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Pathways #13

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bdd9ceb
pathway queries, local consensusdb
Nov 7, 2018
efcb008
dict entry fix
Nov 7, 2018
087e6be
resetting wikipathways
Nov 7, 2018
cbaaa55
resetting wikipathways
Nov 7, 2018
97afa76
resetting wikipathways
Nov 7, 2018
52151c2
wikipathways as submodule
Nov 7, 2018
8c8239c
consensus path db automated update, get_pathways()
Nov 8, 2018
b064261
exclude directly queried databases from cpdb
Nov 8, 2018
0a99861
clearer list uniquification
Nov 8, 2018
ee08028
more efficient result output
Nov 8, 2018
9b95c03
removed unnecessary conversion
Nov 8, 2018
056b877
building pathway db
Nov 9, 2018
d451fb1
pathway db
Nov 9, 2018
876c5e8
pathway db
Nov 9, 2018
13c79ee
Merge pull request #7 from Genome3d/lucas
Nov 9, 2018
9e3c86c
Merge pull request #8 from Genome3d/lucas
Nov 11, 2018
7f514e9
wikipathways edit
Nov 13, 2018
f143819
wikipathways
Nov 13, 2018
2c7e5ab
improvements regarding robustness
Nov 13, 2018
9103f09
naming
Nov 13, 2018
6d4150d
secure encoding
Nov 13, 2018
2e20b7e
return produce_summary()
Nov 13, 2018
dbe115b
ConnectionError
Nov 13, 2018
bf04338
ConnectionError Wikipathways specific
Nov 13, 2018
9a71887
encoding incompatibilities
Nov 13, 2018
8daa0b7
logging
Nov 14, 2018
8ee74e8
minor changes, logging, typos
Nov 14, 2018
da653c4
fixed timeout handling
Nov 14, 2018
aa8f037
fixed timeout handling
Nov 14, 2018
104194f
handling ConnectionError
Nov 14, 2018
cd14016
pathway summary integration
Nov 14, 2018
ba89435
run pathway summary separately
Nov 14, 2018
0c9421a
wikipathways as forked submodule, significant expression variation ac…
Nov 22, 2018
3d2f8b6
tracking master
Nov 22, 2018
a78289a
removed submodule
Nov 22, 2018
20053f6
wikipathways on branch master
Nov 22, 2018
0ea624d
wikipathways track master
Nov 22, 2018
d0573b1
wikipathways at master
Nov 22, 2018
76e75ed
removed submodule
Nov 22, 2018
85b8921
wikipathways on master
Nov 22, 2018
032fa44
saving to dict, no output files
Nov 22, 2018
7f108da
gene expression z-scores mapped to pathways - current state
Nov 26, 2018
d50bebc
no wp api client needed
Nov 29, 2018
77214bd
up/downstream for wikipathways
Nov 30, 2018
95c396d
up/downstream for reactome, queries robust via requests not pycurl
Dec 5, 2018
c5abfd2
relocated file io setup to function
Dec 5, 2018
9cd1c19
code relocated to main file
Dec 6, 2018
013d9f0
up/downstream for kegg, pathway versions for kegg, db version for wik…
Dec 12, 2018
a853d9d
robustness regarding input/style/processing input line by line
Dec 12, 2018
019e85c
robustness: kegg: gene exists but has no pathways associated
Dec 13, 2018
e5120db
robustness: previously unknown tag in wp interaction xml/reactome: po…
Dec 13, 2018
464776e
reduced queries for kegg
Dec 14, 2018
4ea343c
reduced queries for kegg
Dec 14, 2018
7518b65
wikipathways: hard coding namespace map
Dec 15, 2018
8401c05
csv writing improved
Dec 17, 2018
587bf46
csv writing
Dec 17, 2018
04ec253
wp: excluding metabolites from interactions/expression integration
Dec 18, 2018
9cd9745
HPM Protein Expression Data integrated
Dec 19, 2018
654622d
wp: gene products only as up/downstream, hpm: peptide and gene level
Jan 6, 2019
153d993
argument order fixed
Jan 7, 2019
f781192
hpm: fixes, file names as in original data set
Jan 7, 2019
4c4e287
summary: overview of set sizes during multiprocessing, pathway_summar…
Jan 7, 2019
ba2a700
logging: number of genes queried etc
Jan 8, 2019
8d2a2b1
pathway summary: snp-gene mappings
Jan 8, 2019
9a71748
HTML parsing error altered
Jan 8, 2019
4f9d9d8
multiprocessing db queries
Jan 8, 2019
3c99ca3
pathway summary
Jan 11, 2019
0649e7d
pathway summary
Jan 14, 2019
1bbbf82
rebased added wikipathways
Oct 31, 2018
02ec163
reduced globals
Nov 1, 2018
d08ef36
removed globals
Nov 2, 2018
d3e4759
beginning pathway integration
Nov 2, 2018
51d1947
pathway query
Nov 2, 2018
300f505
unecessary import
Nov 2, 2018
d5f71a1
formatting
Nov 3, 2018
99f00f9
clean up, preparation for pull
Nov 4, 2018
812c8c2
produce_summary() return
Nov 4, 2018
ac24739
shebang
Nov 4, 2018
4e730c6
alphabetic order unecessary
Nov 5, 2018
a6988df
alphabetic order unecessary
Nov 5, 2018
da96b95
dict iteration fix
Nov 6, 2018
b60253f
pathway import not necessary
Nov 6, 2018
7dbd03c
cell lines ordered
Nov 7, 2018
538fb7c
pathway queries, local consensusdb
Nov 7, 2018
b560bf4
dict entry fix
Nov 7, 2018
9bd8de7
resetting wikipathways
Nov 7, 2018
4fb81f5
resetting wikipathways
Nov 7, 2018
dee35d4
resetting wikipathways
Nov 7, 2018
0988af2
wikipathways as submodule
Nov 7, 2018
f72d7af
consensus path db automated update, get_pathways()
Nov 8, 2018
b716c44
exclude directly queried databases from cpdb
Nov 8, 2018
e392ad5
clearer list uniquification
Nov 8, 2018
46b7998
more efficient result output
Nov 8, 2018
4fbd455
removed unnecessary conversion
Nov 8, 2018
3f24aea
building pathway db
Nov 9, 2018
46b20c2
Revert "clearer list uniquification"
Nov 9, 2018
4f1bca3
pathway db
Nov 9, 2018
6b3b4f8
robust against missing genes.txt
Nov 9, 2018
cd51431
code style
Nov 11, 2018
8f534c3
code style
Nov 11, 2018
b534871
wikipathways edit
Nov 13, 2018
1e193a5
wikipathways
Nov 13, 2018
14358e8
improvements regarding robustness
Nov 13, 2018
5c7295c
naming
Nov 13, 2018
d0b622d
secure encoding
Nov 13, 2018
cc714cb
return produce_summary()
Nov 13, 2018
a736366
ConnectionError
Nov 13, 2018
bab42b7
ConnectionError Wikipathways specific
Nov 13, 2018
a6fd890
encoding incompatibilities
Nov 13, 2018
830aa71
logging
Nov 14, 2018
042ff44
minor changes, logging, typos
Nov 14, 2018
7d268b8
fixed timeout handling
Nov 14, 2018
5a7731b
fixed timeout handling
Nov 14, 2018
bef72f0
handling ConnectionError
Nov 14, 2018
17bac73
pathway summary integration
Nov 14, 2018
7ea2b97
run pathway summary separately
Nov 14, 2018
f1fd829
wikipathways as forked submodule, significant expression variation ac…
Nov 22, 2018
295d0ba
tracking master
Nov 22, 2018
dd4d073
removed submodule
Nov 22, 2018
5e6a138
wikipathways on branch master
Nov 22, 2018
0b0ed7b
wikipathways track master
Nov 22, 2018
8e815a5
wikipathways at master
Nov 22, 2018
2cf0424
removed submodule
Nov 22, 2018
7b93fdc
wikipathways on master
Nov 22, 2018
b59f239
saving to dict, no output files
Nov 22, 2018
cdb2154
gene expression z-scores mapped to pathways - current state
Nov 26, 2018
36fbcb3
no wp api client needed
Nov 29, 2018
5196e07
up/downstream for wikipathways
Nov 30, 2018
7ccbc80
up/downstream for reactome, queries robust via requests not pycurl
Dec 5, 2018
b14cb6c
relocated file io setup to function
Dec 5, 2018
272546a
code relocated to main file
Dec 6, 2018
c924066
up/downstream for kegg, pathway versions for kegg, db version for wik…
Dec 12, 2018
63f5965
robustness regarding input/style/processing input line by line
Dec 12, 2018
3a6b6d0
robustness: kegg: gene exists but has no pathways associated
Dec 13, 2018
bc3795f
robustness: previously unknown tag in wp interaction xml/reactome: po…
Dec 13, 2018
958c9f9
reduced queries for kegg
Dec 14, 2018
288f6da
reduced queries for kegg
Dec 14, 2018
08e27e1
wikipathways: hard coding namespace map
Dec 15, 2018
7dfb843
csv writing improved
Dec 17, 2018
b368469
csv writing
Dec 17, 2018
0a9cfff
wp: excluding metabolites from interactions/expression integration
Dec 18, 2018
e0f0dc9
HPM Protein Expression Data integrated
Dec 19, 2018
304e8f4
wp: gene products only as up/downstream, hpm: peptide and gene level
Jan 6, 2019
9d4d733
argument order fixed
Jan 7, 2019
ff7b133
hpm: fixes, file names as in original data set
Jan 7, 2019
373601f
summary: overview of set sizes during multiprocessing, pathway_summar…
Jan 7, 2019
ce27c91
logging: number of genes queried etc
Jan 8, 2019
c712f9f
pathway summary: snp-gene mappings
Jan 8, 2019
759ed5a
HTML parsing error altered
Jan 8, 2019
f4f8ba2
multiprocessing db queries
Jan 8, 2019
a4db83f
pathway summary
Jan 11, 2019
54950f9
pathway summary
Jan 14, 2019
9dc5de9
Merge branch 'pathways' of https://github.com/Genome3d/codes3d-v1 int…
Jan 14, 2019
ebf1f81
fixes
Jan 14, 2019
6d66628
kegg: limiting URL length; wikipathways: curation tags
Jan 14, 2019
b0a173c
wp: handling of broken gpml gene names
Jan 15, 2019
4022187
react: specificity of stripping modfications via regex
Jan 16, 2019
1b908ae
wp: capitalizing gene names according to hgnc
Jan 16, 2019
26fec97
fixed naming problem
Jan 16, 2019
a7754e5
wp: excluding homology mappings
Jan 16, 2019
898e02f
wp: only gene names with xref
Jan 16, 2019
f55bfd6
wp: regex modifications
Jan 17, 2019
23ddaca
reactome: different access; comments
Jan 17, 2019
88eedd4
cleaned up using class
Jan 18, 2019
36cdae2
one buffer size, 2 threads per process
Jan 22, 2019
9edd568
altered reactome query, gene name correction
Jan 22, 2019
e8cbfa4
kegg: robust against failing queries
Jan 22, 2019
3905d44
wp: up/down regulation
Jan 23, 2019
6031774
expression data
Jan 24, 2019
d28b3e3
wp only
Jan 24, 2019
d3a3264
print gene_ids removed
Jan 24, 2019
047e11a
gene synonym mapping
Jan 25, 2019
b0c1b6d
dynamic nsmap
Jan 25, 2019
7ccbd0a
GTEX integration
Jan 25, 2019
c55d5f8
gtex integration
Jan 26, 2019
149616b
gtex
Jan 26, 2019
8620520
gene synonyms: efficient handling
Jan 29, 2019
ad47989
naming error
Jan 29, 2019
2426c1b
pathway summary
Jan 29, 2019
f34309c
more gene remapping, hpm: gene 0 => prot 0
Jan 29, 2019
950d53b
pathway queries and summary changes
Jan 30, 2019
4bfde55
plots phosphorylation
Jan 31, 2019
53beee4
merged, retry requests
Feb 5, 2019
260fe85
misc dir removed
Feb 5, 2019
48be168
gitignore updated
Feb 5, 2019
5aa142b
logging
Feb 5, 2019
36d9434
sqllite queries, heatmap layout
Feb 7, 2019
fccdabf
heatmap layout
Feb 7, 2019
423894d
plots: p added
Feb 10, 2019
ce0b3de
optional numbers
Feb 13, 2019
9f8ac10
clustering
Feb 15, 2019
a8dd0f3
gene-only mode; legend
Mar 2, 2019
7ee950f
integration
Mar 3, 2019
bcdeec2
merge conflicts addressed
Mar 3, 2019
c8d5310
Merge pull request #12 from Genome3d/pathways_to_version1
Mar 3, 2019
6466bbd
merge conflict in produce summary
Mar 3, 2019
345bcd5
fixed integration problems
Mar 6, 2019
088b8e8
integration issue, global class
Mar 7, 2019
01fb86b
clustering genes only when 3 or more
Mar 9, 2019
aec1a96
Merge branch 'version1' into pathways
Apr 10, 2019
4d77824
static wspace
Apr 10, 2019
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6 changes: 4 additions & 2 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
.gitignore
*.pyc
lib/
lib
lib/*
!lib/gene_names.tsv
codes3d_summary/
codes3d_pathway/
codes3d_output/
.gitignore
4 changes: 4 additions & 0 deletions .gitmodules
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
[submodule "wikipathways-api-client-py"]
path = wikipathways-api-client-py
url = https://github.com/lucasfein/wikipathways-api-client-py
branch = master
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