Skip to content

Commit f0b3c19

Browse files
shaicoh3nshaicoh3n
committed
initial commit (no data+models+annotations)
initial commit (no data+models+annotations)
1 parent 9fb1934 commit f0b3c19

11 files changed

+3542
-0
lines changed

‎.gitignore

+40
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,40 @@
1+
2+
code/Models/TITER/titer_canon_sc_scores_sorted.pickle
3+
*.pkl
4+
*.json
5+
code/Data/clinvar_transc_sites.csv
6+
code/Data/clinvar_trans_init_sites.csv
7+
code/Data/clinvar_splicing_sites.csv
8+
code/Data/clinvar_sites.csv
9+
code/Data/Chromosome/hg38.fa.fai
10+
code/Data/Chromosome/hg38.fa
11+
code/Data/annotations/chr_table_Y.csv
12+
code/Data/annotations/chr_table_X.csv
13+
code/Data/annotations/chr_table_9.csv
14+
code/Data/annotations/chr_table_8.csv
15+
code/Data/annotations/chr_table_7.csv
16+
code/Data/annotations/chr_table_6.csv
17+
code/Data/annotations/chr_table_5.csv
18+
code/Data/annotations/chr_table_4.csv
19+
code/Data/annotations/chr_table_3.csv
20+
code/Data/annotations/chr_table_22.csv
21+
code/Data/annotations/chr_table_21.csv
22+
code/Data/annotations/chr_table_20.csv
23+
code/Data/annotations/chr_table_2.csv
24+
code/Data/annotations/chr_table_19.csv
25+
code/Data/annotations/chr_table_18.csv
26+
code/Data/annotations/chr_table_17.csv
27+
code/Data/annotations/chr_table_16.csv
28+
code/Data/annotations/chr_table_15.csv
29+
code/Data/annotations/chr_table_14.csv
30+
code/Data/annotations/chr_table_13.csv
31+
code/Data/annotations/chr_table_12.csv
32+
code/Data/annotations/chr_table_11.csv
33+
code/Data/annotations/chr_table_10.csv
34+
code/Data/annotations/chr_table_1.csv
35+
code/Data/all_genome_genes.csv
36+
code/Data/all_genome_transcripts.csv
37+
*.pyc
38+
*.pyc
39+
*.pyc
40+
*.pyc

‎EXPosition.jpg

645 KB
Loading

‎code/EXPosition_utils.py

+336
Large diffs are not rendered by default.

‎code/Exposition_GUI.py

+2,660
Large diffs are not rendered by default.

‎code/Results/Results_man_muts_example.csv

+13
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,13 @@
1+
serial,gene_symbol,ensembl_id,use_mut_predictor,do_transcription,do_splicing,do_initiation,site_chr,INS_prob,INS_ins_pos,INS_ins_mut,DEL_prob,DEL_del_start,DEL_del_nts,SUB_prob,SUB_ins_mut,SUB_del_start,SUB_del_nts,increased_sensitivity,N_muts,init_search_dist,final_search_dist,titer_threshold,SAI_interesting,TITER_interesting,splicing_score,transcription_score,trans_init_score,all_int_genes_transcription_score,all_int_genes_trans_init_score,all_int_genes_splicing_score,mult_gene_affect,mut_df,comment,do_adj_srch,in_range_splicing,in_range_transcription,in_range_trans_init,max_transcription_name,max_trans_init_name,max_splicing_name,Class,eff,DEL_names,significant_transcription,significant_splicing,significant_trans_init,INS_names,SUB_names
2+
0,AADAT,No Interest Transcript,0,1,1,1,chr4,0,,,1.0,170089678,GTGCGTAATTCAT,0,,,,0,4,10,400,0.05,No missplicing!,/ST_DEL_0,0.00074,0.14092,0.00602, AADAT: 0.14092181780894047 , AADAT: 0.0060158617395979636 , AADAT: 0.0007428031922645349 ,0,"Empty DataFrame
3+
Columns: []
4+
Index: []",Success!,0,1,1,1,Not Analyzed,Not Analyzed,Not Analyzed,Not Classified,1.0,D,Significant,Significant,Significant,,
5+
1,A2ML1,No Interest Transcript,0,1,1,1,chr12,1.0,8847690,AC,0.0,,,0,,,,0,4,10,400,0.05,No missplicing!,No alt init!,0.00476,6e-05,0.0, A2ML1: 6.239495922035942e-05 , A2ML1: 0 , A2ML1: 0.004756862642716825 ,0,"Empty DataFrame
6+
Columns: []
7+
Index: []",Success!,0,1,1,0,Not Analyzed,Not Analyzed,Not Analyzed,Not Classified,1.0,,Not Significant,Significant,Not Significant,I,
8+
2,A2ML1,No Interest Transcript,0,1,1,1,chr12,0,,,1.0,8822631,AAATCT,0,,,,0,4,10,400,0.05,No missplicing!,/ST_DEL_0,0.0,0.14812,0.00138, A2ML1: 0.14811960254050247 , A2ML1: 0.0013798404510316274 , A2ML1: 0 ,0,"Empty DataFrame
9+
Columns: []
10+
Index: []",Success!,0,1,1,1,Not Analyzed,Not Analyzed,Not Analyzed,Not Classified,1.0,D,Significant,Not Significant,Significant,,
11+
3,A2ML1,No Interest Transcript,0,1,1,1,chr12,0,8822631,AAA,0.0,,,1.0,AAA,8822631,AAATCT,0,4,10,400,0.05,No missplicing!,/ST_SUB_0,0.0,0.03284,0.00077, A2ML1: 0.03283981843367389 , A2ML1: 0.0007705174194735922 , A2ML1: 0 ,0,"Empty DataFrame
12+
Columns: []
13+
Index: []",Success!,0,1,1,1,Not Analyzed,Not Analyzed,Not Analyzed,Not Classified,1.0,,Significant,Not Significant,Not Significant,,S

‎code/Results/Results_pred_muts_example.csv

+21
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,21 @@
1+
serial_row,gene_symbol,ensembl_id,use_mut_predictor,do_transcription,do_splicing,do_initiation,site_chr,target_seq,site_strand,site_start_pos,increased_sensitivity,N_muts,init_search_dist,final_search_dist,titer_threshold,SAI_interesting,TITER_interesting,splicing_score,transcription_score,trans_init_score,all_int_genes_transcription_score,all_int_genes_trans_init_score,all_int_genes_splicing_score,mult_gene_affect,mut_df,comment,do_adj_srch,in_range_splicing,in_range_transcription,in_range_trans_init,max_transcription_name,max_trans_init_name,max_splicing_name,Class,GuidePro,VBC,eff,DEL_prob,DEL_del_start,DEL_del_nts,DEL_names,INS_prob,INS_ins_pos,INS_ins_mut,INS_names,significant_transcription,significant_splicing,significant_trans_init
2+
0,No Interest Gene,No Interest Transcript,1,1,1,1,chr19,GTGTGCCGAGGTGTGCTGCG,-,58352485,0,4,10,400,0.05,No missplicing!,No alt init!,0.00217,0.03335,0.0, A1BG: 0.03334644253182871 , A1BG: 0 , A1BG: 0.0021655515502202846 ,0," indels frequency mut_type del_len del_start ins_nt del_nts
3+
1 I1+T 0.926175 I -1 -1 A
4+
2 D3 -1 0.026057 D 3 58352466 NaN
5+
3 D16 -2 0.025715 D 16 58352454 NaN
6+
4 D14 -2 0.022053 D 14 58352456 NaN ",Success!,0,1,1,0,Not Analyzed,Not Analyzed,Not Analyzed,Silencing,0.468,0.598,0.610305928448505,0.015902545423620722/0.015694299471409684/0.013459148481908314,58352466/58352454/58352456,GCA/AAGTCACACCCCGCAG/GTCACACCCCGCAG,D3 -1/D16 -2/D14 -2,0.5652499350715663,58352467,A,I1+T,Significant,Significant,Not Significant
7+
1,A1BG,No Interest Transcript,1,1,1,1,chr19,GGAAGTCTGGAGTCTCCAGG,+,58353093,0,4,10,400,0.05,No missplicing!,No alt init!,0.00166,0.0321,0.0, A1BG: 0.03209800732383983 , A1BG: 0 , A1BG: 0.0016585767168001881 ,0," indels frequency mut_type del_len del_start ins_nt del_nts
8+
1 I1+C 0.412697 I -1 -1 C
9+
2 D18 -7 0.265245 D 18 58353103 NaN
10+
3 D14 -12 0.172598 D 14 58353098 NaN
11+
4 D7 -5 0.149459 D 7 58353105 NaN ",Success!,0,1,1,0,Not Analyzed,Not Analyzed,Not Analyzed,Non-Silencing,0.255,0.578,0.5034364763754479,0.13353389935500276/0.08689235023833249/0.07524331123923213,58353103/58353098/58353105,AGTCTCCAGGTGGGCCTG/TCTGGAGTCTCCAG/TCTCCAG,D18 -7/D14 -12/D7 -5,0.20776691554288046,58353109,C,I1+C,Significant,Significant,Not Significant
12+
2,A4GALT,No Interest Transcript,1,1,1,1,chr22,CTTGAAGCCGATGATGAACA,+,42693865,0,4,10,400,0.05,No missplicing!,/ST_INS_0/ST_INS_1/ST_DEL_0/ST_DEL_1,0.00036,0.01334,0.00868, A4GALT: 0.013344770839137023 , A4GALT: 0.00868385350526222 , A4GALT: 0.00036060373574892124 ,0," indels frequency mut_type del_len del_start ins_nt del_nts
13+
1 I1+A 0.597856 I -1 -1 A
14+
2 D1 0 0.285086 D 1 42693882 NaN
15+
4 D2 1 0.063697 D 2 42693883 NaN
16+
5 I1+T 0.053361 I -1 -1 T ",Success!,0,1,1,1,Not Analyzed,Not Analyzed,Not Analyzed,Non-Silencing,0.283,0.578,0.4492484145262343,0.12807457357220867/0.02861557074791305,42693882/42693883,A/CA,D1 0/D2 1,0.26858581940100235/0.02397245080511033,42693881/42693881,A/T,I1+A/I1+T,Significant,Significant,Significant
17+
3,AACS,No Interest Transcript,1,1,1,1,chr12,GCAGATGGACCGCTTCCGGG,+,125065665,0,4,10,400,0.05,No missplicing!,/ST_INS_0/ST_DEL_0/ST_DEL_1/ST_DEL_2,0.00076,0.0866,0.00798, AACS: 0.08660109194870898 , AACS: 0.007979915731502701 , AACS: 0.0007587146130918718 ,0," indels frequency mut_type del_len del_start ins_nt del_nts
18+
1 I1+C 0.479357 I -1 -1 C
19+
2 D1 -1 0.288019 D 1 125065681 NaN
20+
3 D11 -9 0.141167 D 11 125065673 NaN
21+
4 D15 -5 0.091457 D 15 125065677 NaN ",Success!,0,1,1,1,Not Analyzed,Not Analyzed,Not Analyzed,Silencing,0.215,0.755,0.6317418852727085,0.18195374590315/0.08918098630960788/0.05777734296290251,125065681/125065673/125065677,C/ACCGCTTCCGG/CTTCCGGGCGGCTGT,D1 -1/D11 -9/D15 -5,0.30282981009704807,125065681,C,I1+C,Significant,Significant,Significant

‎code/man_muts_example.csv

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
serial,gene_symbol,ensembl_id,use_mut_predictor,do_transcription,do_splicing,do_initiation,site_chr,INS_prob,INS_ins_pos,INS_ins_mut,DEL_prob,DEL_del_start,DEL_del_nts,SUB_prob,SUB_ins_mut,SUB_del_start,SUB_del_nts
2+
0,AADAT,No Interest Transcript,0,1,1,1,chr4,0,,,1,170089678,GTGCGTAATTCAT,0,,,
3+
1,A2ML1,No Interest Transcript,0,1,1,1,chr12,1,8847690,AC,0,,,0,,,
4+
2,A2ML1,No Interest Transcript,0,1,1,1,chr12,0,,,1,8822631,AAATCT,0,,,
5+
3,A2ML1,No Interest Transcript,0,1,1,1,chr12,0,8822631,AAA,0,,,1,AAA,8822631,AAATCT

‎code/pred_muts_example.csv

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
serial_row,gene_symbol,ensembl_id,use_mut_predictor,do_transcription,do_splicing,do_initiation,site_chr,target_seq,site_strand,site_start_pos
2+
0,No Interest Gene,No Interest Transcript,1,1,1,1,chr19,GTGTGCCGAGGTGTGCTGCG,-,58352485
3+
1,A1BG,No Interest Transcript,1,1,1,1,chr19,GGAAGTCTGGAGTCTCCAGG,+,58353093
4+
2,A4GALT,No Interest Transcript,1,1,1,1,chr22,CTTGAAGCCGATGATGAACA,+,42693865
5+
3,AACS,No Interest Transcript,1,1,1,1,chr12,GCAGATGGACCGCTTCCGGG,+,125065665

‎code/setup.py

+25
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,25 @@
1+
import sys
2+
from cx_Freeze import setup, Executable
3+
import os
4+
5+
include_files = [os.path.join('.','EXPosition_utils.py'),
6+
os.path.join('.','Data'),
7+
os.path.join('.','Models'),
8+
os.path.join('.','transcription'),
9+
os.path.join('.','annotations'),
10+
os.path.join('.','Results'),
11+
os.path.join('.','man_muts_example.csv'),
12+
os.path.join('.','pred_muts_example.csv')]
13+
14+
packages = ['numpy', 'pandas','sklearn','scipy','tensorflow','keras','statsmodels','tqdm','termplotlib']
15+
setup(
16+
name='EXPostion',
17+
version='1.0',
18+
options={
19+
'build_exe': {
20+
'include_files': include_files,
21+
'packages': packages,
22+
}
23+
},
24+
executables=[Executable('Exposition_GUI.py')]
25+
)

0 commit comments

Comments
 (0)