barcode.py

import logging
import os

from pbsmrtpipe.resource_types import (MovieFofn, BarcodeFofn, BarcodeFasta,
                                       MappingCmph5, BarcodeFastq)
from pbsmrtpipe.model import (TaskTypes, TaskBase,
                              TaskOption, TaskChoiceOption,
                              P_Module, TempDir)

log = logging.getLogger(__name__)


class LabelZmwsTask(TaskBase):
    INPUTS = (MovieFofn, BarcodeFasta)
    OUTPUTS = BarcodeFofn
    NPROC = 1
    TASK_TYPE = TaskTypes.DistributableTask

    score_mode = TaskOption('barcode_mode', 'symmetric', str)
    adapterSidePad = TaskOption('adapterSidePad', 4, int)
    insertSidePad = TaskOption('insertSidePad', 4, int)
    fastqType = TaskChoiceOption('readType', 'subreads', str, ('subreads', 'CCS'))

    def to_cmd(self):
        mfofn, bfasta = self.inputs[:2]
        bfofn = self.outputs[0]
        output_dir = os.path.dirname(bfofn.path)

        d = dict(n=self.nproc, b=bfofn.path, s=self.score_mode, d=output_dir,
                 a=self.adapterSidePad, i=self.insertSidePad, fa=bfasta.path,
                 m=mfofn.path)
        cmd = "pbbarcode.py -vv labelZMWs --nProcs {n} --outFofn {b} --outDir {d} --scoreMode {s} --adapterSidePad {a} --insertSidePad {i} {fa} {m}"
        return cmd.format(**d)


class CopyBarcodesToCmpH5Task(TaskBase):
    INPUTS = (BarcodeFofn, MappingCmph5)
    OUTPUTS = MappingCmph5WithBarcode
    NPROC = 1
    TASK_TYPE = TaskTypes.LocallyDistributableTask

    def to_cmd(self):
        d = dict(f=self.inputs[0].path, a=self.inputs[1].path)
        return "pbbarcode.py labelAlignments {f} {a}".format(**d)


class EmitFastqTask(TaskBase):
    INPUTS = (MovieFofn, BarcodeFofn)
    OUTPUTS = BarcodeFastq
    NPROC = 1
    TASK_TYPE = TaskTypes.LocallyDistributableTask

    TMP_DIR = TempDir('barcode_fqs_tmp')

    def to_cmd(self):
        mfofn, bfofn = self.inputs[:2]
        fastq = self.outputs[0]

        output_dir = fastq.path.replace(".")
        d = dict(m=mfofn.path, b=bfofn.path, fq=fastq.path)
        cmds = []
        cmds.append("mkdir {s}".format(s=output_dir)
        cmds.append("pbbarcode.py emitFastqs {s} --outDir {o} {b} {q}".format(o=output_dir, b=bfofn.path, q=fastq.path)
        cmds.append("pushd %s && tar czf ../%s *.fastq && popd")
        return cmds


class P_Barcode(P_Module):
    TASKS = (LabelZmwsTask, CopyBarcodesToCmpH5Task, EmitFastqTask)