Merge pull request #1360 from deeptools/mbs

Mbs

Cargo.toml

@@ -17,4 +17,6 @@ bigtools = "0.5.3"
 tokio = "*"
 flate2 = "*"
 tempfile = "*"
-ndarray = "0.16.1"
+ndarray = "0.16.1"
+npyz = "*"
+zip = "*"

pydeeptools/deeptools/multiBamSummary2.py

@@ -0,0 +1,340 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import os
+import sys
+import argparse
+import numpy as np
+
+import deeptools.countReadsPerBin as countR
+from deeptools import parserCommon
+from deeptools.utilities import smartLabels
+from importlib.metadata import version
+old_settings = np.seterr(all='ignore')
+
+from deeptools.hp import r_mbams
+
+def parse_arguments(args=None):
+    parser = \
+        argparse.ArgumentParser(
+            formatter_class=argparse.RawDescriptionHelpFormatter,
+            description="""
+
+``multiBamSummary`` computes the read coverages for genomic regions for typically two or more BAM files.
+The analysis can be performed for the entire genome by running the program in 'bins' mode.
+If you want to count the read coverage for specific regions only, use the ``BED-file`` mode instead.
+The standard output of ``multiBamSummary`` is a compressed numpy array (``.npz``).
+It can be directly used to calculate and visualize pairwise correlation values between the read coverages using the tool 'plotCorrelation'.
+Similarly, ``plotPCA`` can be used for principal component analysis of the read coverages using the .npz file.
+Note that using a single bigWig file is only recommended if you want to produce a bedGraph file (i.e., with the ``--outRawCounts`` option; the default output file cannot be used by ANY deepTools program if only a single file was supplied!).
+
+A detailed sub-commands help is available by typing:
+
+  multiBamSummary bins -h
+
+  multiBamSummary BED-file -h
+
+
+""",
+            epilog='example usages:\n'
+                   'multiBamSummary bins --bamfiles file1.bam file2.bam -o results.npz \n\n'
+                   'multiBamSummary BED-file --BED selection.bed --bamfiles file1.bam file2.bam \n'
+                   '-o results.npz'
+                   ' \n\n',
+            conflict_handler='resolve')
+
+    parser.add_argument('--version', action='version',
+                        version='%(prog)s {}'.format(version('deeptools')))
+    subparsers = parser.add_subparsers(
+        title="commands",
+        dest='command',
+        description='subcommands',
+        help='subcommands',
+        metavar='')
+
+    parent_parser = parserCommon.getParentArgParse(binSize=False)
+    read_options_parser = parserCommon.read_options()
+
+    # bins mode options
+    subparsers.add_parser(
+        'bins',
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        parents=[bamcorrelate_args(case='bins'),
+                 parent_parser, read_options_parser,
+                 parserCommon.gtf_options(suppress=True)
+                 ],
+        help="The coverage calculation is done for consecutive bins of equal "
+             "size (10 kilobases by default). This mode is useful to assess the "
+             "genome-wide similarity of BAM files. The bin size and "
+             "distance between bins can be adjusted.",
+        add_help=False,
+        usage='%(prog)s '
+              '--bamfiles file1.bam file2.bam '
+              '-o results.npz \n'
+              'help: multiBamSummary bins -h / multiBamSummary bins --help\n')
+
+    # BED file arguments
+    subparsers.add_parser(
+        'BED-file',
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        parents=[bamcorrelate_args(case='BED-file'),
+                 parent_parser, read_options_parser,
+                 parserCommon.gtf_options()
+                 ],
+        help="The user provides a BED file that contains all regions "
+             "that should be considered for the coverage analysis. A "
+             "common use is to compare ChIP-seq coverages between two "
+             "different samples for a set of peak regions.",
+        usage='%(prog)s --BED selection.bed --bamfiles file1.bam file2.bam -o results.npz\n'
+        'help: multiBamSummary BED-file -h / multiBamSummary bins --help\n',
+        add_help=False)
+
+    return parser
+
+
+def bamcorrelate_args(case='bins'):
+    parser = argparse.ArgumentParser(add_help=False)
+    required = parser.add_argument_group('Required arguments')
+
+    # define the arguments
+    required.add_argument('--bamfiles', '-b',
+                          metavar='FILE1 FILE2',
+                          help='List of indexed bam files separated by spaces.',
+                          nargs='+',
+                          required=True)
+
+    required.add_argument('--outFileName', '-out', '-o',
+                          help='File name to save the coverage matrix. This matrix '
+                               'can be subsequently plotted using plotCorrelation or '
+                               'or plotPCA.',
+                          type=parserCommon.writableFile)
+
+    optional = parser.add_argument_group('Optional arguments')
+
+    optional.add_argument("--help", "-h", action="help",
+                          help="show this help message and exit")
+    optional.add_argument('--labels', '-l',
+                          metavar='sample1 sample2',
+                          help='User defined labels instead of default labels from '
+                               'file names. '
+                               'Multiple labels have to be separated by a space, e.g. '
+                               '--labels sample1 sample2 sample3',
+                          nargs='+')
+    optional.add_argument('--smartLabels',
+                          action='store_true',
+                          help='Instead of manually specifying labels for the input '
+                          'BAM files, this causes deepTools to use the file name '
+                          'after removing the path and extension.')
+
+    optional.add_argument('--genomeChunkSize',
+                          type=int,
+                          default=None,
+                          help='Manually specify the size of the genome provided to each processor. '
+                          'The default value of None specifies that this is determined by read '
+                          'density of the BAM file.')
+
+    if case == 'bins':
+        optional.add_argument('--binSize', '-bs',
+                              metavar='INT',
+                              help='Length in bases of the window used '
+                                   'to sample the genome. (Default: %(default)s)',
+                              default=10000,
+                              type=int)
+
+        optional.add_argument('--distanceBetweenBins', '-n',
+                              metavar='INT',
+                              help='By default, multiBamSummary considers consecutive '
+                              'bins of the specified --binSize. However, to '
+                              'reduce the computation time, a larger distance '
+                              'between bins can by given. Larger distances '
+                              'result in fewer bins considered. (Default: %(default)s)',
+                              default=0,
+                              type=int)
+
+        required.add_argument('--BED',
+                              help=argparse.SUPPRESS,
+                              default=None)
+    else:
+        optional.add_argument('--binSize', '-bs',
+                              help=argparse.SUPPRESS,
+                              default=10000,
+                              type=int)
+
+        optional.add_argument('--distanceBetweenBins', '-n',
+                              help=argparse.SUPPRESS,
+                              metavar='INT',
+                              default=0,
+                              type=int)
+
+        required.add_argument('--BED',
+                              help='Limits the coverage analysis to '
+                              'the regions specified in these files.',
+                              metavar='FILE1.bed FILE2.bed',
+                              nargs='+',
+                              required=True)
+
+    group = parser.add_argument_group('Output optional options')
+
+    group.add_argument('--outRawCounts',
+                       help='Save the counts per region to a tab-delimited file.',
+                       type=parserCommon.writableFile,
+                       metavar='FILE')
+
+    group.add_argument('--scalingFactors',
+                       help='Compute scaling factors (in the DESeq2 manner) '
+                       'compatible for use with bamCoverage and write them to a '
+                       'file. The file has tab-separated columns "sample" and '
+                       '"scalingFactor".',
+                       type=parserCommon.writableFile,
+                       metavar='FILE')
+
+    return parser
+
+
+def process_args(args=None):
+    args = parse_arguments().parse_args(args)
+
+    if len(sys.argv) == 1:
+        parse_arguments().print_help()
+        sys.exit()
+
+    if args.labels and len(args.bamfiles) != len(args.labels):
+        print("The number of labels does not match the number of bam files.")
+        exit(0)
+    if not args.labels:
+        if args.smartLabels:
+            args.labels = smartLabels(args.bamfiles)
+        else:
+            args.labels = [os.path.basename(x) for x in args.bamfiles]
+
+    if not args.BED:
+        args.BED = "None"
+    if not args.region:
+        args.region = []
+    if not args.blackListFileName:
+        args.blackListFileName = "None"
+    if not args.outRawCounts:
+        args.outRawCounts = "None"
+    if not args.scalingFactors:
+        args.scalingFactors = "None"
+    # defaults for the filtering options
+    if not args.samFlagInclude:
+        args.samFlagInclude = 0
+    if not args.samFlagExclude:
+        args.samFlagExclude = 0
+    if not args.minFragmentLength:
+        args.minFragmentLength = 0
+    if not args.maxFragmentLength:
+        args.maxFragmentLength = 0
+    if not args.minMappingQuality:
+        args.minMappingQuality = 0
+    return args
+
+
+def main(args=None):
+    """
+    1. get read counts at different positions either
+    all of same length or from genomic regions from the BED file
+
+    2. save data for further plotting
+
+    """
+    args = process_args(args)
+    print(f"args = {args}")
+    print("running r_mbams")
+    r_mbams(
+        args.command,
+        args.bamfiles,
+        args.outFileName,
+        args.outRawCounts,
+        args.scalingFactors,
+        args.labels,
+        args.binSize,
+        args.distanceBetweenBins,
+        args.numberOfProcessors,
+        args.BED,
+        args.region,
+        args.blackListFileName,
+        args.verbose,
+        args.extendReads,
+        args.centerReads,
+        args.samFlagInclude,
+        args.samFlagExclude,
+        args.minFragmentLength,
+        args.maxFragmentLength,
+        args.minMappingQuality,
+        args.keepExons,
+        args.transcriptID,
+        args.exonID,
+        args.transcript_id_designator
+    )
+
+    # if 'BED' in args:
+    #     bed_regions = args.BED
+    # else:
+    #     bed_regions = None
+
+    # if len(args.bamfiles) == 1 and not (args.outRawCounts or args.scalingFactors):
+    #     sys.stderr.write("You've input a single BAM file and not specified "
+    #                      "--outRawCounts or --scalingFactors. The resulting output will NOT be "
+    #                      "useful with any deepTools program!\n")
+
+    # stepsize = args.binSize + args.distanceBetweenBins
+    # c = countR.CountReadsPerBin(
+    #     args.bamfiles,
+    #     args.binSize,
+    #     numberOfSamples=None,
+    #     genomeChunkSize=args.genomeChunkSize,
+    #     numberOfProcessors=args.numberOfProcessors,
+    #     verbose=args.verbose,
+    #     region=args.region,
+    #     bedFile=bed_regions,
+    #     blackListFileName=args.blackListFileName,
+    #     extendReads=args.extendReads,
+    #     minMappingQuality=args.minMappingQuality,
+    #     ignoreDuplicates=args.ignoreDuplicates,
+    #     center_read=args.centerReads,
+    #     samFlag_include=args.samFlagInclude,
+    #     samFlag_exclude=args.samFlagExclude,
+    #     minFragmentLength=args.minFragmentLength,
+    #     maxFragmentLength=args.maxFragmentLength,
+    #     stepSize=stepsize,
+    #     zerosToNans=False,
+    #     out_file_for_raw_data=args.outRawCounts)
+
+    # num_reads_per_bin = c.run(allArgs=args)
+
+    # sys.stderr.write("Number of bins "
+    #                  "found: {}\n".format(num_reads_per_bin.shape[0]))
+
+    # if num_reads_per_bin.shape[0] < 2:
+    #     exit("ERROR: too few non zero bins found.\n"
+    #          "If using --region please check that this "
+    #          "region is covered by reads.\n")
+
+    # # numpy will append .npz to the file name if we don't do this...
+    # if args.outFileName:
+    #     f = open(args.outFileName, "wb")
+    #     np.savez_compressed(f,
+    #                         matrix=num_reads_per_bin,
+    #                         labels=args.labels)
+    #     f.close()
+
+    # if args.scalingFactors:
+    #     f = open(args.scalingFactors, 'w')
+    #     f.write("sample\tscalingFactor\n")
+    #     scalingFactors = countR.estimateSizeFactors(num_reads_per_bin)
+    #     for sample, scalingFactor in zip(args.labels, scalingFactors):
+    #         f.write("{}\t{:6.4f}\n".format(sample, scalingFactor))
+    #     f.close()
+
+    # if args.outRawCounts:
+    #     # append to the generated file the
+    #     # labels
+    #     header = "#'chr'\t'start'\t'end'\t"
+    #     header += "'" + "'\t'".join(args.labels) + "'\n"
+    #     f = open(args.outRawCounts, 'r+')
+    #     content = f.read()
+    #     f.seek(0, 0)
+    #     f.write(header + content)
+    #     f.close()

pyproject.toml

@@ -88,3 +88,4 @@ bamCoverage2 = "deeptools.bamCoverage2:main"
 bamCompare2 = "deeptools.bamCompare2:main"
 computeMatrix2 = "deeptools.computeMatrix2:main"
 alignmentSieve2 = "deeptools.alignmentSieve2:main"
+multiBamSummary2 = "deeptools.multiBamSummary2:main"

src/alignmentsieve.rs

@@ -27,6 +27,9 @@ pub fn r_alignmentsieve(
     _blacklist: &str, // blacklist file name.
     min_fragment_length: u32, // minimum fragment length.
     max_fragment_length: u32, // maximum fragment length.
+    extend_reads: u32,
+    center_reads: bool,
+
 ) -> PyResult<()> {
     // Input bam file
     let mut bam = Reader::from_path(bamifile).unwrap();

src/bamcompare.rs

@@ -143,12 +143,12 @@ pub fn r_bamcompare(
     Ok(())
 }
 
-struct ParsedBamFile<'a> {
-    bamfile: &'a str,
-    ispe: bool,
-    bg: Vec<TempPath>,
-    mapped: u32,
-    unmapped: u32,
-    readlen: f32,
-    fraglen: f32
+pub struct ParsedBamFile<'a> {
+    pub bamfile: &'a str,
+    pub ispe: bool,
+    pub bg: Vec<TempPath>,
+    pub mapped: u32,
+    pub unmapped: u32,
+    pub readlen: f32,
+    pub fraglen: f32
 }

src/calc.rs

@@ -155,4 +155,4 @@ pub fn calc_ratio(
             return (num / den).log2();
         }
     }
-}
+}