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| 1 | -------------------------------- PARAMETERS -------------------------------- | 1 | -------------------------------- PARAMETERS -------------------------------- |
| 2 | --inputPath Path of training data set : /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 | --outputPath Output path to place output files: /home/egaytan/automatic-extraction-growth-conditions/predict-annot/output/ | 3 | --outputPath Output path to place output files: /home/egaytan/automatic-extraction-growth-conditions/predict-annot/output/ |
| 4 | ---outputFileI Output tagged file I : annot-input_bg_outputI_v5.txt | 4 | +--outputFileI Output tagged file I : annot-input_bg_outputI_v6 |
| 5 | ---outputFileII Output tagged file II : annot-input_bg_outputII_v5 | 5 | +--outputFileII Output tagged file II : annot-input_bg_outputII_v6 |
| 6 | ---outputFileII Output tagged file III : annot-input_bg_outputIII_v5 | 6 | +--outputFileII Output tagged file III : annot-input_bg_outputIII_v6 |
| 7 | --modelPath Path to read CRF model : /home/egaytan/automatic-extraction-growth-conditions/CRF/models | 7 | --modelPath Path to read CRF model : /home/egaytan/automatic-extraction-growth-conditions/CRF/models |
| 8 | --modelName Model name : model_Run3_v10_S1_False_S2_True_S3_False_S4_False_Run3_v10 | 8 | --modelName Model name : model_Run3_v10_S1_False_S2_True_S3_False_S4_False_Run3_v10 |
| 9 | --infoPath Path of GSE-GSM index file : /home/egaytan/automatic-extraction-growth-conditions/predict-annot/mapping | 9 | --infoPath Path of GSE-GSM index file : /home/egaytan/automatic-extraction-growth-conditions/predict-annot/mapping |
| ... | @@ -15,16 +15,14 @@ | ... | @@ -15,16 +15,14 @@ |
| 15 | --S4 Semantic features : False | 15 | --S4 Semantic features : False |
| 16 | -------------------------------- PROCESSING -------------------------------- | 16 | -------------------------------- PROCESSING -------------------------------- |
| 17 | Reading CRF model... | 17 | Reading CRF model... |
| 18 | -Reading CRF model done in: 0.009225s | 18 | +Reading CRF model done in: 0.009524s |
| 19 | Processing corpus... | 19 | Processing corpus... |
| 20 | Preprocessing file...annot-input_bg_v4.txt | 20 | Preprocessing file...annot-input_bg_v4.txt |
| 21 | Sentences input data: 90688 | 21 | Sentences input data: 90688 |
| 22 | Predicting tags with model... | 22 | Predicting tags with model... |
| 23 | -Prediction done in: 27.733279s | 23 | +Prediction done in: 27.458162s |
| 24 | Tagging file... | 24 | Tagging file... |
| 25 | -GSE100233 GSM2675514 GPL18006-GPL18133-PMID:29186514 library_strategy.1 <Technique> ChIP-Seq </Technique> Technique | ||
| 26 | -GSE100233 GSM2675514 GPL18006-GPL18133-PMID:29186514 growth_protocol_ch1.1 Cultures of Caulobacter -LRB- TLS1631-TLS1633 -RRB- were grown at 30oC in PYE and supplemented with antibiotics , as necessary , at appropriate concentrations . To deplete wild-type non-tagged ParB , exponential-phase cells were washed off xylose and re-introduced to PYE +0.2 % glucose for an additional <Supp> 5 hours </Supp> . After 4 hours , vanillate was added to induce the expression of flag-parB -LRB- WT -RRB- or flag-parB -LRB- G101S/R104A -RRB- for an hour . Cultures of Escherichia coli -LRB- TLS1637-TLS1650 -RRB- were grown at 30oC in LB and supplemented with antibiotics , as necessary , at appropriate concentrations . IPTG -LRB- 0.5 mM -RRB- was added to induce the production of T18-ParB -LRB- WT -RRB- or T18-ParB -LRB- G101S -RRB- . After an hour , formadehyde -LRB- 1 % final concentration -RRB- were added to fix cells for ChIP-seq . Supp | ||
| 27 | Saving Ouput I... | 25 | Saving Ouput I... |
| 28 | Saving Ouput II... | 26 | Saving Ouput II... |
| 29 | Saving Ouput III... | 27 | Saving Ouput III... |
| 30 | -Pssing corpus done in: 258.328259s | 28 | +Passing corpus done in: 257.970281s | ... | ... |
| 1 | --------------------------------- PARAMETERS -------------------------------- | ||
| 2 | ---inputPath Path of training data set : /home/egaytan/automatic-extraction-growth-conditions/predict-annot/input/ | ||
| 3 | ---outputPath Output path to place output files: /home/egaytan/automatic-extraction-growth-conditions/predict-annot/output/ | ||
| 4 | ---outputFileI Output tagged file I : annot-input_bg_outputI_v4.txt | ||
| 5 | ---outputFileII Output tagged file II : annot-input_bg_outputII_v4 | ||
| 6 | ---modelPath Path to read CRF model : /home/egaytan/automatic-extraction-growth-conditions/CRF/models | ||
| 7 | ---modelName Model name : model_Run3_v10_S1_False_S2_True_S3_False_S4_False_Run3_v10 | ||
| 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_v4.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 | ||
| 17 | -Filtering symbols ['.', ',', ':', ';', '?', '!', "'", '"', '<', '>', '(', ')', '-', '_', '/', '\\', '¿', '¡', '+', '{', '}', '[', ']', '*', '%', '$', '#', '&', '°', '`', '...']: False | ||
| 18 | --------------------------------- PROCESSING -------------------------------- | ||
| 19 | -Reading CRF model... | ||
| 20 | -Reading CRF model done in: 0.009363s | ||
| 21 | -Processing corpus... | ||
| 22 | -Preprocessing file...annot-input_bg_v3.txt | ||
| 23 | -Sentences input data: 14716 | ||
| 24 | -Predicting tags with model | ||
| 25 | -Prediction done in: 1.737334s | ||
| 26 | -Tagging file | ||
| 27 | -Preprocessing file...annot-input_bg_v4.txt | ||
| 28 | -Sentences input data: 90688 | ||
| 29 | -Predicting tags with model | ||
| 30 | -Prediction done in: 26.434549s | ||
| 31 | -Tagging file | ||
| 32 | -Processing corpus done in: 58.304885s |
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