Metadata-Version: 2.1
Name: sdrf-pipelines
Version: 0.0.2
Summary: Translate, convert SDRF to configuration pipelines
Home-page: https://github.com/bigbio/sdrf-pipelines
Author: BigBio Team
Author-email: ypriverol@gmail.com
License: 'Apache 2.0
Description: # sdrf-pipelines
        
        The SDRF pipelines provide a set of tools to validate and convert SDRF files to different workflow configuration files such as MSstats and OpenMS.
        
        ### Installation
        
        ```bash
        pip install sdrf-pipelines
        ```
        
        ## Validate the SDRF
        
        # How to use it:
        
        Then, you can use the tool by executing the following command:
        
        ```bash
        parse_sdrf validate-sdrf --sdrf_file {here_the_path_to_sdrf_file}
        ```
        
        ## Convert to OpenMS: Usage
        
        ```bash
        parse_sdrf convert-openms -s sdrf.tsv
        ```
        
        ### Description:
        
        - experiment settings (search engine settings etc.)
        - experimental design
        
        The experimental settings file contains one row for every raw file. Columns contain relevevant parameters like precursor mass tolerance, modifications etc. These settings can usually be derived from the sdrf file.
        
        | URI | Filename | FixedModifications | VariableModifications | Label | PrecursorMassTolerance | PrecursorMassToleranceUnit | FragmentMassTolerance | FragmentMassToleranceUnit | DissociationMethod | Enzyme |
        |------| ------------- |-------------|-----|---| ------------- |-------------|-----|---| ------------- |-------------|
        | ftp://ftp.pride.ebi.ac.uk/pride/data/archive/XX/PXD324343/A0218_1A_R_FR01.raw | A0218_1A_R_FR01.raw | Acetyl (Protein N-term) | Gln->pyro-glu (Q),Oxidation (M) | label free sample| 10 | ppm | 10 | ppm | HCD | Trypsin |
        | ftp://ftp.pride.ebi.ac.uk/pride/data/archive/XX/PXD324343/A0218_1A_R_FR02.raw | A0218_1A_R_FR02.raw | Acetyl (Protein N-term) | Gln->pyro-glu (Q),Oxidation (M) | label free sample| 10 | ppm | 10 | ppm | HCD | Trypsin |
        
        
        The experimental design file contains information how to unambiguously map a single quantitative value. Most entries can
        be derived from the sdrf file. However, definition of conditions might need manual changes.
        
        - **Fraction_Group** identifier that indicates which fractions belong together. In the case of label-free data, the fraction group identifier has the same cardinality as the sample identifier.
        - The **Fraction** identifier indicates which fraction was measured in this file. In the case of unfractionated data the fraction identifier is 1 for all samples.
        - The **Label** identifier. 1 for label-free, 1 and 2 for SILAC light/heavy, e.g. 1-10 for TMT10Plex
        - The **Spectra_Filepath** (e.g., path = "/data/SILAC_file.mzML")
        - **MSstats_Condition** the condition identifier as used by MSstats
        - **MSstats_BioReplicate** an identifier to indicate replication. (MSstats requires that there are no duplicate entries. E.g., if MSstats_Condition, Fraction_Group group and Fraction number are the same - as in the case of biological or technical replication, one uses the MSstats_BioReplicate to make entries non-unique)
        
        | Fraction_Group| Fraction      | Spectra_Filepath  | Label | MSstats_Condition      | MSstats_BioReplicate  |
        | ------------- |-------------|-----|---| ------------- |-----------|
        | 1 | 1 | A0218_1A_R_FR01.raw | 1 | 1 | 1 | 1 |
        | 1 | 2 | A0218_1A_R_FR02.raw | 1 | 1 | 1 | 1 |
        | . | . | ... | . | . | . | . |
        | 1 | 15 | A0218_2A_FR15.raw | 1 | 1 | 1 | 1 |
        | 2 | 1 | A0218_2A_FR01.raw | 1 | 2 | 2 | 1 |
        | . | . | ... | . | . | . | . |
        | . | . | ... | . | . | . | . |
        | 10 | 15 | A0218_10A_FR15.raw | 1 | 10 | 10 | 1 |
        
        For details, please see the MSstats documentation
        
Keywords: sdrf python multiomics proteomics
Platform: any
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.5
Description-Content-Type: text/markdown
