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- format_functions.convert_oligos(path='.', adapter_type='^', barcode_length=7)
Converts the Mothur “oligo” format to .fasta files containing the barcodes, for use with Cutadapt.
The function reads the barcode pairs present in the oligo files with the .file extension used in the Mothur software. Those barcode pairs are reformatted in two different .fasta files that can be used as inputs to operate the demultiplexing of NGS reads with Cutadapt. It outputs .fasta files in the directory where the oligo files are present.
- Parameters:
- pathstring
The path where the oligo files are stored, this directory will also be the output directory. Default path = ‘.’
- adapter_typestring
Specify the type of adapter for Cutadapt, according to the ones listed here. Default adapter_type = ‘’ that corresponds to an anchored 5’ adapter.
- barcode_lengthinteger
Specify the length of the barcodes in the oligo files. Default barcode_length = 7
- format_functions.mothur_to_cutadapt(string_list, adapter_type='^', barcode_length=7)
Used from the “Convert Oligo” function to actually operate the conversion. It reads line by line the previous file and reformats every line with a new string.
- Parameters:
- string_list
This parameter is created during the call of ‘Convert_oligos’.
- adapter_typestring
Specify the type of adapter for Cutadapt, according to the ones listed here. Default adapter_type = ‘’ that corresponds to an anchored 5’ adapter.
- barcode_lengthinteger
Specify the length of the barcodes in the oligo files. Default barcode_length = 7
- manifest_create.read_folder_content(raw_files_path='.')
It reads the content of a folder to retrieve a list of .fastq.gz files.
- Parameters:
- raw_files_path
The path where the raw .fastq.gz files are stored.
- manifest_create.write_manifest(raw_files_path='.')
It writes a manifest file to use as import with Qiime2 from a folder of ´.fastq.gz’files. The content of the folder is read and all the ´.gz´ files included in the manifest. The manifest file can then be used normally with Qiime2 to start the analysis pipeline.
- Parameters:
- raw_files_path
The path where the raw .fastq.gz files are stored.