- El corpus de entrenamiento y el modelo entrenado (son dos archivos grandes).
- Python, Skalearn, Gensim (latest version).
Sea el corpus en "GUs_literature.txt" y sea una lista de TFs "AraC", "YdeO", "ArgP", "Ada", "AcrR" y "XylR":
$ nl ../corpus/GUs_literature.txt | grep AraC | head -n1
15 AraC . arabinose AraC-arabinose . fucose AraC-fucose . araBAD araBAD_mRNA AraB RXN0-5116 ...
$ nl /almac/ignacio/data/GUsDany/corpus/GUs_literature.txt | grep AcrR | head -n1
5 AcrR . ethidium AcrR-ethidium . proflavin AcrR-proflavin . rhodamine 6G AcrR-rhodamine 6G ...
$ nl /almac/ignacio/data/GUsDany/corpus/GUs_literature.txt | grep Ada | head -n1
6 Ada . methyl Ada-methyl . ada-alkB ada-alkB_mRNA Ada Ada-methyl . ada-alkB ada-alkB_mRNA AlkB...
$ nl /almac/ignacio/data/GUsDany/corpus/GUs_literature.txt | grep ArgP | head -n1
16 ArgP . arginine ArgP-arginine . lysine ArgP-lysine . argO argO_mRNA ArgO RXN66-448 arginine_Ext...
$ nl /almac/ignacio/data/GUsDany/corpus/GUs_literature.txt | grep XylR | head -n1
180 XylR . xylose XylR-xylose . xylAB xylAB_mRNA XylA XYLISOM-RXN xylopyranose xylulose . xylAB ...
$ nl /almac/ignacio/data/GUsDany/corpus/GUs_literature.txt | grep YdeO | head -n1
57 EvgA . phosphate EvgA-phosphate . acrD acrD_mRNA AcrD AcrD-AcrA-TolC TRANS-RXN-92 drug_Ext ...$ python most_similars.py -h
usage: most_similars.py [-h] [--indexes indexes] [--corpus corpus]
[--inlines inlines] [--model model] [--dims dims]
[--top top] [--train train] [--save save]
This script gives a ranking for ach sentence of a given list (list of
'indexes') or for each string inside a file ('inlines').
optional arguments:
-h, --help show this help message and exit
--indexes indexes A list of indexes separed by comma.
--corpus corpus A file containing train text a [sentence|document] per
line.
--inlines inlines A file containing a sentence by row.
--model model A file containing the sentence embeddings model (gensim).
--dims dims Dimension of word embeddings.
--top top number of sentences returned for each ranking.
--train train Toggles whether a new model must be trained
(unspecified=False).
--save save Toggles whether results must be saved into automaticly
named files (unspecified=False).Give the list to the ranking script:
$ python most_similars.py --corpus ../GUs_literature.txt --indexes 15,5,6,16,180,57 --model ./d2v_raw_GUs-literature-wiki_H300_W5_A1.model
This prints out to stdout the ranking:
index | similaity | GU
# The most similars to this GU:
# 'AraC . arabinose AraC-arabinose . fucose AraC-fucose . araBAD araBAD_mRNA AraB R'
10 0.99226 AllR . glyoxylate AllR-glyoxylate . allA allA_mRNA AllA UREIDOGLYCOLATE-LYASE-RX
5 0.99199 Ada . methyl Ada-methyl . ada-alkB ada-alkB_mRNA Ada Ada-methyl . ada-alkB ada-a
4 0.99137 AcrR . ethidium AcrR-ethidium . proflavin AcrR-proflavin . rhodamine 6G AcrR-rho
6 0.99095 AdiY . adiA adiA_mRNA AdiA ARGDECARBOX-RXN arginine agmatine CO2 . gadAX gadAX_m
7 0.99053 AgaR . agaR agaR_mRNA AgaR . agaS-kbaY-agaBCDI agaS-kbaY-agaBCDI_mRNA AgaS . aga
11 0.98684 AllS . allantoin AllS-allantoin . allDCE allDCE_mRNA AllD RXN0-7024 ureidoglycol
13 0.98683 AppY . appCBXA appCBXA_mRNA AppC AppC-AppB RXN0-5266 ubiquinol_Ext oxygen_Ext ub
12 0.98499 AlsR . allose AlsR-allose . rpiB rpiB_mRNA RpiB RXN0-303 aldehydo-D-allose-6-P a
3 0.98437 AccB . accBC accBC_mRNA AccB AccD-AccA-AccC-AccB ACETYL-COA-CARBOXYLTRANSFER-RXN
9 0.97129 AlaS . alanine AlaS-alanine . alaS alaS_mRNA AlaS AlaS-alanine .
# The most similars to this GU:
# 'AcrR . ethidium AcrR-ethidium . proflavin AcrR-proflavin . rhodamine 6G AcrR-rho'
6 0.99968 AdiY . adiA adiA_mRNA AdiA ARGDECARBOX-RXN arginine agmatine CO2 . gadAX gadAX_m
5 0.99963 Ada . methyl Ada-methyl . ada-alkB ada-alkB_mRNA Ada Ada-methyl . ada-alkB ada-a
10 0.99963 AllR . glyoxylate AllR-glyoxylate . allA allA_mRNA AllA UREIDOGLYCOLATE-LYASE-RX
7 0.99954 AgaR . agaR agaR_mRNA AgaR . agaS-kbaY-agaBCDI agaS-kbaY-agaBCDI_mRNA AgaS . aga
13 0.99844 AppY . appCBXA appCBXA_mRNA AppC AppC-AppB RXN0-5266 ubiquinol_Ext oxygen_Ext ub
12 0.99793 AlsR . allose AlsR-allose . rpiB rpiB_mRNA RpiB RXN0-303 aldehydo-D-allose-6-P a
11 0.99738 AllS . allantoin AllS-allantoin . allDCE allDCE_mRNA AllD RXN0-7024 ureidoglycol
3 0.99274 AccB . accBC accBC_mRNA AccB AccD-AccA-AccC-AccB ACETYL-COA-CARBOXYLTRANSFER-RXN
14 0.99137 AraC . arabinose AraC-arabinose . fucose AraC-fucose . araBAD araBAD_mRNA AraB R
9 0.98198 AlaS . alanine AlaS-alanine . alaS alaS_mRNA AlaS AlaS-alanine .
# The most similars to this GU:
# 'Ada . methyl Ada-methyl . ada-alkB ada-alkB_mRNA Ada Ada-methyl . ada-alkB ada-a'
4 0.99963 AcrR . ethidium AcrR-ethidium . proflavin AcrR-proflavin . rhodamine 6G AcrR-rho
10 0.99959 AllR . glyoxylate AllR-glyoxylate . allA allA_mRNA AllA UREIDOGLYCOLATE-LYASE-RX
6 0.99957 AdiY . adiA adiA_mRNA AdiA ARGDECARBOX-RXN arginine agmatine CO2 . gadAX gadAX_m
7 0.99940 AgaR . agaR agaR_mRNA AgaR . agaS-kbaY-agaBCDI agaS-kbaY-agaBCDI_mRNA AgaS . aga
13 0.99807 AppY . appCBXA appCBXA_mRNA AppC AppC-AppB RXN0-5266 ubiquinol_Ext oxygen_Ext ub
12 0.99758 AlsR . allose AlsR-allose . rpiB rpiB_mRNA RpiB RXN0-303 aldehydo-D-allose-6-P a
11 0.99706 AllS . allantoin AllS-allantoin . allDCE allDCE_mRNA AllD RXN0-7024 ureidoglycol
3 0.99286 AccB . accBC accBC_mRNA AccB AccD-AccA-AccC-AccB ACETYL-COA-CARBOXYLTRANSFER-RXN
14 0.99199 AraC . arabinose AraC-arabinose . fucose AraC-fucose . araBAD araBAD_mRNA AraB R
9 0.98166 AlaS . alanine AlaS-alanine . alaS alaS_mRNA AlaS AlaS-alanine .
# The most similars to this GU:
# 'ArgP . arginine ArgP-arginine . lysine ArgP-lysine . argO argO_mRNA ArgO RXN66-4'
11 0.96595 AllS . allantoin AllS-allantoin . allDCE allDCE_mRNA AllD RXN0-7024 ureidoglycol
7 0.96445 AgaR . agaR agaR_mRNA AgaR . agaS-kbaY-agaBCDI agaS-kbaY-agaBCDI_mRNA AgaS . aga
10 0.96392 AllR . glyoxylate AllR-glyoxylate . allA allA_mRNA AllA UREIDOGLYCOLATE-LYASE-RX
6 0.96369 AdiY . adiA adiA_mRNA AdiA ARGDECARBOX-RXN arginine agmatine CO2 . gadAX gadAX_m
12 0.96237 AlsR . allose AlsR-allose . rpiB rpiB_mRNA RpiB RXN0-303 aldehydo-D-allose-6-P a
14 0.96222 AraC . arabinose AraC-arabinose . fucose AraC-fucose . araBAD araBAD_mRNA AraB R
5 0.96203 Ada . methyl Ada-methyl . ada-alkB ada-alkB_mRNA Ada Ada-methyl . ada-alkB ada-a
4 0.96194 AcrR . ethidium AcrR-ethidium . proflavin AcrR-proflavin . rhodamine 6G AcrR-rho
13 0.96039 AppY . appCBXA appCBXA_mRNA AppC AppC-AppB RXN0-5266 ubiquinol_Ext oxygen_Ext ub
3 0.95761 AccB . accBC accBC_mRNA AccB AccD-AccA-AccC-AccB ACETYL-COA-CARBOXYLTRANSFER-RXN
# The most similars to this GU:
# 'XylR . xylose XylR-xylose . xylAB xylAB_mRNA XylA XYLISOM-RXN xylopyranose xylul'
172 0.86116 TrpR . tryptophan TrpR-tryptophan . aroH aroH_mRNA AroH DAHPSYN-RXN P-enol-pyruv
169 0.82007 TdcR . tdcABCDEFG tdcABCDEFG_mRNA TdcA . tdcABCDEFG tdcABCDEFG_mRNA TdcB . tdcAB
176 0.81844 UlaR . ulaABCDEF ulaABCDEF_mRNA UlaA UlaC-UlaB-UlaA RXN0-2461 HPr - phosphorylat
173 0.79348 TyrR . tryptophan TyrR-tryptophan . phenylalanine TyrR-phenylalanine . tyrosine
174 0.78728 UhpA . phosphate UhpA-phosphate . uhpT uhpT_mRNA UhpT TRANS-RXN0-534 GAP_Ext GAP
166 0.77735 SoxS . acnA acnA_mRNA AcnA ACONITATEHYDR-RXN cis-aconitate I-CIT ACONITATEDEHYDR
180 0.76551 YdeO . appCBXA appCBXA_mRNA AppC AppC-AppB RXN0-5266 ubiquinol_Ext oxygen_Ext ub
167 0.76202 StpA . bglG bglG_mRNA BglG . bglGFB bglGFB_mRNA BglG . bglGFB bglGFB_mRNA BglF .
161 0.75943 RutR . thymine RutR-thymine . uracil RutR-uracil . carAB carAB_mRNA CarA CarB-Ca
170 0.75093 TorR . phosphate TorR-phosphate . TorI TorR-TorI . gadAX gadAX_mRNA GadA GLUTDEC
# The most similars to this GU:
# 'EvgA . phosphate EvgA-phosphate . acrD acrD_mRNA AcrD AcrD-AcrA-TolC TRANS-RXN-9'
64 0.79245 FucR . fuculose-1-P FucR-fuculose-1-P . fucAO fucAO_mRNA FucA FUCPALDOL-RXN fucu
43 0.79137 CytR . cytidine CytR-cytidine . cdd cdd_mRNA Cdd CYTIDEAM2-RXN cytidine ammonium
46 0.77583 DeoR . 2-deoxy-D-ribose 5-phosphate DeoR-2-deoxy-D-ribose 5-phosphate . deoCABD
51 0.77244 DpiA . phosphate DpiA-phosphate . appY appY_mRNA AppY . citCDEFXG citCDEFXG_mRNA
49 0.76499 DinJ-YafQ . cspE cspE_mRNA CspE . dinJ-yafQ dinJ-yafQ_mRNA DinJ YafQ-DinJ . dinJ
40 0.76081 CusR . phosphate CusR-phosphate . cusCFBA cusCFBA_mRNA CusC CusC-CusB-CusF-CusA
41 0.75702 CynR . cyanate CynR-cyanate . cynR cynR_mRNA CynR CynR-cyanate . cynTS cynTS_mRN
48 0.75559 DicA . dicB-ydfDE-insD-intQ dicB-ydfDE-insD-intQ_mRNA DicB . dicB-ydfDE-insD-int
47 0.75532 DhaR . DhaK DhaR-DhaK . dhaKLM dhaKLM_mRNA DhaK DhaR-DhaK . dhaKLM dhaKLM_mRNA D
80 0.74344 HcaR . hcaEFCBD hcaEFCBD_mRNA HcaE HcaC-HcaD-HcaF-HcaE RXN-12072 cinnamate oxyge
Happy linking