common.Misc Namespace Reference

Miscellaneous functions useful all over the project. More...

Functions
def	FileType (pathname)
	Low level compression determination. More...
def	OpenFile4Reading (pathname, mode="r")
	Opens file for reading. More...
def	TypeConvert (value, toType, warn=True)
	Data conversion with error logging. More...
def	GetGRChVersion (dver)
	Get the human Genome Reference Consortium genome build version used by Ensembl. More...
def	SplitGenomicCoord (coord, dver, warn=True, retainBuild=False)
	Splits a standard string for genomic location. More...
def	SplitSNPGenomicCoord (coord, dver, warn=True)
	Splits genomic coordinates from a SNP. More...
def	GetGenomicCoordinateString (build, chromosome, startPos, endPos=None, warn=True)
	Create the Genomic Coordinate string in the format Build:Chromosome:Start -End or Build:Chromosome:Start (in the case where start and end are equal). More...
def	ComplementaryDNA (seq, reverse=False)
	Compute the complementary DNA sequence of a given sequence string. More...
def	WCheckInputColumns (writer, cols, line, lineNr, permissiveness, warn=True, exitCode=1, index0=True)
	Check applicability of column indices and apply permissiveness mode. More...
def	CheckInputColumns (cols, nrCols, lineNr, stop, warn=True, exitCode=1, index0=True, lastLen=None)
	Check applicability of column indices. More...
def	CheckInputLengths (len, lastLen, lineNr, warn=True)
	Check the length of an input line by comparing it to the last line. More...
def	ConvertInputIndices (cols, warn=True, exit=False)
	Convert input column(s) to table indices. More...

Variables
list	VALID_HS_CHROMOSOMES = [str(x) for x in range(1,23)] + ["X", "Y", "MT"];
int	FT_FAILED = -1;
	Error when trying to peek into file. More...
int	FT_UNK = 0;
	No compression detected. More...
int	FT_COMPRESS = 1;
	Unix compress file. More...
int	FT_GZIP = 2;
	GZIP file. More...
int	FT_BZIP2 = 3;
	BZIP2 file. More...

Detailed Description

Miscellaneous functions useful all over the project.

Author

Chris X. Weichenberger

Date

2012-02-17

Copyright

See LICENSE file.

Function Documentation

CheckInputColumns()

def common.Misc.CheckInputColumns	(		cols,
			nrCols,
			lineNr,
			stop,
			warn = True,
			exitCode = 1,
			index0 = True,
			lastLen = None
	)

Check applicability of column indices.

Checks if indices are appropriate for indexing into a list with a certain
number of columns. This function may terminate the program!
@param cols  See @ref WCheckInputColumns.
@param nrCols  Number of columns of the list to be checked.
@param lineNr  See @ref WCheckInputColumns.
@param stop  If a value in @c cols failed to index into a list with
 @c lineNr elements, the program execution is aborted when this parameter
 is set to @c True.
@param warn  See @ref WCheckInputColumns.
@param exitCode  See @ref WCheckInputColumns.
@param index0  See @ref WCheckInputColumns.
@return  See @ref WCheckInputColumns.

CheckInputLengths()

def common.Misc.CheckInputLengths	(		len,
			lastLen,
			lineNr,
			warn = True
	)

Check the length of an input line by comparing it to the last line.

@param len Lengths of the current input line
@param lastLen Lengths of the last input line
@param lineNr  Line number of the input file, used for reporting
@param warn  If set to @c False, warnings will not be issued.
@return @c True, if the lengths are the same. @c False, if the lengths are
 different.

ComplementaryDNA()

def common.Misc.ComplementaryDNA	(		seq,
			reverse = False
	)

Compute the complementary DNA sequence of a given sequence string.

For a given sequence of DNA bases, compute the case sensitive sequence on
the reverse strand, allowing also gap characters.
@param seq  DNA sequence as a @c String, can be single character.
@param reverse  If set to @c True, the string is also position-reversed.
@return Complementary DNA sequence.

ConvertInputIndices()

def common.Misc.ConvertInputIndices	(		cols,
			warn = True,
			exit = False
	)

Convert input column(s) to table indices.

This function is meant for checking the validity of column indices passed
by the command line interface. A check for applicability of the indices in
the context of an input line is done by @ref CheckInputColumns and @ref
WCheckInputColumns.
@param cols  Input columns as a List of Strings.
@param warn  If set to @c False, prevent printing of error messages.
@param exit  If set to @c True, the program execution stops with exit code
 1.
@return flag,columns  @c flag is @c True, if the conversion was successful
 and @c columns holds the converted indices (starting from 0). If @c flag
 is @c False, an empty list is returned indicating an error in conversion,
 ie. not an integer.

FileType()

def common.Misc.FileType

(

pathname

)

Low level compression determination.

This function tells reliably if the file is GZIP or COMPRESS compressed,
independently of the extension by reading the magic number.

@param pathname  Full path name of file.
@return  FT_FAILED, FT_UNK, FT_COMPRESS, FT_GZIP, FT_BZIP2

GetGenomicCoordinateString()

def common.Misc.GetGenomicCoordinateString	(		build,
			chromosome,
			startPos,
			endPos = None,
			warn = True
	)

Create the Genomic Coordinate string in the format Build:Chromosome:Start -End or Build:Chromosome:Start (in the case where start and end are equal).

Parameters

build	The genome build version String as retrieved from a call to cls.Misc.GetGRChVersion.
chromosome	The chromosome where start (and if present, end) are located.
startPos	The start position on the above chromosome.
endPos	The end position on the above chromosome. Can be omited in case of single nucleotide positions.
build	Use this build string instead of the current one.
warn	If set to False, prevent printing of warnings.

Returns

The Genomic Coordinate string. Is None if an invalid combination of start and end is provided, or the chromosome name is not one of the (case insensitive) human chromosomes (1,2,...,22, X, Y, MT).

GetGRChVersion()

def common.Misc.GetGRChVersion

(

dver

)

Get the human Genome Reference Consortium genome build version used by Ensembl.

Parameters

dver	Data version String to access the corresponding section in the configuration file.

Returns

The GRCh version name (String) or None, if the data version is not contained in the configuration file.

OpenFile4Reading()

def common.Misc.OpenFile4Reading	(		pathname,
			mode = "r"
	)

Opens file for reading.

@param pathname  Full path name of file.
@param mode  Reading mode for pure ASCII files. Can only be 'r' or 'rb'.
@return  File handle. To be closed by user. @c None if the file could not
 be opened.

SplitGenomicCoord()

def common.Misc.SplitGenomicCoord	(		coord,
			dver,
			warn = True,
			retainBuild = False
	)

Splits a standard string for genomic location.

Most generic location of a nucleotide in a genome in our system is given
by 'build:chromosome:position'. In case @c build is missing, it is
replaced with the current Ensembl build version string.

@param coord  Genomic location @c String.
@param dver  Data version @c String for config file lookup.
@param warn  If set to @c False, prevent printing of warnings.
@param retainBuild If set to @c True, the function returns the exact
 genomic build given, even if it is not equal to the default genome build
 version.
@return (build, chromosome, position) as (@c String, @c String, @c Int),
 all of them @c None if an error occurred.

SplitSNPGenomicCoord()

def common.Misc.SplitSNPGenomicCoord	(		coord,
			dver,
			warn = True
	)

Splits genomic coordinates from a SNP.

A SNP position in the genome can either be a single base pair, or it can
also be a short interval, as insertions and deletions affect more than a
single base pair. As for an example, rs60709680 codes for an insertion and
is represented as GRCh37:8:67970310-67970311 (build, chromosome, fromPos,
toPos).

@param coord  Genomic SNP location @c String.
@param dver  Data version @c String for config file lookup.
@param warn  If set to @c False, prevent printing of warnings.
@return (build, chromosome, fromPos, toPos) as
 (@c String, @c String, @c Int, @c Int). All @c None if an error
 occurred. It is guaranteed that @c fromPos <= @c toPos.

TypeConvert()

def common.Misc.TypeConvert	(		value,
			toType,
			warn = True
	)

Data conversion with error logging.

Converts between built-in Python data types and conditionally issues an
error message if the conversion failed.
@param value  Value to be converted, can be any built-in data type.
@param toType  Data type to convert to, eg. @c int.
@param warn  If set to @c False, prevent printing of warnings.
@return conv. If conversion failed, @c conv will be set to @c None,
 otherwise it holds the converted @c value.

WCheckInputColumns()

def common.Misc.WCheckInputColumns	(		writer,
			cols,
			line,
			lineNr,
			permissiveness,
			warn = True,
			exitCode = 1,
			index0 = True
	)

Check applicability of column indices and apply permissiveness mode.

This function checks if the values in @c cols are valid indices for
accessing columns represented in a @c list in @c line. Depending on the
permissiveness model, a call to this function may lead to program
abortion!
@param writer  A @ref cls.DefaultTable.CDefaultTableWriter instance.
@param cols  A @c list of @c ints to be checked if they can be used as
 indices for a line. For convenience, this can also be an @c int in case
 of a single column.
@param line  A @c list of @c strings, representing the line to be
 checked for indexing validity.
@param lineNr  An @c int, indicating the line number in the file. Used for
 reporting errors/warnings.
@param  permissiveness  One of the three possible permissiveness models:
 @c PERMISSIVENESS_ECHO, write the line using parameter @c writer;
 @c PERMISSIVENESS_SKIP, do not write the line;
 @c PERMISSIVENESS_STOP, stop processing and exit with an error code.
@param warn  If set to @c False, warnings will not be issued.
@param exitCode If the @c permissiveness is set to @c PERMISSIVENESS_STOP,
 the program exits with this exit code.
@param index0 If set to @c True, values in @c cols are interpreted as
 Python indices starting with 0. If set to @c False, indices are
 interpreted to be starting with 1.
@return @c True, if all checks were fulfilled and the values in @c cols
 can be used for indexing into the list @c line. @c False, if one of the
 values would produce an indexing error in @c line. If the permissiveness
 model equals to @c PERMISSIVENESS_STOP, the program has been terminated
 and does not return! Otherwise, warning messages have been written
 accordingly (@c warn flag), the line has been written if
 @c PERMISSIVENESS_ECHO was used.

Variable Documentation

FT_BZIP2

int common.Misc.FT_BZIP2 = 3;

BZIP2 file.

FT_COMPRESS

int common.Misc.FT_COMPRESS = 1;

Unix compress file.

FT_FAILED

int common.Misc.FT_FAILED = -1;

Error when trying to peek into file.

FT_GZIP

int common.Misc.FT_GZIP = 2;

GZIP file.

FT_UNK

int common.Misc.FT_UNK = 0;

No compression detected.

May right be an ASCII file.

VALID_HS_CHROMOSOMES

list common.Misc.VALID_HS_CHROMOSOMES = [str(x) for x in range(1,23)] + ["X", "Y", "MT"];