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Great changes to incorporate… #1

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eb310b6
Update README
THinnerichs Dec 9, 2021
b95ebb7
Update 2to3 .py files and upload full data
THinnerichs Dec 13, 2021
d646389
Update RetrieveGene.py for checkpointing
THinnerichs Dec 16, 2021
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24 changes: 12 additions & 12 deletions AllGenes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,13 +24,13 @@ def QueryAPI(model,criteriaString,includeString="",optionsString="",writeOut=[])
api = RmaApi()
# Settings for retrieval
rows = []
blockSize = 2000
blockSize = 5000
done = False
startRow = 0
# for i in range(0, total_rows, blockSize):

while not done:
print "Row %d, attempting to retrieve %d rows..." % (startRow, blockSize)
print("Row %d, attempting to retrieve %d rows..." % (startRow, blockSize))

tot_rows = len(rows)
if len(includeString)==0:
Expand All @@ -50,16 +50,16 @@ def QueryAPI(model,criteriaString,includeString="",optionsString="",writeOut=[])
numRows = len(rows) - tot_rows # additional rows retrieved on running the query
startRow += numRows

print "%d rows retrieved." % numRows
print("%d rows retrieved." % numRows)

# Check if we're at the end of the road
if numRows == 0 or numRows < blockSize:
done = True

# Write out the results as they come in, if requested
if isinstance(writeOut, basestring):
if isinstance(writeOut, str):
json_utilities.write(json_file_name, rows)
print "Wrote to %s" % json_file_name
print("Wrote to %s" % json_file_name)

return rows
#-------------------------------------------------------------------------------
Expand Down Expand Up @@ -106,7 +106,7 @@ def SaveSectionsToCSV(sections):
})
# To dataframe:
df_sections = pd.DataFrame.from_records(sectionList) #,index='section_id')
df_sections = df_sections.sort('section_id')
df_sections = df_sections.sort_values(by=['section_id'])

# Save as a .csv file:
df_sections.to_csv(sectionDatasetFilename)
Expand All @@ -123,19 +123,19 @@ def SaveSectionsToCSV(sections):
})
# To dataframe:
df_genes = pd.DataFrame.from_records(geneList) #,index='entrez_id')
df_genes = df_genes.sort('entrez_id')
df_genes = df_genes.sort_values(by=['entrez_id'])
numGenesFull = df_genes.shape[0]
df_genes = df_genes.drop_duplicates()
numGenesFiltered = df_genes.shape[0]
print "Genes filtered from %u to %u" % (numGenesFull, numGenesFiltered)
print("Genes filtered from %u to %u" % (numGenesFull, numGenesFiltered))
# Save as a .csv file:
df_genes.to_csv(geneInfoFilename)
#-------------------------------------------------------------------------------
def SaveListCSV(stringList,fileName):
# Outputs a csv from a given list of strings
resultFile = open(fileName,'wb')
wr = csv.writer(resultFile, dialect='excel')
wr.writerow(stringList)
with open(file=fileName, mode='w') as resultFile:
wr = csv.writer(resultFile, dialect='excel')
wr.writerow(stringList)

#-------------------------------------------------------------------------------

Expand All @@ -154,7 +154,7 @@ def SaveListCSV(stringList,fileName):
entrezSet = set(geneEntrezList)
geneEntrezList = list(entrezSet)
geneEntrezList.sort()
print "There are %u unique genes in section datasets" % len(entrezSet)
print("There are %u unique genes in section datasets" % len(entrezSet))
SaveListCSV(geneEntrezList,entrezIDFilename)

# Saves to:
Expand Down
9 changes: 9 additions & 0 deletions README.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
# AllenSDK

This is a python 3 ported version of [https://github.com/benfulcher/AllenSDK](https://github.com/benfulcher/AllenSDK), enhanced through some parallelism using `joblib` and others.

[![DOI](https://zenodo.org/badge/104984017.svg)](https://zenodo.org/badge/latestdoi/104984017)
[![Twitter](https://img.shields.io/twitter/url/https/twitter.com/bendfulcher.svg?style=social&label=Follow%20%40bendfulcher)](https://twitter.com/bendfulcher)

Expand All @@ -10,6 +12,13 @@ This repository contains code for:
Requires Matlab and python.
The [AllenSDK package](http://alleninstitute.github.io/AllenSDK/install.html) for python must be installed.

Commands to install AllenSDK (As incompatible with newer versions)
```
conda create -n allensdk python=3.7
conda activate allensdk
pip install allensdk
```

If anything is unclear or needs improvement, please send questions by [raising an Issue](https://docs.github.com/en/github/managing-your-work-on-github/creating-an-issue) or [sending me an email](mailto:ben.d.fulcher@gmail.com).

This pipeline is based on code developed for [Fulcher and Fornito, _PNAS_ (2016)](https://doi.org/10.1073/pnas.1513302113), and used for [Fulcher et al., _PNAS_ (2019)](https://doi.org/10.1073/pnas.1814144116).
Expand Down
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