geo-alchemy 0.0.6

a Python library and command line tool to make GEO data into gold.

geo-alchemy

a Python library and command line tool to make GEO data into gold.

1. why geo-alchemy
2. installation
3. usage
   • parse metadata from GEO
     • parse platform
     • parse sample
     • parse series
   • serialization and deserialization

why geo-alchemy

GEO is like a gold mine that contains a huge many gold ore. But processing these gold ore(GEO series) into gold(expression matrix, clinical data) is not very easy:

1. how to map microarray probe to gene?
2. how about multiple probes map to same gene?
3. hot to get clinical data?
4. ...

geo-alchemy was born to deal with it.

installation

pip install geo-alchemy

usage

parse metadata from GEO

parse platform

from geo_alchemy import PlatformParser


parser = PlatformParser.from_accession('GPL570')
platform1 = parser.parse()


# or
platform2 = PlatformParser.from_accession('GPL570').parse()


print(platform1 == platform2)

parse sample

from geo_alchemy import SampleParser


parser = SampleParser.from_accession('GSM1885279')
sample1 = parser.parse()

# or
sample2 = SampleParser.from_accession('GSM1885279').parse()

print(sample1 == sample2)

parse series

from geo_alchemy import SeriesParser


parser = SeriesParser.from_accession('GSE73091')
series1 = parser.parse()


# don't parse samples, samples attribute will be a blank list
series2 = parser.parse(parse_samples=False)
print(series2.samples == [])


# or
series3 = SeriesParser.from_accession('GSE73091').parse()


print(series1 == series3)

additional computed attributes can be access by:

print(series.sample_count)  # how many samples
print(series.platforms)  # duplication removal platforms
print(series.organisms)  # duplication removal organisms

serialization and deserialization

For the convenience of saving, all objects in geo-alchemy can be converted to dict, and this dict can be directly saved to a file in json form.

Moreover, geo-alchemy also provides methods to convert these dicts into objects.

from geo_alchemy import SeriesParser


series1 = SeriesParser.from_accession('GSE73091').parse()
data = series1.to_dict()
series2 = SeriesParser.parse_dict(data)


print(series1 == series2)