#!/usr/bin/env python
# -*- coding: utf-8 -*-
import argparse
import sys
import os
## own functions
# scriptdir=os.path.abspath(os.path.join(__file__, "../../sincei"))
# sys.path.append(scriptdir)
from sincei._version import __version__
[docs]def parse_arguments(args=None):
parser = argparse.ArgumentParser(
formatter_class=argparse.RawDescriptionHelpFormatter,
description="""
sincei is a suite of command-line tools developed for a user-friendly analysis of single-cell sequencing data.
Version: {}
Each tool begins with the prefix sc<tool_name>, such as:
$ scBulkCoverage -b file1.bam -g groupinfo.txt -o coverage
[ Tools for a typical single-cell analysis workflow ] (WIP: work in progress/not available yet)
scFilterBarcodes Identify and filter cell barcodes from BAM file (for droplet-based single-cell seq)
scFilterStats Produce per-cell statistics after filtering reads by user-defined criteria.
scCountReads Counts reads for each barcode on genomic bins or user-defined features.
scCountQC Perform quality control and filter the output of scCountReads.
scCombineCounts [WIP] Concatenate/merge the counts from different samples/batches or modalities
scClusterCells Perform dimensionality reduction and clustering on the output of scCountReads.
scBulkCoverage Get pseudo-bulk coverage per group using a user-supplied cell->group mapping (output of scClusterCells).
scBAMops Modify a BAM file to group cells (using cell barcodes), or filter/shift mapped reads.
scFindMarkers [WIP] Find marker genes per group, given the output of scCountReads and a user-defined group.
scFeaturePlot [WIP] Plot the counts for a given feature on a UMAP or on a (IGV-style) genomic-track.
""".format(
__version__
),
)
return parser
[docs]def process_args(args=None):
args = parse_arguments().parse_args(args)
return args
[docs]def main(args=None):
if args is None and len(sys.argv) == 1:
args = ["--help"]
process_args(args)