msphy-SCNAClonal

Introduction

msphy-SCNAClonal is a SCNA's subclonal reconstruction pipeline based on multi-stage tree structure learning, which could infer the tree structure of tumor's evolution process from various kinds of sequencing data from a tumor's multiple samples, such as multiple samples' NGS data obtained at different time points, or, multiple NGS/Target sequencing/Single cell sequencing or their combination data.

Structure of msphy-SCNAClonal

Bias correction model

Segment merging model

SCNA's probabilistic model

Multi-stage tree structure learning model

Requirements

seaborn
pymc 
ete2
pydp
python2-backports.functools_lru_cache
gwpy
pysam
scipy
numpy
matplotlib

Usage

usage: run.py preprocess [-h] [--nBamName NBAMNAME]
                        [--tBamNameL TBAMNAMEL [TBAMNAMEL ...]]
                        [--bedNameL BEDNAMEL [BEDNAMEL ...]]
                        [--refFaName REFFANAME] [--pathPreFix PATHPREFIX]
                        [--subcloneNumL SUBCLONENUML [SUBCLONENUML ...]]
                        [--coverageL COVERAGEL [COVERAGEL ...]]
                        [--maxCopyNumber MAXCOPYNUMBER]
                        [--baselineThredLOH BASELINETHREDLOH]
                        [--baselineThredAPM BASELINETHREDAPM]
                        [--minDepth MINDEPTH] [--minBqual MINBQUAL]
                        [--minMqual MINMQUAL] [--processNum PROCESSNUM]
                        [--bedCorrectedPath BEDCORRECTEDPATH]
                        [--pklPath PKLPATH] [--answerFilePath ANSWERFILEPATH]
                        [--gcCorrectionMethod GCCORRECTIONMETHOD]
                        [--readFromBed READFROMBED] [--mergeSeg MERGESEG]
                        [--pklFlag PKLFLAG] [--isFixedC ISFIXEDC]

optional arguments:
  -h, --help            show this help message and exit
  --nBamName NBAMNAME   BAM file for normal sample.
  --tBamNameL TBAMNAMEL [TBAMNAMEL ...]
                        BAM files for tumor samples sorted in chronological
                        order.
  --bedNameL BEDNAMEL [BEDNAMEL ...]
                        BED files for segments of each sample in chronological
                        order.
  --refFaName REFFANAME
                        FASTA file for reference genome.
  --pathPreFix PATHPREFIX
                        Base name of the preprocessed input file to be
                        created.
  --subcloneNumL SUBCLONENUML [SUBCLONENUML ...]
                        Set the subclone numbers
  --coverageL COVERAGEL [COVERAGEL ...]
                        Set the coverage numbers
  --maxCopyNumber MAXCOPYNUMBER
                        Set the maximum copy number
  --baselineThredLOH BASELINETHREDLOH
                        baseline Thred of LOH
  --baselineThredAPM BASELINETHREDAPM
                        baseline Thred of APM
  --minDepth MINDEPTH   Minimum reads depth required for both normal and tumor
                        samples. Default is 20.
  --minBqual MINBQUAL   Minimum base quality required. Default is 10.
  --minMqual MINMQUAL   Minimum mapping quality required. Default is 10.
  --processNum PROCESSNUM
                        Number of processes to launch for preprocessing.
                        Default is 1.
  --bedCorrectedPath BEDCORRECTEDPATH
                        The name of corrected BICseq result file
  --pklPath PKLPATH     Load the pkl path
  --answerFilePath ANSWERFILEPATH
                        Load the answer file path
  --gcCorrectionMethod GCCORRECTIONMETHOD
                        The gc correction method, one of auto and visual
  --readFromBed READFROMBED
                        get read from Bed (True), from bam file if set it
                        False
  --mergeSeg MERGESEG   to merge segment or not to
  --pklFlag PKLFLAG     The pkl flag
  --isFixedC ISFIXEDC   Fix Copy number



usage: run.py model [-h] [-b WRITEBACKUPSEVERY] [-S WRITESTATEEVERY]
                    [-k TOPKTREES] [-f CLONALFREQS] [-B BURNINSAMPLENUM]
                    [-s MCMCSAMPLENUM] [-i MHITERATIONS] [-r RANDOMSEED]
                    [-t TMPDIR] [-p PARAMSFILE]
                    [--inputDataFile INPUTDATAFILE]
                    [--inputDataTextFile INPUTDATATEXTFILE]
                    [--isMerged ISMERGED] [--isCrossing ISCROSSING]
                    [--crossingFile CROSSINGFILE]
                    [--isSingleCell ISSINGLECELL]
                    [--singleCellFile SINGLECELLFILE]
                    [--maxCopyNumber MAXCOPYNUMBER] [--noTag NOTAG]
                    [--isParameterized ISPARAMETERIZED]

optional arguments:
  -h, --help            show this help message and exit
  -b WRITEBACKUPSEVERY, --write-backups-every WRITEBACKUPSEVERY
                        Number of iterations to go between writing backups of
                        program state
  -S WRITESTATEEVERY, --write-state-every WRITESTATEEVERY
                        Number of iterations between writing program state to
                        disk. Higher values reduce IO burden at the cost of
                        losing progress made if program is interrupted.
  -k TOPKTREES, --top-k-trees TOPKTREES
                        Output file to save top-k trees in text format
  -f CLONALFREQS, --clonal-freqs CLONALFREQS
                        Output file to save clonal frequencies
  -B BURNINSAMPLENUM, --burnin-samples BURNINSAMPLENUM
                        Number of burnin samples
  -s MCMCSAMPLENUM, --mcmc-samples MCMCSAMPLENUM
                        Number of MCMC samples
  -i MHITERATIONS, --mh-iterations MHITERATIONS
                        Number of Metropolis-Hastings iterations
  -r RANDOMSEED, --random-seed RANDOMSEED
                        Random seed for initializing MCMC sampler
  -t TMPDIR, --tmp-dir TMPDIR
                        Path to directory for temporary files
  -p PARAMSFILE, --params PARAMSFILE
                        JSON file listing run parameters, generated by the
                        parser
  --inputDataFile INPUTDATAFILE
                        File listing data(SCNA data, either semgent or
                        stripe). For proper format, see README.md.
  --inputDataTextFile INPUTDATATEXTFILE
                        Text file listing data(SCNA stripes). For proper
                        format, see README.md.
  --isMerged ISMERGED   is merged data file
  --isCrossing ISCROSSING
                        using crossing file
  --crossingFile CROSSINGFILE
                        The crossing file.
  --isSingleCell ISSINGLECELL
                        using single cell file
  --singleCellFile SINGLECELLFILE
                        The single cell file.
  --maxCopyNumber MAXCOPYNUMBER
                        Max copy number
  --noTag NOTAG         to remove all tag or not
  --isParameterized ISPARAMETERIZED
                        to make only one subpopulation in each time tag

usage: run.py postprocess [-h] [--treeFile TREEFILE]
                          [--SCNAPoolFile SCNAPOOLFILE]
                          [--answerFilePath ANSWERFILEPATH]
                          [--outputFolder OUTPUTFOLDER]

optional arguments:
  -h, --help            show this help message and exit
  --treeFile TREEFILE   File containing sampled trees
  --SCNAPoolFile SCNAPOOLFILE
                        File containing SCNA pool
  --answerFilePath ANSWERFILEPATH
                        Answer file path
  --outputFolder OUTPUTFOLDER
                        Output folder