Notebook

Demonstrate Genome for REPositioning drugs¶

Cautions:

noted as version 1.0.0 which means not touched since first made.
horribly named program makes me question computational sophistication of developers or at least their understanding of branding. Or how much reviewers considered the manuscript. (Explanation: grep is a very common, often used Unix command, and so naming your program that insures no one will ever be able to find the code or anything related.)
involves a database and hasn't been updated in four years

This won't be necessary if running from link provided as requirments will already be installed:

If running this elsewhere and getting errors saying cannot import scipy, argparse, numpy, or pandas, then run this code block in a cell in the notebook:

%pip install scipy
%pip install argparse
%pip install numpy
%pip install pandas

Show usage with example¶

In [1]:

#show first few lines of example input
!head example/RA_trans.genes

PANK4
HES5
LOC115110
TNFRSF14
C1orf93
MMEL1
MFAP2
ATP13A2
SDHB
PADI2

In [2]:

#show directory contents before run
!ls

 data						     LICENSE.md
'Demonstrate Genome for REPositioning drugs.ipynb'   README.md
 example					     requirements.txt
 grep.py					     update_database

In [3]:

%run grep.py --genelist example/RA_trans.genes --out example --test ATC

In [4]:

#show directory contents to see what was made
!ls

 data						     grep.py
'Demonstrate Genome for REPositioning drugs.ipynb'   LICENSE.md
 example					     README.md
 example.ATC.detail.txt				     requirements.txt
 example.ATC.large.txt				     update_database

In [5]:

# show first 30 lines of result file
!head -30 example.ATC.detail.txt

#Group	GroupName	OddsRatio	FisherExactP
A01	STOMATOLOGICAL PREPARATIONS	0.0	1.0
A02	DRUGS FOR ACID RELATED DISORDERS	0.0	1.0
A03	DRUGS FOR FUNCTIONAL GASTROINTESTINAL DISORDERS	1.696969696969697	0.45866618350054966
A04	ANTIEMETICS AND ANTINAUSEANTS	0.0	1.0
A05	BILE AND LIVER THERAPY	0.0	1.0
A06	DRUGS FOR CONSTIPATION	0.0	1.0
A07	ANTIDIARRHEALS, INTESTINAL ANTIINFLAMMATORY/ANTIINFECTIVE AGENTS	0.0	1.0
A08	ANTIOBESITY PREPARATIONS, EXCL. DIET PRODUCTS	0.0	1.0
A09	DIGESTIVES, INCL. ENZYMES	0.0	1.0
A10	DRUGS USED IN DIABETES	0.0	1.0
A11	VITAMINS	0.0	1.0
A12	MINERAL SUPPLEMENTS	0.0	1.0
A14	ANABOLIC AGENTS FOR SYSTEMIC USE	0.0	1.0
A16	OTHER ALIMENTARY TRACT AND METABOLISM PRODUCTS	0.0	1.0
B01	ANTITHROMBOTIC AGENTS	1.648989898989899	0.46790118087197186
B02	ANTIHEMORRHAGICS	0.0	1.0
B03	ANTIANEMIC PREPARATIONS	0.0	1.0
B05	BLOOD SUBSTITUTES AND PERFUSION SOLUTIONS	0.0	1.0
B06	OTHER HEMATOLOGICAL AGENTS	0.0	1.0
C01	CARDIAC THERAPY	1.6224662162162162	0.36633761423573746
C02	ANTIHYPERTENSIVES	0.0	1.0
C03	DIURETICS	2.7176308539944904	0.3234969317058849
C04	PERIPHERAL VASODILATORS	3.5258467023172906	0.2632265400754351
C05	VASOPROTECTIVES	0.0	1.0
C07	BETA BLOCKING AGENTS	0.0	1.0
C08	CALCIUM CHANNEL BLOCKERS	2.7176308539944904	0.3234969317058849
C09	AGENTS ACTING ON THE RENIN-ANGIOTENSIN SYSTEM	0.0	1.0
C10	LIPID MODIFYING AGENTS	0.0	1.0
D01	ANTIFUNGALS FOR DERMATOLOGICAL USE	0.0	1.0

In [6]:

# show first 30 lines of other result file
!head -30 example.ATC.large.txt

#Group	GroupName	OddsRatio	FisherExactP
A	ALIMENTARY TRACT AND METABOLISM	0.4175084175084175	0.9073586755836576
B	BLOOD AND BLOOD FORMING ORGANS	0.9292929292929293	0.6667409120705736
C	CARDIOVASCULAR SYSTEM	1.1098790322580645	0.52288230144114
D	DERMATOLOGICALS	0.6980649872216137	0.7653438054311404
G	GENITO URINARY SYSTEM AND SEX HORMONES	0.0	1.0
H	SYSTEMIC HORMONAL PREPARATIONS, EXCL. SEX HORMONES AND INSULINS	0.0	1.0
J	ANTIINFECTIVES FOR SYSTEMIC USE	0.0	1.0
L	ANTINEOPLASTIC AND IMMUNOMODULATING AGENTS	3.7395833333333335	0.0016006128913752943
M	MUSCULO-SKELETAL SYSTEM	1.4580792682926829	0.41483225119822686
N	NERVOUS SYSTEM	0.3700581978727674	0.9307597129365626
P	ANTIPARASITIC PRODUCTS, INSECTICIDES AND REPELLENTS	0.0	1.0
R	RESPIRATORY SYSTEM	2.3784119106699753	0.1517209311834251
S	SENSORY ORGANS	0.7069475240206947	0.761171048831641
V	VARIOUS	0.0	1.0

Try with different contents¶

Make a list of genes with each gene on a separate line. Like so:

ABCC10
ABI2
ATXN2
BGLAP
BLM
BMPR2
BNIP1
BRAP
BZRAP1
BZRAP1-AS1
CDKN1A
COL4A2
CORO1C
CREBRF
CRIP3
CTLA4
CTTNBP2NL
CUX2
CYLC2
F11
FAM109A
FAM216A
FAM222A
FAM222A-AS1
FARP1
FES
FGA
FGB
FGG
FICD
FOXC1
FOXF2
FOXN4
FOXQ1
FURIN
GIT2
GLTP
GMDS
GMNN
HTRA1
HVCN1
ICA1L
IFT81
ILF3
ILF3-AS1
IQCD
ISCU
KCNK3
KCTD10
KDM4A
KLKB1
LDLR
LPA
LRCH1
MAN2A2
MAPKAPK5
MAPKAPK5-AS1
MIR142
MIR22
MIR22HG
MIR638
MMAB
MMP12
MMP13
MMP3
MPO
MTMR4
MVK
MYL2
MYO1H
NAA25
NBEAL1
NEDD4
NKX2-5
NOP58
OAS1
OAS2
OAS3
OBFC1
PAQR6
PDE3A
PITX2
PLEKHA1
PLG
PLRG1
PMF1
PMF1-BGLAP
PPM1E
PPP1CC
PPTC7
PRPF8
PRRX1
PTPN11
PTPRF
QTRT1
RAB44
RAD51C
RAD9B
RAPH1
RASAL1
RGS7
RILP
RNF43
RPH3A
RPL6
SART3
SBF2
SBF2-AS1
SCARF1
SELPLG
SEPT4
SH2B3
SH3PXD2A
SLC22A7
SMARCA4
SMG5
SNORD11
SNORD11B
SNORD70
SSH1
ST7L
SUMO1
SUPT4H1
TMEM119
TPCN1
TRAFD1
TRIM37
TRPV4
TSPAN2
TTBK1
UBE3B
UNG
USP30
ZNF474

Normally, you'd make such a file with a text editor; however, here we'll use Python. A text editor is critical; use SublimeText, or Atom, or VScode. Nothing else, besides VSCode, made by Microsoft will do this. This is a common tripping point, as novices aren't away Microsoft Word and Wordpad on their computer aren't suitable for this.

In [7]:

s='''ABCC10
ABI2
ATXN2
BGLAP
BLM
BMPR2
BNIP1
BRAP
BZRAP1
BZRAP1-AS1
CDKN1A
COL4A2
CORO1C
CREBRF
CRIP3
CTLA4
CTTNBP2NL
CUX2
CYLC2
F11
FAM109A
FAM216A
FAM222A
FAM222A-AS1
FARP1
FES
FGA
FGB
FGG
FICD
FOXC1
FOXF2
FOXN4
FOXQ1
FURIN
GIT2
GLTP
GMDS
GMNN
HTRA1
HVCN1
ICA1L
IFT81
ILF3
ILF3-AS1
IQCD
ISCU
KCNK3
KCTD10
KDM4A
KLKB1
LDLR
LPA
LRCH1
MAN2A2
MAPKAPK5
MAPKAPK5-AS1
MIR142
MIR22
MIR22HG
MIR638
MMAB
MMP12
MMP13
MMP3
MPO
MTMR4
MVK
MYL2
MYO1H
NAA25
NBEAL1
NEDD4
NKX2-5
NOP58
OAS1
OAS2
OAS3
OBFC1
PAQR6
PDE3A
PITX2
PLEKHA1
PLG
PLRG1
PMF1
PMF1-BGLAP
PPM1E
PPP1CC
PPTC7
PRPF8
PRRX1
PTPN11
PTPRF
QTRT1
RAB44
RAD51C
RAD9B
RAPH1
RASAL1
RGS7
RILP
RNF43
RPH3A
RPL6
SART3
SBF2
SBF2-AS1
SCARF1
SELPLG
SEPT4
SH2B3
SH3PXD2A
SLC22A7
SMARCA4
SMG5
SNORD11
SNORD11B
SNORD70
SSH1
ST7L
SUMO1
SUPT4H1
TMEM119
TPCN1
TRAFD1
TRIM37
TRPV4
TSPAN2
TTBK1
UBE3B
UNG
USP30
ZNF474
'''
%store s >mygenes.txt 

Writing 's' (str) to file 'mygenes.txt'.

In [8]:

#run with my genes as input
%run grep.py --genelist mygenes.txt --out amazing_results --test ATC

different way of saving gene names¶

Can make the list of gene names using the bash shel

In [9]:

!echo SUMO1 > another_genelist.txt
!echo SUPT4H1 >> another_genelist.txt
!echo TMEM119 >> another_genelist.txt
!echo TPCN1 >> another_genelist.txt
!echo TRAFD1 >> another_genelist.txt
!echo TRIM37 >> another_genelist.txt
!echo TRPV4 >> another_genelist.txt
!echo TSPAN2 >> another_genelist.txt
!echo TTBK1 >> another_genelist.txt
!echo UBE3B >> another_genelist.txt

OR another way

In [10]:

#to set up demonstrate another way, first delete last example
!rm another_genelist.txt

In [11]:

%%bash
myArray=("SUMO1" "SUPT4H1" "TMEM119" "TPCN1" "TRAFD1" "TRIM37" "TRPV4" "TSPAN2" "TTBK1" "UBE3B")
for str in ${myArray[@]}; do
  echo $str >> another_genelist.txt
done

In [12]:

#run with another set of genes as input
%run grep.py --genelist mygenes.txt --out another_genelist --test ATC

Enjoy!