Initial commit

FDSTools v0.0.1 with Stuttermark v1.3.
Other tools will come later.

.gitignore

+*.pyc
+dist/*
+*.egg-info/*

README.rst

+Forensic DNA Sequencing Tools
+=============================
+
+Tools for filtering and interpretation of Next Generation Sequencing data of
+forensic DNA samples. To obtain a list of included tools with a brief
+description of each tool, run:
+
+    ``fdstools -h``
+
+For a complete description of the command line arguments of a specific tool,
+run:
+
+    ``fdstools -h TOOLNAME``
+
+
+Installation
+------------
+
+The recommended way to install FDSTools is by using the ``pip`` package
+installer. If you have ``pip`` installed, you can easily install FDSTools by
+typing:
+
+    ``pip install fdstools``
+
+Alternatively, FDSTools can be installed by running:
+    ``python setup.py install``
+
+
+FDSTools Changelog
+------------------
+v0.0.1
+    - Initial version
+    - Includes Stuttermark v1.3
+
+
+Stuttermark
+-----------
+
+Mark potential stutter products by assuming a fixed maximum percentage of
+stutter product vs the parent allele.
+
+Input
+    Tab-seperated file with at least these three columns:
+        - 'name': the name of the marker
+        - 'allele': the allele name, as a TSSV-style sequence, e.g.,
+          "``AGAT(12)TGAT(4)``"
+        - 'total': the total number of reads
+
+    This format is compatible with 'knownalleles.csv' files created by TSSV.
+
+Output
+    The same file, with an additional column (named 'annotation' by default).
+    The new column contains '``STUTTER``' for possible stutter products, or
+    '``ALLELE``' otherwise. Lines that were not evaluated are annotated as
+    '``UNKNOWN``'. The ``STUTTER`` annotation contains additional information.
+    For example,
+
+        ``STUTTER:146.6x1(2-1):10.4x2(2-1x9-1)``
+
+    This is a stutter product for which at most 146.6 reads have come from the
+    first sequence in the output file ("``146.6x1``") and at most 10.4 reads
+    have come from the second sequence in the output file ("``10.4x2``"). This
+    sequence differs from the first sequence in the output file by a loss of
+    one repeat of the second repeat block ("``2-1``") and it differs from the
+    second sequence by the loss of one repeat in the second block *and* one
+    repeat in the ninth block ("``2-1x9-1``").
+
+
+Changelog
+~~~~~~~~~
+
+v1.3
+    - First version of Stuttermark to be included in ``fdstools``
+    - Fixed crash that occurred when an empty allele (e.g., a primer dimer)
+      was encountered
+    - Stuttermark now prints a warning if an allele is encountered that is
+      not a TSSV-style sequence
+
+v1.2
+    - All settings are now available from the command line
+    - Use 1-based indexing in ``STUTTER`` annotations
+
+v1.1
+    - Stuttermark now accepts file names and the minimum number of reads to
+      evaluate as command line arguments
+
+v1.0
+    - Initial version
+
+

fdstools/__init__.py

+"""
+Tools for characterisation and filtering of PCR stutter artefacts and other
+systemic noise in Next Generation Sequencing data of forensic STR markers.
+"""
+
+__version_info__ = ('0', '0', '1')
+__version__ = '.'.join(__version_info__)
+usage = __doc__.split("\n\n\n")
+
+def version(name, toolname=None, toolversion=None):
+    """Return a version string for the package or a given tool."""
+    verformat = "%s %s"
+    toolverformat = "%s (part of %s)"
+    if toolname is None:
+        return verformat % (name, __version__)
+    if toolversion is None:
+        return toolverformat % (toolname, verformat % (name, __version__))
+    return toolverformat % (verformat % (toolname,toolversion),
+                            verformat % (name, __version__))

fdstools/fdstools.py

+#!/usr/bin/env python
+
+import argparse, pkgutil, os
+import tools
+
+from . import usage, version
+
+
+# Map tool names to argument parsers.
+__tools__ = {}
+
+
+class _HelpAction(argparse.Action):
+    def __call__(self, parser, namespace, values, option_string=None):
+        # If valid 'tool' argument is given, call that tool's help.
+        if values and values[0] in __tools__:
+            __tools__[values[0]].print_help()
+            __tools__[values[0]].exit()
+        else:
+            parser.print_help()
+            parser.exit()
+    #__call__
+#_HelpAction
+
+
+class _VersionAction(argparse.Action):
+    def __call__(self, parser, namespace, values, option_string=None):
+        # If valid 'tool' argument is given, print that tool's version.
+        if values and values[0] in __tools__:
+            parser = __tools__[values[0]]
+        formatter = parser._get_formatter()
+        formatter.add_text(parser.version)
+        parser.exit(message=formatter.format_help())
+    #__call__
+#_VersionAction
+
+
+def main():
+    """
+    Main entry point.
+    """
+    parser = argparse.ArgumentParser(add_help=False, description=usage[0],
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.version = version(parser.prog)
+    parser.add_argument('-v', "--version", action=_VersionAction,
+                        default=argparse.SUPPRESS, nargs=argparse.REMAINDER,
+                        help="show version number and exit")
+    parser.add_argument('-h', '--help', action=_HelpAction,
+                        default=argparse.SUPPRESS, nargs=argparse.REMAINDER,
+                        help="show this help message, or help for the "
+                             "specified TOOL, and exit")
+    subparsers = parser.add_subparsers(title='available tools', dest='tool',
+                                       metavar='TOOL', help="specify which "
+                                       "tool to run")
+    subparsers.required = True
+
+    prefix = tools.__name__ + "."
+    for importer, name, ispkg in pkgutil.iter_modules(
+            path=[os.path.join(
+                os.path.dirname(os.path.abspath(__file__)),
+                "tools")]):
+        module = importer.find_module(prefix + name).load_module(prefix + name)
+        subparser = subparsers.add_parser(
+            name, help=module.__doc__, description=module.__doc__,
+            version=version(parser.prog, name, module.__version__))
+        __tools__[name] = subparser
+        module.add_arguments(subparser)
+        subparser.set_defaults(func=module.run)
+    try:
+        args = parser.parse_args()
+        args.func(args)
+    except OSError as error:
+        parser.error(error)
+#main
+
+
+if __name__ == "__main__":
+    main()

fdstools/lib.py

+#!/usr/bin/env python
+
+import re
+
+# Patterns that match entire sequences.
+PAT_SEQ_RAW = re.compile("^[ACGT]*$")
+PAT_SEQ_TSSV = re.compile("^(?:[ACGT]+\(\d+\))*$")
+PAT_SEQ_ALLELENAME = re.compile(
+    "^(?:(?:\d+(?:\.\d+)?_(?:[ACGT]+\[\d+\])+)|[XY])"  # nn_ACGT[nn]...
+    "(?:_[-+]\d+(?:\.1)?(?P<a>(?:(?<=\.1)-)|(?<!\.1)[ACGT]+)>"  # _+3A>
+        "(?!(?P=a))(?:[ACTG]+|-))*$")  # Portion of variants after '>'.
+
+# Pattern that matches blocks of TSSV-style sequences.
+PAT_TSSV_BLOCK = re.compile("([ACTG]+)\((\d+)\)")
+
+
+def detect_sequence_format(seq):
+    """Return format of seq.  One of 'raw', 'tssv', or 'allelename'."""
+    if not seq:
+        raise ValueError("Empty sequence.")
+    if PAT_SEQ_RAW.match(seq):
+        return 'raw'
+    if PAT_SEQ_TSSV.match(seq):
+        return 'tssv'
+    if PAT_SEQ_ALLELENAME.match(seq):
+        return 'allelename'
+    raise ValueError("Unrecognised sequence format.")
+#detect_sequence_format
+
+
+def get_column_ids(column_names, *names):
+    """Find all names in column_names and return their indices."""
+    result = []
+    for name in names:
+        try:
+            result.append(column_names.index(name))
+        except ValueError:
+            raise Exception("Column not found in input file: %s" % name)
+    if len(result) == 1:
+        return result[0]
+    return tuple(result)
+#get_column_ids
+
+
+def pos_int_arg(value):
+    """Convert str to int, raise ArgumentTypeError if not positive."""
+    if not value.isdigit() or not int(value):
+        raise argparse.ArgumentTypeError(
+            "invalid positive int value: '%s'" % value)
+    return int(value)
+#pos_int_arg
+
+
+def print_db(text, debug):
+    """Print text if debug is True."""
+    if debug:
+        print(text)
+#print_db

fdstools/tools/stuttermark.py

+#!/usr/bin/env python
+"""
+Mark potential stutter products by assuming a fixed maximum percentage
+of stutter product vs the parent allele.
+"""
+import argparse
+import sys
+import re
+
+from ..lib import pos_int_arg, print_db, PAT_TSSV_BLOCK, get_column_ids
+
+__version__ = "1.3"
+
+
+# Default values for parameters are specified below.
+
+# Link a difference in repeat count to a minimum occurrance percentage
+# for stutter peaks.  Any repeat count differences other than listed
+# here are taken to have zero probability.
+# This value can be overridden by the -s command line option.
+_DEF_STUTTERDEF = "-1:15,+1:4"
+
+# Any peaks with less than this number of reads are not evaluated.
+# This value can be overridden by the -m command line option.
+_DEF_MIN_READS = 2
+
+# Stutters are not expected to appear for blocks with less than
+# _DEF_MIN_REPEATS repeats.  If two alleles have a different repeat count
+# for any block with less than _DEF_MIN_REPEATS repeats, it is not possible
+# that one of them is a stutter of the other.  Therefore, no comparison
+# is made between any two such sequences.
+# This value can be overridden by the -n command line option.
+_DEF_MIN_REPEATS = 3
+
+# Peaks are only annotated as a stutter peak of some other peak if the
+# expected number of stutter occurances of this other peak is above
+# this value.
+# This value can be overridden by the -r command line option.
+_DEF_MIN_REPORT = 0.1
+
+# Default name of the column we are adding.
+# This value can be overridden by the -c command line option.
+_DEF_COLNAME = "annotation"
+
+
+def load_data(infile, colname_annotation=_DEF_COLNAME):
+    """
+    Read data from the file handle infile and return a tuple
+    (colum_names, data_rows).
+
+    The input file is expected to have tab-delimited columns with
+    column names on the first line and one allele per data row.
+    There are three required columns:
+        name    The name of the marker this allele belongs to.
+        allele  The allele sequence in TSSV output format.
+                E.g., AGAT(7)TGAT(3).
+        total   The total number of reads with this sequence.
+
+    An additional column "annotation" is appended.  All data rows
+    are given a value of "UNKNOWN" for this column.
+
+    :arg infile: Open readable handle to data file.
+    :type infile: stream
+
+    :returns: A 2-tuple (column_names, data_rows).
+    :rtype: tuple(list, list)
+    """
+    # Get column numbers.  We are adding a column as well.
+    column_names = infile.readline().rstrip("\r\n").split("\t")
+    colid_total, colid_allele, colid_name = get_column_ids(column_names,
+        "total", "allele", "name")
+    column_names.append(colname_annotation)
+
+    # Step through the file line by line to build the allele list.
+    allelelist = []
+    for line in infile:
+        columns = line.rstrip("\r\n").split("\t")
+
+        # Skip empty/malformed lines (NOTE: allowing additional columns
+        # beyond the expected 4 columns).
+        if len(columns) != len(column_names)-1:
+            if len(line.strip()):
+                print("WARNING: skipped line: %s" % line)
+            continue
+
+        # Split the allele column into a list of tuples:
+        # [('ACTG','4'),('CCTC','12'),...]
+        columns[colid_allele] = PAT_TSSV_BLOCK.findall(columns[colid_allele])
+        if columns[colid_allele] == None:
+            print("WARNING: skipped line: %s" % line)
+            continue
+
+        # String to integer conversion...
+        columns[colid_allele] = map(
+            lambda x: [x[0], int(x[1])], columns[colid_allele])
+        columns[colid_total] = int(columns[colid_total])
+
+        # Repeat unit deduplication (data may contain stuff like
+        # "AGAT(7)AGAT(5)" instead of "AGAT(12)").
+        if columns[colid_allele]:
+            dedup = [columns[colid_allele][0]]
+            for i in range(1, len(columns[colid_allele])):
+                if columns[colid_allele][i][0] == dedup[-1][0]:
+                    dedup[-1][1] += columns[colid_allele][i][1]
+                else:
+                    dedup.append(columns[colid_allele][i])
+            columns[colid_allele] = dedup
+
+        # Add the allele to the list, including our new column.
+        columns.append("UNKNOWN")
+        allelelist.append(columns)
+    return column_names, allelelist
+#load_data
+
+
+def annotate_alleles(infile, outfile, stutter, min_reads=_DEF_MIN_READS,
+                     min_repeats=_DEF_MIN_REPEATS, min_report=_DEF_MIN_REPORT,
+                     colname_annotation=_DEF_COLNAME, debug=False):
+    """
+    Read data from the file handle infile and write annotated data to
+    file handle outfile.
+
+    The input file is expected to have tab-delimited columns with
+    column names on the first line and one allele per data row.
+    There are three required columns:
+        name    The name of the marker this allele belongs to.
+        allele  The allele sequence in TSSV output format.
+                E.g., AGAT(7)TGAT(3).
+        total   The total number of reads with this sequence.
+
+    An additional annotation column is appended.  All data rows
+    are given a value of "ALLELE", "STUTTER:...", or "UNKNOWN".
+    Alleles that are annotated as "STUTTER" are given a colon-separated
+    description of their expected origins.  For each originating allele
+    a description of the form AxB(C) is given, with A the maximum
+    expected number of stutter reads from this origin, B the allele
+    number of the originating allele (where the first allele in the
+    output file is allele 1), and C a 'x'-separated list of repeat
+    blocks that had stuttered.
+
+    Example stutter description:
+        STUTTER:123.8x1(3-1):20.2x2(4+1)
+    This stutter allele has two originating alleles: a maximum of 123.8
+    reads from allele 1 plus a maximum of 20.2 reads from 2.  Compared
+    to allele 1, this is a -1 stutter in the third repeat block.
+    Compared to allele 2, this is a +1 stutter of the fourth repeat
+    block.  (If this allele had more than 144 total reads, it would have
+    been annotated as "ALLELE".)
+
+    :arg infile: Open readable handle to data file.
+    :type infile: stream
+
+    :arg outfile: Open writable handle for output data.
+    :type outfile: stream
+
+    :arg stutter: A dict mapping stutter size (keys) to a maximum
+                  expected percentage of stutter of this size.
+    :type stutter: dict{int: float}
+
+    :arg min_reads: Any alleles with less than this number of reads are
+                    not evaluated (annotation=UNKNOWN).
+    :type min_reads: int
+
+    :arg min_repeats: Stutters are not expected to appear for blocks
+                      with less than this number of repeats.
+    :type min_repeats: int
+
+    :arg min_report: Stutters with an expected number of reads below
+                     this value are not reported.
+    :type min_report: float
+
+    :arg colname_annotation: Name of the newly added column.
+    :type colname_annotation: str
+
+    :arg debug: If True, print debug output to stdout.
+    :type debug: bool
+    """
+    column_names, allelelist = load_data(infile, colname_annotation)
+    colid_total, colid_allele, colid_name = get_column_ids(column_names,
+        "total", "allele", "name")
+
+    # Sort (descending total reads).
+    allelelist.sort(key=lambda allele:
+        [allele[colid_name], -allele[colid_total]])
+
+    for iCurrent in range(len(allelelist)):
+
+        # See if this allele appeared a reasonable number of times.
+        if allelelist[iCurrent][colid_total] < min_reads:
+            continue
+
+        isStutterPeakOf = {}
+        maximumOccurrenceExpected = 0
+
+        # Find all ways to reach allele iCurrent by mutating the other
+        # alleles that appeared more often.
+        for iOther in range(iCurrent):
+
+            # Must be same marker.
+            if (allelelist[iCurrent][colid_name] !=
+                    allelelist[iOther][colid_name]):
+                continue
+
+            print_db('%i vs %i' % (iCurrent+1, iOther+1), debug)
+
+            # Must be same number of blocks.
+            if (len(allelelist[iCurrent][colid_allele]) !=
+                    len(allelelist[iOther][colid_allele])):
+                print_db('Different number of blocks', debug)
+                continue
+
+            maximumOccurrenceExpectedForThisOther = 1.0
+            blocksThatDiffer = {}
+
+            # What is needed to get from sequence iOther to iCurrent?
+            # We will look at each block in turn.
+            for block in range(len(allelelist[iCurrent][colid_allele])):
+
+                # If mutations are needed to get from iOther to
+                # iCurrent, iCurrent can't be a stutter of iOther.
+                if (allelelist[iCurrent][colid_allele][block][0] !=
+                        allelelist[iOther][colid_allele][block][0]):
+                    print_db('Block %i has different sequence' % (block+1),
+                             debug)
+                    break
+
+                # See how many times the current block appears more or
+                # less often in iCurrent as compared to iOther.
+                deltaRepeats = (allelelist[iCurrent][colid_allele][block][1] -
+                                allelelist[iOther][colid_allele][block][1])
+                if deltaRepeats == 0:
+                    continue
+
+                # iCurrent is not a stutter of iOther if any one of its
+                # blocks differs in count while either count is below
+                # min_repeats.  It is not a stutter of iOther because
+                # those are expected not to occur for such low repeat
+                # counts.  At the same time any further analysis
+                # between the two is invalid because this block was not
+                # the same.  Note that if this truly was a stutter of
+                # iOther, maximumOccurrenceExpected is going to be a
+                # bit too low now.
+                if min(allelelist[iCurrent][colid_allele][block][1],
+                     allelelist[iOther][colid_allele][block][1]) < min_repeats:
+                    print_db('Block %i has low-count difference: %i and %i' %
+                        (block+1, allelelist[iCurrent][colid_allele][block][1],
+                         allelelist[iOther][colid_allele][block][1]), debug)
+                    break
+
+                # Depending on the repeat count difference, iCurrent
+                # may appear at most a certain amount of times.
+                # This is expressed as a percentage of the occurrence
+                # of iOther.
+
+                # If the repeat count difference is highly improbable,
+                # this can't be a stutter.
+                elif deltaRepeats not in stutter:
+                    print_db('Improbable difference in number of repeats of '
+                             'block %i: %i' % (block+1, deltaRepeats), debug)
+                    break
+
+                # Based on this block only, sequence iCurrent could be
+                # a stutter of sequence iOther.  It may appear only a
+                # limited number of times, however.
+                else:
+                    blocksThatDiffer[block] = deltaRepeats
+                    maximumOccurrenceExpectedForThisOther *= \
+                        stutter[deltaRepeats] / 100.0
+                    print_db('Occurence percentage now %d' %
+                             maximumOccurrenceExpectedForThisOther, debug)
+
+            else:
+                # If we end up here, iCurrent could very well be a
+                # stutter peak of iOther, but it might be below the
+                # reporting threshold.
+                thisStutterOccurrenceExpected = \
+                    (maximumOccurrenceExpectedForThisOther *
+                     allelelist[iOther][colid_total])
+                if thisStutterOccurrenceExpected < min_report:
+                    print_db('Expected occurrence of stutter from '
+                             '%i to %i is only %d' %
+                             (iOther+1, iCurrent+1,
+                              thisStutterOccurrenceExpected), debug)
+                else:
+                    isStutterPeakOf[iOther] = (blocksThatDiffer,
+                        thisStutterOccurrenceExpected)
+                    maximumOccurrenceExpected += thisStutterOccurrenceExpected
+                    print_db('Expected occurence now %d' %
+                             maximumOccurrenceExpected, debug)
+
+        # Now we'll just need to check whether it does not appear
+        # unrealistically often.
+        if allelelist[iCurrent][colid_total] > maximumOccurrenceExpected:
+            print_db('Occurs too often (%i > %d)' %
+                     (allelelist[iCurrent][colid_total],
+                      maximumOccurrenceExpected), debug)
+            allelelist[iCurrent][-1] = "ALLELE"
+        else:
+            # Stutter peak detected.
+            allelelist[iCurrent][-1] = "STUTTER:%s" % ":".join(map(
+                lambda iOther: "%.1fx%i(%s)" % (
+                    isStutterPeakOf[iOther][1],
+                    iOther+1,
+                    "x".join(map(
+                        lambda block: "%i%+i" % (
+                            block+1,
+                            isStutterPeakOf[iOther][0][block]),
+                        isStutterPeakOf[iOther][0]))),
+                isStutterPeakOf))
+            print_db("%2i is a stutter peak of %s; occur=%i, maxOccur=%s" %
+                     (iCurrent+1, isStutterPeakOf,
+                      allelelist[iCurrent][colid_total],
+                      maximumOccurrenceExpected), debug)
+
+    # Reconstruct the allele sequence and write out the findings.
+    for i in range(len(allelelist)):
+        allelelist[i][colid_allele] = "".join(map(
+            lambda block: "%s(%i)" % tuple(block),
+            allelelist[i][colid_allele]))
+    outfile.write("\t".join(column_names))
+    outfile.write("\n")
+    outfile.write("\n".join(map(
+        lambda allele: "\t".join(map(str, allele)), allelelist)))
+    outfile.write("\n")
+#annotate_alleles
+
+
+def stutter_def_arg(value):
+    """
+    Convert a stutter definition string to dict, raise ArgumentTypeError
+    on failure.
+
+    The stutter definition string is a comma-separated list of int:float
+    pairs, e.g., "-1:15,+1:3.5".  Whitespace around interpunction is
+    permitted, e.g., "-1: 15, +1: 3.5".
+
+    :arg min_reads: A valid stutter definition string.
+    :type min_reads: str
+
+    :returns: A dict mapping stutter size (keys) to a maximum expected
+              percentage of stutter of this size.
+    :rtype: dict{int: float}
+    """
+    if ":" not in value:
+        return {}
+    try:
+        return {int(x[0]): float(x[1])
+                for x in map(lambda x: x.split(":"), value.split(","))}
+    except ValueError as e:
+        raise argparse.ArgumentTypeError(
+            "invalid stutter definition value: '%s' (%s)" % (value, str(e)))
+#stutter_def_arg
+
+
+def add_arguments(parser):
+    parser.add_argument('infile', nargs='?', metavar="IN", default=sys.stdin,
+        type=argparse.FileType('r'),
+        help="the CSV data file to process (default: read from stdin)")
+    parser.add_argument('outfile', nargs='?', metavar="OUT",
+        default=sys.stdout, type=argparse.FileType('w'),
+        help="the file to write the output to (default: write to stdout)")
+    parser.add_argument('-s', '--stutter', metavar="DEF", type=stutter_def_arg,
+        default=_DEF_STUTTERDEF,
+        help="Define maximum expected stutter percentages.  The default value "
+             "of '%(default)s' sets -1 stutter (loss of one repeat) to 15%%, "
+             "+1 stutter (gain of one repeat) to 4%%.  Any unspecified "
+             "stutter amount is assumed not to occur directly but e.g., a -2 "