parsing_scripts.sample package¶
Submodules¶
parsing_scripts.sample.cel_sample module¶
-
parsing_scripts.sample.cel_sample.main()¶ Parse a CEL (Affymetrix) file and extract SAMPLE raw data
The probe original id is given by X.Y
- PARAMETERS:
- None
parsing_scripts.sample.gpr_sample module¶
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parsing_scripts.sample.gpr_sample.main()¶ Parse a GPR file and extract SAMPLE raw data
A GPR file is a TAB-delimited file with headers and complete sample raw data information
- PARAMETERS:
param1 (string): The column header of the original probe id to parse out. If it is composed by more than one field, put all of them separated with a |. For example X|Y (actual probe ids will be concatenated with dots . in that case)
param2 (string): The column header of the data value you want to parse out
param3 (int): Number of lines to skip
param4 (int): The sample channel (optional)
parsing_scripts.sample.pair_sample module¶
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parsing_scripts.sample.pair_sample.main()¶ Parse a PAIR file and extract SAMPLE raw data
A PAIR file is a TAB-delimited file with headers and complete sample raw data information The probe id is given by X.Y to ensure uniqueness and the raw data value is taken from the PM column
- PARAMETERS:
- param1 (int): Number of lines to skip
parsing_scripts.sample.soft_sample module¶
-
parsing_scripts.sample.soft_sample.main()¶ Parse a SOFT file and extract SAMPLE description and optionally raw data
- PARAMETERS:
- param1 (string): The raw data value field, if empty it will be assigned automatically using the sample_column_identifier function
parsing_scripts.sample.trim_quantify module¶
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parsing_scripts.sample.trim_quantify.main()¶ Trim a FASTQ file using Trimmomatic and quantify using KALLISTO
The result counts will be added to the SAMPLE OBJECT
- PARAMETERS:
- param1 (bool): True if this FASTQ file has a PAIRED file (forward or reverse), default False