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~/Projects/gene-converter $ p build_and_convert.py | |
docker build -t convert/elegene10st --build-arg package=pd.elegene.1.0.st_3.12.0.tar.gz --build-arg db=elegene10st -f Dockerfile.pd . | |
Sending build context to Docker daemon 3.904GB | |
Step 1/13 : FROM convert/base | |
---> d958adf36199 | |
Step 2/13 : WORKDIR /home/user | |
Removing intermediate container a0118890d985 | |
---> 47b27a4c2473 | |
Step 3/13 : USER root | |
---> Running in 475050347cd0 |
We can make this file beautiful and searchable if this error is corrected: No tabs found in this TSV file in line 0.
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organism internal_accession | |
Homo sapiens hgu133plus2 | |
Mus musculus mouse4302 | |
Homo sapiens hgu133a | |
Homo sapiens hugene10st | |
Mus musculus mogene10st | |
Rattus norvegicus rat2302 | |
Homo sapiens hgu133a2 | |
Homo sapiens hgu219 | |
Homo sapiens hthgu133pluspm |
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## | |
# Hacked together, sorry.. | |
# Required CSVs were tediously exported manually from GEO web interface. | |
## | |
import csv | |
import json | |
import requests | |
import pdb | |
import pprint |
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SRP004164 | |
SRP085379 | |
GSE62322 | |
SRP030508 | |
SRP030509 | |
SRP030506 | |
SRP030507 | |
SRP030504 | |
SRP030505 | |
SRP030502 |
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SRP068364 | |
SRP041343 | |
E-GEOD-24528 | |
SRP020008 | |
SRP084292 | |
E-GEOD-39842 | |
SRP111553 | |
SRP069839 | |
SRP058956 | |
GSE94532 |
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# GPL1319 | |
GSE1894 | |
GSE1995 | |
GSE3303 | |
GSE3667 | |
GSE4201 | |
GSE4585 | |
GSE4859 | |
GSE4989 | |
GSE5048 |
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[ | |
{ | |
"gpl": "GPL570", | |
"num_samples": 137985, | |
"organism": "Homo sapiens", | |
"title": "[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array" | |
}, | |
{ | |
"gpl": "GPL13112", | |
"num_samples": 99869, |
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[ | |
{ | |
"gpl": "GPL570", | |
"num_samples": 137981, | |
"title": "[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array" | |
}, | |
{ | |
"gpl": "GPL13112", | |
"num_samples": 99869, | |
"title": "Illumina HiSeq 2000 (Mus musculus)" |
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GSE10080 | |
GSE10241 | |
GSE10842 | |
GSE11567 | |
GSE11913 | |
GSE11915 | |
GSE12215 | |
GSE12243 | |
GSE12771 | |
GSE13201 |
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GSE7701 | |
GSE7702 | |
GSE9067 | |
GSE9187 | |
GSE10057 | |
GSE10107 | |
GSE10864 | |
GSE10956 | |
GSE10959 | |
GSE11132 |