Source code for demux.Demux_Barcode_Command

from classes.ChewbaccaCommand import ChewbaccaCommand
from Demux_Name_Program_Chewbacca import Demux_Program_Chewbacca
from Demux_Barcode_Program_Fastx import Demux_Program_Fastx


class Demux_Barcode_Command(ChewbaccaCommand):
    """Given a set of files, each file is assigned a file offeset (value between sampleId and sequenceId).  Each file is then split into separate child files where
        each file holds only sequences belonging to a single sample.  These child files are named using the sample name
        for the sequences it lists, and the file offset of the file it came from.  Demuxing is based on the nucleotide
        barcode prefixing each sequence.

    **Inputs**:
        * One or more fasta/fastq files to demux.
        * A single .barcodes file: A :ref:`.barcodes`.

    **Outputs**:
        * <sample_name>_<file_id#>_ demux.<ext> file(s) - <fasta/fastq> files, containing all the sequences from file \
            <file_id#>, which had a barcode corresponding to sample <sample_name>.
        * unmatched_<file_id#>_ demux.<ext> file(s) - <fasta/fastq> files, containing sequences from file \
            <file_id#>, whose barcode did not match any of those listed in the .barcodes file.

    **Notes**:
        * The assignment of the offset to file should be treated as an arbitrary process and should not used for record \
            keeping.
        * Each input file will generate its own unmatched_* file (if applicable).

    **Example**:

    ::

        data/
            Data1.fasta:
                @Seq4
                AGACGCAAAAAA
                @Seq5
                AGTGTAAAAAAT


            Data2.fasta:
                @Seq6
                AGACGCAAAAAC
                @Seq7
                AGTGTAAAAAAG
                @Seq8
                CGTGTAAAAAAG
        ./
            Data.barcodes:
                SampleA        AGACGC
                SampleB        AGTGTA

    ``$ python chewbacca.py demux_samples -i data/ -b Data.barcodes -o rslt``

    Here, we see that Data1.fasta was assigned '0' as an offset, while Data2.fasta was assigned '1' as an offset.  Because \
    both files had sequences from SampleA, the sequences from Data1.fasta  were written to SampleA_0_demux.fastq, \
    and those sequences from Data2.fasta were written to SampleA_1_demux.fastq.  The same is true for SampleB.

    ::

        rslt/
            SampleA_0_demux.fastq:
                @Seq4
                AGACGCAAAAAA

            SampleB_0_demux.fastq:
                @Seq5
                AGTGTAAAAAAT

            SampleA_1_demux.fastq:
                @Seq6
                AGACGCAAAAAC

            SampleB_1_demux.fastq:
                @Seq7
                AGTGTAAAAAAG

        rslt_aux/
            unmatched_0_demux.fastq:
                @Seq8
                CGTGTAAAAAAG
    """
    supported_programs = [Demux_Program_Fastx]
    default_program = Demux_Program_Fastx
    command_name = "Demux"