Merge pull request #177 from prasham21/refactor-analysis-module

Refactor analysis module

.github/workflows/tests.yml

@@ -34,6 +34,6 @@ jobs:
         run:
           tox -e py
         env:
-          INDRA_NEO4J_URL: ${{ secrets.INDRA_NEO4J_URL }}
+          INDRA_NEO4J_URL: "bolt://indra-cogex-lb-1eac1a3f066c0e52.elb.us-east-1.amazonaws.com:7687"
           INDRA_NEO4J_USER: ${{ secrets.INDRA_NEO4J_USER }}
           INDRA_NEO4J_PASSWORD: ${{ secrets.INDRA_NEO4J_PASSWORD }}

.gitignore

@@ -132,3 +132,4 @@ import.report
 .idea
 .idea/*
 .DS_Store
+src/indra_cogex/apps/static/source_badges.css

notebooks/phosphoproteomics_geffen/phosphoprot_explanation.ipynb

@@ -1543,6 +1543,16 @@
     "# Explore specific examples of site annotations\n",
     "[s for s in stmts_by_site.items() if s[0][0] == 'EXO1']"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bc02f41e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "protmapper.ann"
+   ]
   }
  ],
  "metadata": {

src/indra_cogex/analysis/__init__.py

@@ -0,0 +1,4 @@
+from pathlib import Path
+
+HERE = Path(__file__).parent.resolve().absolute()
+gene_continuous_analysis_example_data = HERE / "example_gene_data.csv"

src/indra_cogex/analysis/example_gene_data.csv

@@ -0,0 +1,201 @@
+gene_name,log2FoldChange
+YWHAB,-0.007834918
+YWHAE,-0.015973798
+YWHAH,0.06525256
+YWHAG,0.044404462
+SFN,-0.02976365
+YWHAQ,0.027458748
+YWHAZ,-0.004621383
+PPP2R5A,0.172823826
+PPP2R5D,0.023434448
+PPP2R5E,-0.216846213
+PPP2R5C,-0.36182941
+PPP2R1A,-0.076917203
+PPP2R1B,0.104152273
+PPP2R2A,0.031030455
+SH3BP1,0.042832082
+MPG,-0.051368183
+EIF4ENIF1,-0.113104564
+SLC3A2,0.213079298
+BZW2,0.066744158
+BZW1,0.100280513
+NT5C3A,0.011070345
+PGD,0.004263778
+PGLS,-0.098158149
+A1CF,0.105347041
+APP,-0.174194188
+AAAS,-0.03014477
+SLC1A5,-0.027154538
+AAGAB,0.090027177
+AAK1,-0.082737155
+PRKAA1,0.140364596
+AAR2,-0.0125346
+AATF,-0.016067206
+APOBEC3A,0.1357998
+APOBEC3B,-0.037393152
+APOBEC3C,-0.002644567
+APOBEC3F,0.013894275
+APOBEC3G,-0.086607048
+ABCA3,-0.014380271
+ABCB10,0.003477282
+ABCD1,-0.100460811
+ABCD2,0.10783447
+ABCD3,-0.060373037
+ABCE1,-0.04365049
+ABCF1,-0.036172563
+ABCF2,-0.021618789
+ABCF3,-0.12688348
+ABHD12,0.002547447
+ABHD14B,0.026315795
+ABI1,0.02447343
+ABI2,0.070248284
+ABL1,0.183487775
+ABL2,0.241480286
+ABR,-0.116763081
+ABRAXAS1,0.001991917
+ABRAXAS2,0.320259547
+ABT1,-0.044982617
+ACACA,-0.038471683
+ACACB,-0.100024725
+ACAD9,-0.037848093
+ACADVL,0.00558187
+ACAP2,0.135190119
+ACBD5,-0.085880794
+ACBD6,0.166240241
+DBI,1.442972627
+ACAD10,0.070417774
+ACIN1,0.00742579
+ACTL6A,-0.063511887
+ACLY,-0.065682931
+ACOT13,-0.133994534
+ACO1,0.065871895
+ACOT8,-0.025752905
+ACOT9,-0.015982487
+ACSL3,-0.140558871
+ACSL4,-0.064293962
+ACTB,-0.084677564
+ACTBL2,0.080023292
+POTEKP,-0.013939517
+ACTN1,-0.110658673
+ACTN2,-0.012408017
+ACTN3,-0.054429647
+ACTN4,0.00539965
+ACTA1,-0.319373889
+ACTR1B,0.37213006
+ACTR1A,-0.069172151
+ADAM10,-0.03588429
+ADA2,-0.059794758
+ADAP1,0.07604121
+AGPS,-0.007960316
+ADD1,0.062595835
+ADD2,-0.055540585
+ADD3,0.208582702
+ADNP,-0.077781022
+ADPGK,0.131806442
+AASDHPPT,0.011900425
+ADRM1,0.041529672
+SLC25A4,-0.153934351
+SLC25A5,-0.032218808
+SLC25A6,0.037894924
+SLC25A31,-0.238749677
+AEBP2,0.032025799
+AFAP1,0.203362454
+AFF1,-0.036545192
+AFF4,-0.231393839
+AFG3L2,-0.032413874
+AFTPH,-0.287103952
+ALG10B,0.147116305
+AGAP2,-0.045127754
+AGAP3,-0.071432392
+AGFG1,-0.009055862
+AGGF1,-0.040537547
+AGK,0.275372803
+PGM3,0.004758125
+AGO1,0.024745067
+AGO2,0.021592856
+AGO3,0.025918375
+AGO4,-0.06253178
+ADGRF1,-0.121486812
+AGRN,0.396592437
+ADGRL2,-0.234385362
+ADGRL3,-0.024146725
+AHNAK,0.025674463
+AHNAK2,-0.089995924
+AIFM1,0.114048943
+AIMP1,0.027067928
+AIMP2,0.037915793
+AIP,0.099089107
+AKAP17A,-0.012553814
+AKAP1,-0.084242638
+AKAP8,-0.012928769
+AKR1E2,-0.118821286
+AKAP13,-0.103937162
+AKAP8L,-0.090616788
+AKT1S1,0.05396134
+ARL14EP,0.051670537
+ALDH1A1,-0.349704002
+ALDH1L2,-0.050594502
+ALDH3A1,-0.114951935
+ALDH3A2,-0.144257648
+ALDH3B1,-0.055511291
+ALOX5AP,0.006343954
+ALB,0.139695178
+ALDH2,-0.160142862
+ALDOA,0.01128666
+ALG12,0.083480407
+ALG2,0.679985121
+ALG3,-0.177158303
+ALG6,-0.031067381
+ALG8,-0.058193464
+ALKBH2,0.059667416
+ALKBH5,0.082637821
+ALS2,-0.039450835
+ALX1,-0.239469009
+AMOTL1,-0.051765201
+AMPH,0.044654061
+LAP3,0.337433365
+ANPEP,-0.011590467
+LRPAP1,-0.00286531
+ANP32A,0.001475451
+ANP32B,-0.074659255
+ANP32E,-0.089343646
+ANAPC2,-0.043485259
+ANK2,-0.023399971
+ANKHD1,-0.008324687
+ANKLE2,-0.063650571
+ANKZF1,-0.038645576
+ANLN,0.031970411
+PRMT1,0.080859473
+PRMT3,-0.360830799
+PRMT5,-0.01841515
+ANO2,-0.039607757
+ANKRD11,-0.211484382
+ANKRD17,-0.025024948
+ANKRD24,-0.454340643
+ANKRD27,-0.215153685
+ANKRD28,0.183323872
+ANKRD44,0.074745409
+ANKRD50,0.028595357
+ANKS1A,-0.06003762
+ANXA11,-0.183730502
+ANXA1,0.046383985
+ANXA2,0.035745291
+ANXA4,-0.021593695
+ANXA5,0.087132071
+ANXA6,-0.061374351
+SNAP91,-0.0599222
+AP1B1,0.038324903
+AP1G1,-0.002652249
+AP1M1,-0.10669982
+AP1S1,-0.164372562
+AP1S2,-0.104389145
+AP2A1,0.048914821
+AP2A2,-0.035667563
+AP2B1,-0.005440283
+AP2M1,-0.041691207
+AP2S1,-0.011319567
+AP3B1,-0.023396396
+AP3B2,-0.003882796
+AP3D1,-0.000783146
+AP3M1,-0.061487117
+AP3M2,0.037356862