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1 # RAS Generator
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2
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3 Compute Reaction Activity Scores (RAS) from gene expression data.
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4
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5 ## Overview
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6
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7 RAS Generator computes reaction activity scores by evaluating GPR rules with gene expression values.
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8
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9 ## Galaxy Interface
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10
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11 In Galaxy: **COBRAxy → Expression2RAS**
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12
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13 1. Select built-in model or upload custom GPR rules
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14 2. Upload gene expression data
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15 3. Click **Run tool**
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16
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17 ## Command-line console
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18
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19 ```bash
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20 ras_generator -rs ENGRO2 \
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21 -in expression_data.tsv \
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22 -ra ras_scores.tsv \
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23 -ol ras_generation.log
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24 ```
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25
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26 ## Parameters
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27
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28 | Parameter | Flag | Description | Default |
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29 |-----------|------|-------------|---------|
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30 | Rules Selector | `-rs` | ENGRO2, Recon, or Custom | ENGRO2 |
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31 | Input Data | `-in` | Gene expression TSV file | - |
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32 | Output RAS | `-ra` | Output RAS scores file | - |
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33 | Output Log | `-ol` | Log file | - |
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34 | Custom Rules | `-rl` | Custom GPR rules file | - |
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35 | Gene Names | `-gn` | Gene ID type | HGNC_Symbol |
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36 | Remove Gene | `-rg` | Remove missing genes | true |
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37 | Ignore NaN | `--none` | Handle missing gene expression | true |
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38
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39 ## Input Format
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40
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41 Gene expression file (TSV):
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42
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43 ```
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44 Gene Sample1 Sample2 Sample3
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45 ALDOA 125.5 98.3 142.7
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46 ENO1 85.2 110.4 95.8
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47 PFKM 200.3 185.6 210.1
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48 ```
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49
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50 **File Format Notes:**
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51 - Use **tab-separated** values (TSV)
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52 - First row must contain column headers (Gene, Sample names)
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53 - Gene names must match the selected gene ID type
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54 - Numeric values only for expression data
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55
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56 ## GPR Rules
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57
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58 - **AND**: All genes required
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59 - **OR**: Any gene sufficient
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60 - Example: `(GENE1 and GENE2) or GENE3`
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61
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62 ## NaN Handling
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63
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64 The `--none` parameter controls how missing gene expression values are treated in GPR rules:
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65
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66 **When `--none true` (default):**
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67 - `(GENE1 and NaN)` → evaluated as `GENE1` value
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68 - `(GENE1 or NaN)` → evaluated as `GENE1` value
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69 - Missing genes don't block reaction activity calculation
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70
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71 **When `--none false` (strict mode):**
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72 - `(GENE1 and NaN)` → `NaN` (reaction cannot be evaluated)
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73 - `(GENE1 or NaN)` → `NaN` (reaction cannot be evaluated)
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74 - Any missing gene propagates NaN through the entire GPR expression
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75
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76 **Recommendation**: Use default (`true`) for datasets with incomplete gene coverage.
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77
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78 ## Output Format
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79
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80 ```
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81 Reaction Sample1 Sample2 Sample3
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82 R00001 125.5 98.3 142.7
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83 R00002 85.2 110.4 95.8
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84 ```
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85
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86 ## Examples
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87
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88 ### Basic Usage
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89
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90 ```bash
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91 ras_generator -rs ENGRO2 \
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92 -in expression.tsv \
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93 -ra ras_scores.tsv
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94 ```
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96 ## Troubleshooting
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98 | Error | Solution |
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99 |-------|----------|
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100 | "Gene not found" | Check gene ID format |
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101 | "Invalid GPR" | Verify GPR rule syntax |
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102
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103 ## See Also
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104
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105 - [RAS to Bounds](tools/ras-to-bounds)
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106 - [MAREA](tools/marea)
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107 - [Built-in Models](reference/built-in-models)
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