geo-alchemy 0.0.8

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. use as Python library
   • parse metadata from GEO
     • parse platform
     • parse sample
     • parse series
   • serialization and deserialization
4. use as command line software
   • preprocessing

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

If you only want use as Python library:

pip install geo-alchemy

If you also want use as command line software:

pip install 'geo-alchemy[cmd]'

use as Python library

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)

# get platform annotation data
platform = PlatformParser.from_accession('GPL570', view='full').parse()
print(platform.internal_data)

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()

# or
series2 = SeriesParser.from_accession('GSE73091').parse()


print(series1 == series2)
print(series1.platforms)
print(series1.samples)
print(series1.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)

use as command line software

preprocessing(microarray series only)

geo-alchemy pp -s GSE174772 -p GPL570 -g 11

1. -s GSE174772 means preprocessing for GSE174772
2. -p GPL570 means preprocessing samples who use GPL570 of GSE174772
3. -g 11 means NO.11 column of GPL570 annotation file is gene

this command generate 2 files under current directory:

1. clinical file GSE174772_clinical.txt
2. gene expression file GSE174772_expression.txt