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exfilms - npm Package Compare versions
Comparing version 1.0.2 to 1.0.3
@@ -0,1 +1,8 @@ | ||
| ## [1.0.3](https://github.com/vmalnathnambiar/exfilms/compare/v1.0.2...v1.0.3) (2024-03-28) | ||
| ### Bug Fixes | ||
| * **input check:** set input defaults appropriately ([67e112a](https://github.com/vmalnathnambiar/exfilms/commit/67e112a3801d4e4d6b190907f96d4b274b265fb8)) | ||
| ## [1.0.2](https://github.com/vmalnathnambiar/exfilms/compare/v1.0.1...v1.0.2) (2024-03-27) | ||
@@ -2,0 +9,0 @@ |
@@ -18,3 +18,4 @@ # Data Conversion to mzML using ProteoWizard | ||
| Data retrieved from MS instruments (from now on referred to as raw MS data) is widely stored in proprietary vendor formats that are optimised to its respective hardware and are only accessibly using vendor-provided software libraries. To enable cross-platform data integration and analysis, mzML was introduced as an open, universal format to store raw MS data acquired independently of vendor-specific instruments. One of the most prominent way of converting these raw MS data files to mzML is using the ProteoWizard _msConvert_ tool.\ | ||
| Data retrieved from MS instruments (from now on referred to as raw MS data) is widely stored in proprietary vendor formats that are optimised to its respective hardware and are only accessibly using vendor-provided software libraries. To enable cross-platform data integration and analysis, mzML was introduced as an open, universal format to store raw MS data acquired independently of vendor-specific instruments. One of the most prominent way of converting these raw MS data files to mzML is using the ProteoWizard _msConvert_ tool. | ||
| <br> | ||
@@ -48,3 +49,4 @@ | ||
| Download [ProteoWizard][pwiz-download]\ | ||
| Download [ProteoWizard][pwiz-download] | ||
| <br> | ||
@@ -51,0 +53,0 @@ |
@@ -1,2 +0,2 @@ | ||
| # How to Create A Target File | ||
| # How to Create a Target File | ||
@@ -43,3 +43,4 @@ > [!NOTE]\ | ||
| \ | ||
|  | ||
| <br> | ||
@@ -55,3 +56,4 @@ | ||
| Once you select the option, you will be prompted a pop-up box allowing you to specify how you would like to publish your content to the web. You can then use the options provided to link or embed your document. | ||
| Once you select the option, you will be prompted a pop-up box allowing you to specify how you would like to publish your content to the web. You can then use the options provided to link or embed your document. | ||
| <br> | ||
@@ -58,0 +60,0 @@ |
@@ -36,3 +36,4 @@ # How to ExfilMS: The Complete Guide | ||
| The `i`, `--inputDirectory` displayed in the error message is known as a command line argument (or "command" or "flag") that is required for the successful execution of ExfilMS. There are both required and non-required flags available for your use. The inclusion of these flags along with the `exfilms` command will configure and establish the behaviour of the tool for running its extraction (and filtering) process.\ | ||
| The `i`, `--inputDirectory` displayed in the error message is known as a command line argument (or "command" or "flag") that is required for the successful execution of ExfilMS. There are both required and non-required flags available for your use. The inclusion of these flags along with the `exfilms` command will configure and establish the behaviour of the tool for running its extraction (and filtering) process. | ||
| <br> | ||
@@ -39,0 +40,0 @@ |
| { | ||
| "name": "exfilms", | ||
| "version": "1.0.2", | ||
| "version": "1.0.3", | ||
| "description": "A cross-platform, command line interface (CLI) tool to extract mass spectrometry (MS) data from mzML formatted files, with spectrum filtering capabilities.", | ||
@@ -5,0 +5,0 @@ "bin": { |
@@ -11,20 +11,62 @@ \ | ||
| ExfilMS is a cross-platform, command line interface (CLI) tool to extract mass spectrometry (MS) data from mzML formatted files, with spectrum filtering capabilities.\ | ||
| ExfilMS is a cross-platform, command line interface (CLI) tool to extract mass spectrometry (MS) data from mzML formatted files, with spectrum filtering capabilities. | ||
| <br> | ||
| ### Features: | ||
| ## Features | ||
| - MS data extraction (spectrum and chromatogram) | ||
| - Precision value rounding | ||
| - Spectra filtering (m/z and intensity) | ||
| - Targeted (target file, m/z tolerance and ppm tolerance) | ||
| - Range (minimum and maximum m/z) | ||
| - Spectrum data filtering | ||
| - Spectrum type (profile / centroid) | ||
| - MS level | ||
| - Polarity (positive / negative) | ||
| - Exclude spectra (m/z and intensity) | ||
| 1. MS data extraction (spectrum and chromatogram) | ||
| 2. Precision value rounding | ||
| 3. Spectra filtering (m/z and intensity) | ||
| - Targeted (target file, m/z tolerance and ppm tolerance) | ||
| - Range (minimum and maximum m/z) | ||
| 4. Spectrum data filtering | ||
| - Spectrum type (profile / centroid) | ||
| - MS level | ||
| - Polarity (positive / negative) | ||
| - Exclude spectra (m/z and intensity) | ||
| <br> | ||
| ## Supported MS Platforms | ||
| Data extraction and spectrum filtration have been tested on data acquired from the following MS platforms: | ||
| <table> | ||
| <tr> | ||
| <th>Instrument Vendor</th> | ||
| <th>MS Platform</th> | ||
| </tr> | ||
| <tr> | ||
| <td rowspan="3">Bruker</td> | ||
| <td>ImpactII QToF-MS</td> | ||
| </tr> | ||
| <tr> | ||
| <td>solariX MRMS</td> | ||
| </tr> | ||
| <tr> | ||
| <td>timsTOFPro TIMS-ToF-MS</td> | ||
| </tr> | ||
| <tr> | ||
| <td rowspan="3">Waters</td> | ||
| <td>XEVOTQXS TQ-MS</td> | ||
| </tr> | ||
| <tr> | ||
| <td>XEVOTQXS DESI-MS</td> | ||
| </tr> | ||
| <tr> | ||
| <td>XEVOG2XSQTOF REIMS</td> | ||
| </tr> | ||
| <tr> | ||
| <td>SCIEX</td> | ||
| <td>QTRAP6500+ TQ-MS</td> | ||
| </tr> | ||
| </table> | ||
| <br> | ||
| ## Installation | ||
@@ -109,3 +151,3 @@ | ||
| - [How to ExfilMS: The Complete Guide](./docs/how-to-exfilms-the-complete-guide.md) | ||
| - [How to Create A Target File](./docs/how-to-create-a-target-file.md) | ||
| - [How to Create a Target File](./docs/how-to-create-a-target-file.md) | ||
@@ -118,6 +160,9 @@ <br> | ||
| > | ||
| > - Unable to extract MS data from Bruker EVOQ instruments (unsupported format by ProteoWizard). | ||
| > - Unable to parse mzML data that has a file size **GREATER THAN** 2GB. | ||
| > - Large MS data may cause Node environment to terminate abruptly due to memory limit exhaustion. | ||
| > - Slow output write speed due to build architecture difference (i.e, Intel vs AMD vs ARM) when running ExfilMS with Docker. | ||
| > 1. Unable to extract MS data from Bruker EVOQ instruments (unsupported format by ProteoWizard). | ||
| > | ||
| > 2. Unable to parse mzML data that has a file size **GREATER THAN** 2GB. | ||
| > | ||
| > 3. Large MS data may cause Node environment to terminate abruptly due to memory limit exhaustion. | ||
| > | ||
| > 4. Slow output write speed due to build architecture difference (i.e, Intel vs AMD vs ARM) when running ExfilMS with Docker. | ||
@@ -124,0 +169,0 @@ <br> |
@@ -18,2 +18,3 @@ #!/usr/bin/env node | ||
| import { setForSpectraFiltering } from './utils/setForSpectraFiltering.js'; | ||
| import { setInquirerDefaults } from './utils/setInquirerDefaults.js'; | ||
| import { writeLog } from './utils/writeLog.js'; | ||
@@ -56,7 +57,4 @@ import { yargsCheck } from './utils/yargsCheck.js'; | ||
| // Configure some parameters to match argv setDefault() settings format | ||
| configParam.outputFormat = configParam.outputFormat[0]; | ||
| if (configParam.msLevel) { | ||
| configParam.msLevel = configParam.msLevel.split(' ').map(Number); | ||
| } | ||
| // Set up configuration parameters appropriately | ||
| configParam = await setInquirerDefaults(configParam); | ||
| console.log(''); | ||
@@ -63,0 +61,0 @@ } else { |
@@ -5,3 +5,3 @@ /** | ||
| import { setDefaults } from './setDefaults.js'; | ||
| import { setYargsDefaults } from './setYargsDefaults.js'; | ||
@@ -64,3 +64,3 @@ /** | ||
| // Set default values (where required) | ||
| configParam = await setDefaults(argv); | ||
| configParam = await setYargsDefaults(argv); | ||
| } | ||
@@ -67,0 +67,0 @@ |
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Improved metrics
- Total package byte prevSize
- increased by0.07%
2253832
- Number of package files
- increased by2.63%
39
- Lines of code
- increased by0.6%
2010
- Number of lines in readme file
- increased by29.22%
199
No dependency changes