Carlos-Francisco Méndez-Cruz / automatic-extraction-growth-conditions

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Estefani Gaytan Nunez
07d3119f 1 parent 582f6ed0

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-------------------------------- PARAMETERS --------------------------------
Path to read input files: /home/egaytan/automatic-extraction-growth-conditions/predict-annot/input/
Mode name: model_Run3_v10_S1_False_S2_True_S3_False_S4_False_Run3_v10
Model path: /home/egaytan/automatic-extraction-growth-conditions/CRF/models
Path to place output files: /home/egaytan/automatic-extraction-growth-conditions/predict-annot/output/
Filtering stop words: False
Levels: S1: FalseS2: FalseS3: FalseS4: False
Run variant: None
--inputPath Path of training data set : /home/egaytan/automatic-extraction-growth-conditions/predict-annot/input/
--outputPath Output path to place output files: /home/egaytan/automatic-extraction-growth-conditions/predict-annot/output/
--outputFileI Output tagged file I : annot-input_bg_outputI.txt
--outputFileII Output tagged file II : annot-input_bg_outputII.txt
--modelPath Path to read CRF model : /home/egaytan/automatic-extraction-growth-conditions/CRF/models
--modelName Model name : model_Run3_v10_S1_False_S2_True_S3_False_S4_False_Run3_v10
--infoPath Path of GSE-GSM index file : /home/egaytan/automatic-extraction-growth-conditions/predict-annot/mapping
--infoFile GSE-GSM index file : bg_sentences_midx.txt
--variant Run variant : 13
--S1 General features : True
--S2 Inner/Complete word features : False
--S3 Extended context features : False
--S4 Semantic features : True
--filteringStopWords Filtering stop words : False
--filterSymbols Filtering punctuation marks : False
Filtering symbols ['.', ',', ':', ';', '?', '!', "'", '"', '<', '>', '(', ')', '-', '_', '/', '\\', '¿', '¡', '+', '{', '}', '[', ']', '*', '%', '$', '#', '&', '°', '`', '...']: False
-------------------------------- PROCESSING --------------------------------
Reading CRF model...
Reading CRF model done in: 0.008342s
Reading CRF model done in: 0.008336s
Processing corpus...
Preprocessing file...annot-input_bg_v3.txt
Sentences input data: 14716
Predicting tags with model
Prediction done in: 0.983480s
Prediction done in: 1.688127s
Tagging file
0 1
0 <Gtype> antibody : Flag <Gtype/> Gtype
1 <Gversion> ChIP-Seq <Gversion/> Gversion
2 Cultures of Caulobacter -LRB- TLS1631-TLS1633 ... Gtype
3 <Gtype> developmental stage : mixed population... Gtype
4 DNA was isolated using the Qiagen Cell Lysis a...
5 Escherichia coli
6 Escherichia coli AB1157
7 For analysis of ChIP-seq data , Hiseq 2500 Ill...
8 For analysis of IDAP-seq data , Hiseq 2500 Ill... Gtype
9 Genome _ build : NC _ 000913.3
10 Genome _ build : NC _ 011916.1
11 <Gtype> genotype : AB1157 ybbD : : parS scramb... Gtype
12 <Gtype> genotype : AB1157 ybbD : : parS scramb... Gtype
13 <Gtype> genotype : AB1157 ybbD : : parS site 1... Gtype
14 <Gtype> genotype : AB1157 ybbD : : parS site 2... Gtype
15 <Gtype> genotype : AB1157 ybbD : : parS site 2... Gtype
16 <Gtype> genotype : AB1157 ybbD : : parS site 3... Gtype
17 <Gtype> genotype : AB1157 ybbD : : parS site 3... Gtype
18 <Gtype> genotype : AB1157 ybbD : : parS site 4... Gtype
19 <Gtype> genotype : AB1157 ybbD : : parS site 4... Gtype
20 <Gtype> genotype : AB1157 ybbD : : parS site 5... Gtype
21 <Gtype> genotype : AB1157 ybbD : : parS site 5... Gtype
22 <Gtype> genotype : AB1157 ybbD : : parS site 6... Gtype
23 <Gtype> genotype : AB1157 ybbD : : parS site 7... Gtype
24 <Gtype> genotype : AB1157 ybbD : : parS site 7... Gtype
25 Hiseq 2500 Illumina short reads -LRB- 50 bp -R...
26 LELab _ ChIP _ seq _ TLS1637 _ anti _ FLAG
27 LELab _ ChIP _ seq _ TLS1638 _ anti _ FLAG
28 LELab _ ChIP _ seq _ TLS1639 _ anti _ FLAG
29 LELab _ ChIP _ seq _ TLS1640 _ anti _ FLAG
... ... ...
14686 <Phase> ESBL019 Coliform <Phase/> Phase
14687 <Gtype> ESBL019 Filamented <Gtype/> Gtype
14688 ESBL019 Reverted
14689 <Phase> ESBL019 Transition <Phase/> Phase
14690 Escherichia coli
14691 Four morphologic states of ESBL019 were used d...
14692 <Gtype> morphology : Coliform <Gtype/> Gtype
14693 <Gtype> morphology : Filamented <Gtype/> Gtype
14694 morphology : Reverted -LRB- reverted back from...
14695 morphology : Transition -LRB- from Coli into F...
14696 RNA isolation was performed using an RNeasy mi...
14697 <Gtype> strain : beta-lactamase -LRB- ESBL -RR... Gtype
14698 The E. coli isolate ESBL019 was originally iso...
14699 Escherichia coli
14700 lexA 10 ' after UV vs. 0 ' , MG1655
14701 <Gtype> lexA 10 min after UV treatment , 25 ug... Gtype
14702 lexA 20 ' after NOuv vs. 0 ' , MG1655
14703 lexA 20 ' after UV vs. 0 ' , MG1655
14704 lexA 20 min after NOuv , 25 ug total RNA , 2 u...
14705 <Gtype> lexA 20 min after UV treatment , 25 ug... Gtype
14706 lexA 40 ' after UV vs. 0 ' , MG1655
14707 <Gtype> lexA 40 min after UV treatment , 25 ug... Gtype
14708 lexA 5 ' after UV vs. 0 ' , MG1655
14709 <Gtype> lexA 5 min after UV treatment , 25 ug ... Gtype
14710 lexA 60 ' after NOuv vs. 0 ' , MG1655
14711 lexA 60 ' after UV vs. 0 ' , MG1655
14712 lexA 60 min after NOuv , 25 ug total RNA , 2 u...
14713 <Gtype> lexA 60 min after UV treatment , 25 ug... Gtype
14714 lexA vs. wt , before UV treatment , MG1655
14715 untreated cells , 25 ug total RNA
[14716 rows x 2 columns]
Processing corpus done in: 3.948320s
......