Metadata-Version: 1.0
Name: readquant
Version: 1.2.0
Summary: Convenience package for parsing RNA-seq quantification results
Home-page: UNKNOWN
Author: Valentine Svensson
Author-email: valentine@nxn.se
License: MIT
Description: ## readquant
        
        This package contains helper functions for parsing both expression values
        and technical features from common RNA-seq quantification tools.
        
        The goal is to simplify going from a collection of quantification results to
        expression table, as well as sample meta data.
        
        A minimal example could look something like this:
        
            In [1]: from readquant import read_quants, read_qcs
        
            In [2]: tpm = read_quants('salmon/*E4_salmon_out', version='0.4.0')
        
            In [3]: tpm.head()
            Out[3]:
                    salmon/1771-026-195-E4_salmon_out  \
            Name
            ERCC-00158                                0.0
            ERCC-00154                                0.0
            ERCC-00150                                0.0
            ERCC-00143                                0.0
            ERCC-00142                                0.0
        
                    salmon/1771-026-190-E4_salmon_out  \
            Name
            ERCC-00158                                0.0
            ERCC-00154                                0.0
            ERCC-00150                                0.0
            ERCC-00143                                0.0
            ERCC-00142                                0.0
        
                    salmon/1771-026-196-E4_salmon_out  \
            Name
            ERCC-00158                              0.000
            ERCC-00154                            906.236
            ERCC-00150                              0.000
            ERCC-00143                              0.000
            ERCC-00142                              0.000
        
                    salmon/1771-026-198-E4_salmon_out  \
            Name
            ERCC-00158                                0.0
            ERCC-00154                                0.0
            ERCC-00150                                0.0
            ERCC-00143                                0.0
            ERCC-00142                                0.0
        
                    salmon/1771-023-118-E4_salmon_out  \
            Name
            ERCC-00158                            0.00000
            ERCC-00154                            9.35988
            ERCC-00150                            0.00000
            ERCC-00143                          724.44800
            ERCC-00142                            0.00000
        
                    salmon/1771-026-193-E4_salmon_out
            Name
            ERCC-00158                                0.0
            ERCC-00154                                0.0
            ERCC-00150                                0.0
            ERCC-00143                                0.0
            ERCC-00142                                0.0
        
            In [4]: sample_info = read_qcs('salmon/*_salmon_out', version='0.4.0', flen_lim=(10, 100))
        
            In [5]: sample_info.head()
            Out[5]:
                                           percent_mapped  num_processed  \
            salmon/1771-026-197-G4_salmon_out         71.8270      2665988.0
            salmon/1771-026-198-D2_salmon_out         67.7853      3841894.0
            salmon/1771-026-195-H7_salmon_out         73.4492      3875822.0
            salmon/1771-026-194-E9_salmon_out         47.5425       979446.0
            salmon/1771-026-195-E4_salmon_out         56.3955      5051277.0
        
                                           global_fl_mode  robust_fl_mode
            salmon/1771-026-197-G4_salmon_out           103.0           103.0
            salmon/1771-026-198-D2_salmon_out           122.0           122.0
            salmon/1771-026-195-H7_salmon_out           110.0           110.0
            salmon/1771-026-194-E9_salmon_out           111.0           111.0
            salmon/1771-026-195-E4_salmon_out           111.0           111.0
        
Platform: UNKNOWN
