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biocore / biom-format

The Biological Observation Matrix (BIOM) Format Project
http://biom-format.org
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BiomTable.iterObservations not working in biom2 #540

Closed george-weingart closed 10 years ago

george-weingart commented 10 years ago

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 commented 10 years ago

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))

— Reply to this email directly or view it on GitHub https://github.com/biocore/biom-format/issues/540.

george-weingart commented 10 years ago

Opened #541

george-weingart commented 10 years ago

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 commented 10 years ago

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 https://github.com/biocore/biom-format/issues/540.

— Reply to this email directly or view it on GitHub https://github.com/biocore/biom-format/issues/540#event-166828805.

george-weingart commented 10 years ago

Thanks !!