Hi George,

Please review the documentation and the changelog before posting issues.
You can find the changelog in this repository, and the documentation is at
biom-format.org. to answer your question, that function has been renamed
simply "iter" and you pass which axis (sample or observation) as an
argument.
On Sep 17, 2014 1:10 PM, "george-weingart" notifications@github.com wrote:

Hello,

I have code that was working in biom1 and now have to modify to work in
biom2.
It was using BiomTable.iterObservations as follows but now in biom2
iterObservations is not working.

What is the easiest way to do it in biom2?

Thanks!
George Weingart

BiomObservations = BiomTable.iterObservations(conv_to_np=True)

for BiomObservationData in BiomObservations:
sBugName = str( BiomObservationData[1])
BiomTaxDataEntry = list()
BiomTaxDataEntry.append(sBugName)
BiomObservationsValues = BiomObservationData[0]
for BiomDataValue in BiomObservationsValues:
BiomTaxDataEntry.append(BiomDataValue)
BiomTaxDataWork.append(tuple(BiomTaxDataEntry))

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#540.

[george-weingart]

Opened #541

[george-weingart]

Hi Adam,

Thanks. Worked.

Where exactly is the change log you referred?
Where exactly it says that iterObservations was changed to iter?

Thanks for your help and prompt response.
George

[wasade]

The change log can be found here:
https://github.com/biocore/biom-format/blob/master/ChangeLog.md

Best,
Daniel
On Sep 17, 2014 3:37 PM, "george-weingart" notifications@github.com wrote:

Reopened #540 #540.

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Reply to this email directly or view it on GitHub
#540 (comment).

[george-weingart]

Thanks !!