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| 1 | -------------------------------- PARAMETERS -------------------------------- | 1 | -------------------------------- PARAMETERS -------------------------------- |
| 2 | -Path to read input files: /home/egaytan/automatic-extraction-growth-conditions/predict-annot/input/ | 2 | +--inputPath Path of training data set : /home/egaytan/automatic-extraction-growth-conditions/predict-annot/input/ |
| 3 | -Mode name: model_Run3_v10_S1_False_S2_True_S3_False_S4_False_Run3_v10 | 3 | +--outputPath Output path to place output files: /home/egaytan/automatic-extraction-growth-conditions/predict-annot/output/ |
| 4 | -Model path: /home/egaytan/automatic-extraction-growth-conditions/CRF/models | 4 | +--outputFileI Output tagged file I : annot-input_bg_outputI.txt |
| 5 | -Path to place output files: /home/egaytan/automatic-extraction-growth-conditions/predict-annot/output/ | 5 | +--outputFileII Output tagged file II : annot-input_bg_outputII.txt |
| 6 | -Filtering stop words: False | 6 | +--modelPath Path to read CRF model : /home/egaytan/automatic-extraction-growth-conditions/CRF/models |
| 7 | -Levels: S1: FalseS2: FalseS3: FalseS4: False | 7 | +--modelName Model name : model_Run3_v10_S1_False_S2_True_S3_False_S4_False_Run3_v10 |
| 8 | -Run variant: None | 8 | +--infoPath Path of GSE-GSM index file : /home/egaytan/automatic-extraction-growth-conditions/predict-annot/mapping |
| 9 | +--infoFile GSE-GSM index file : bg_sentences_midx.txt | ||
| 10 | +--variant Run variant : 13 | ||
| 11 | +--S1 General features : True | ||
| 12 | +--S2 Inner/Complete word features : False | ||
| 13 | +--S3 Extended context features : False | ||
| 14 | +--S4 Semantic features : True | ||
| 15 | +--filteringStopWords Filtering stop words : False | ||
| 16 | +--filterSymbols Filtering punctuation marks : False | ||
| 9 | Filtering symbols ['.', ',', ':', ';', '?', '!', "'", '"', '<', '>', '(', ')', '-', '_', '/', '\\', '¿', '¡', '+', '{', '}', '[', ']', '*', '%', '$', '#', '&', '°', '`', '...']: False | 17 | Filtering symbols ['.', ',', ':', ';', '?', '!', "'", '"', '<', '>', '(', ')', '-', '_', '/', '\\', '¿', '¡', '+', '{', '}', '[', ']', '*', '%', '$', '#', '&', '°', '`', '...']: False |
| 10 | -------------------------------- PROCESSING -------------------------------- | 18 | -------------------------------- PROCESSING -------------------------------- |
| 11 | Reading CRF model... | 19 | Reading CRF model... |
| 12 | -Reading CRF model done in: 0.008342s | 20 | +Reading CRF model done in: 0.008336s |
| 13 | Processing corpus... | 21 | Processing corpus... |
| 14 | Preprocessing file...annot-input_bg_v3.txt | 22 | Preprocessing file...annot-input_bg_v3.txt |
| 15 | Sentences input data: 14716 | 23 | Sentences input data: 14716 |
| 16 | Predicting tags with model | 24 | Predicting tags with model |
| 17 | -Prediction done in: 0.983480s | 25 | +Prediction done in: 1.688127s |
| 18 | Tagging file | 26 | Tagging file |
| 19 | - 0 1 | 27 | +Processing corpus done in: 3.948320s |
| 20 | -0 <Gtype> antibody : Flag <Gtype/> Gtype | ||
| 21 | -1 <Gversion> ChIP-Seq <Gversion/> Gversion | ||
| 22 | -2 Cultures of Caulobacter -LRB- TLS1631-TLS1633 ... Gtype | ||
| 23 | -3 <Gtype> developmental stage : mixed population... Gtype | ||
| 24 | -4 DNA was isolated using the Qiagen Cell Lysis a... | ||
| 25 | -5 Escherichia coli | ||
| 26 | -6 Escherichia coli AB1157 | ||
| 27 | -7 For analysis of ChIP-seq data , Hiseq 2500 Ill... | ||
| 28 | -8 For analysis of IDAP-seq data , Hiseq 2500 Ill... Gtype | ||
| 29 | -9 Genome _ build : NC _ 000913.3 | ||
| 30 | -10 Genome _ build : NC _ 011916.1 | ||
| 31 | -11 <Gtype> genotype : AB1157 ybbD : : parS scramb... Gtype | ||
| 32 | -12 <Gtype> genotype : AB1157 ybbD : : parS scramb... Gtype | ||
| 33 | -13 <Gtype> genotype : AB1157 ybbD : : parS site 1... Gtype | ||
| 34 | -14 <Gtype> genotype : AB1157 ybbD : : parS site 2... Gtype | ||
| 35 | -15 <Gtype> genotype : AB1157 ybbD : : parS site 2... Gtype | ||
| 36 | -16 <Gtype> genotype : AB1157 ybbD : : parS site 3... Gtype | ||
| 37 | -17 <Gtype> genotype : AB1157 ybbD : : parS site 3... Gtype | ||
| 38 | -18 <Gtype> genotype : AB1157 ybbD : : parS site 4... Gtype | ||
| 39 | -19 <Gtype> genotype : AB1157 ybbD : : parS site 4... Gtype | ||
| 40 | -20 <Gtype> genotype : AB1157 ybbD : : parS site 5... Gtype | ||
| 41 | -21 <Gtype> genotype : AB1157 ybbD : : parS site 5... Gtype | ||
| 42 | -22 <Gtype> genotype : AB1157 ybbD : : parS site 6... Gtype | ||
| 43 | -23 <Gtype> genotype : AB1157 ybbD : : parS site 7... Gtype | ||
| 44 | -24 <Gtype> genotype : AB1157 ybbD : : parS site 7... Gtype | ||
| 45 | -25 Hiseq 2500 Illumina short reads -LRB- 50 bp -R... | ||
| 46 | -26 LELab _ ChIP _ seq _ TLS1637 _ anti _ FLAG | ||
| 47 | -27 LELab _ ChIP _ seq _ TLS1638 _ anti _ FLAG | ||
| 48 | -28 LELab _ ChIP _ seq _ TLS1639 _ anti _ FLAG | ||
| 49 | -29 LELab _ ChIP _ seq _ TLS1640 _ anti _ FLAG | ||
| 50 | -... ... ... | ||
| 51 | -14686 <Phase> ESBL019 Coliform <Phase/> Phase | ||
| 52 | -14687 <Gtype> ESBL019 Filamented <Gtype/> Gtype | ||
| 53 | -14688 ESBL019 Reverted | ||
| 54 | -14689 <Phase> ESBL019 Transition <Phase/> Phase | ||
| 55 | -14690 Escherichia coli | ||
| 56 | -14691 Four morphologic states of ESBL019 were used d... | ||
| 57 | -14692 <Gtype> morphology : Coliform <Gtype/> Gtype | ||
| 58 | -14693 <Gtype> morphology : Filamented <Gtype/> Gtype | ||
| 59 | -14694 morphology : Reverted -LRB- reverted back from... | ||
| 60 | -14695 morphology : Transition -LRB- from Coli into F... | ||
| 61 | -14696 RNA isolation was performed using an RNeasy mi... | ||
| 62 | -14697 <Gtype> strain : beta-lactamase -LRB- ESBL -RR... Gtype | ||
| 63 | -14698 The E. coli isolate ESBL019 was originally iso... | ||
| 64 | -14699 Escherichia coli | ||
| 65 | -14700 lexA 10 ' after UV vs. 0 ' , MG1655 | ||
| 66 | -14701 <Gtype> lexA 10 min after UV treatment , 25 ug... Gtype | ||
| 67 | -14702 lexA 20 ' after NOuv vs. 0 ' , MG1655 | ||
| 68 | -14703 lexA 20 ' after UV vs. 0 ' , MG1655 | ||
| 69 | -14704 lexA 20 min after NOuv , 25 ug total RNA , 2 u... | ||
| 70 | -14705 <Gtype> lexA 20 min after UV treatment , 25 ug... Gtype | ||
| 71 | -14706 lexA 40 ' after UV vs. 0 ' , MG1655 | ||
| 72 | -14707 <Gtype> lexA 40 min after UV treatment , 25 ug... Gtype | ||
| 73 | -14708 lexA 5 ' after UV vs. 0 ' , MG1655 | ||
| 74 | -14709 <Gtype> lexA 5 min after UV treatment , 25 ug ... Gtype | ||
| 75 | -14710 lexA 60 ' after NOuv vs. 0 ' , MG1655 | ||
| 76 | -14711 lexA 60 ' after UV vs. 0 ' , MG1655 | ||
| 77 | -14712 lexA 60 min after NOuv , 25 ug total RNA , 2 u... | ||
| 78 | -14713 <Gtype> lexA 60 min after UV treatment , 25 ug... Gtype | ||
| 79 | -14714 lexA vs. wt , before UV treatment , MG1655 | ||
| 80 | -14715 untreated cells , 25 ug total RNA | ||
| 81 | - | ||
| 82 | -[14716 rows x 2 columns] | ... | ... |
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