These utilities are all written in ``Perl'', a widely available public domain interpreted programming language. Some of them work by running one of the other programs in this package and digesting the output one way or another. Others are useful for manipulating genetic marker data files.
For more information about Perl, or to find out how to get it, see http://www.perl.com.
UNIX command syntax:
ligate
[-r]
[-a]
[-n]
[-f]
[-p]
[-b blank]
[-c markers]
[-d markers]
[marker_data ...]
The ligate filter can be used to cut and paste linkage data files
together, and to convert between common file format variants. Any
number of files can be specified, in either Risch or LINKAGE format,
in any combination. The default output is a LINKAGE format file
formed by merging all the input data.
If a linkage file is missing the ASPEX-style header line listing the marker names, then marker names ``M1.1'', ``M1.2'', etc will be generated automatically. The next such file would get marker names ``M2.1'', ``M2.2'', and so on.
Command line parameters:
-rSpecifies that the data should be written in Risch format, as opposed to LINKAGE format.
-aSpecifies ``alphabetic'' codes for gender and blanks. Numeric gender codes (1, 2) will be translated to ``m'' and ``f'', and blank parents and alleles will be coded as ``x''.
-nSpecifies ``numeric'' codes for gender and blanks. Alphabetic gender codes (``m'', ``f'') will be translated to the corresponding numbers, and blanks will be coded as ``0''.
-b blankSpecifies the code for the blank allele. The default is ``0''.
-f blankSpecifies that new rows (with all blank genotype data) should be created in the output file for untyped parents. ASPEX does not require that an untyped parent be listed in the data file, but some linkage programs do.
-p blankSpecifies that the original allele codes should be ``packed'' and recoded as 1, 2, ... for each marker. Some linkage programs require that alleles be coded this way, rather than, say, as raw allele sizes.
-c markersThe list of markers will be included in the output file, in the order given, and all other markers will be omitted.
-d markersThe specified list of markers will be deleted from the output file.
UNIX command syntax:
restrict
[-b blank]
[-kids [+-]n]
[-sick [+-]n]
[-well [+-]n]
[-parents [+-]n]
[-onlysick]
[-pos m[-n]]
[-sib m[-,]n]
[-keep id...]
[-remove id...]
[marker_data]
The restrict filter selects families from a linkage data file
based on family structure. It is structured somewhat like the UNIX
find command. This filter replaces the ``*_kids'', ``*_parent'',
and ``only_sick'' filters in previous ASPEX releases.
Command line parameters:
-b blankSpecifies the code for the blank allele.
-parents [+-]nOnly families with the specified number of typed parents will be accepted. A parameter of the form ``+n'' selects for families with at least ``n'' typed parents; ``-n'' selects for no more than ``n''; and a plain number selects for an exact match.
-kids [+-]nSelects families based on the total number of children.
-sick [+-]nSelects families based on the number of affected children.
-well [+-]nSelects families based on the number of unaffected of children.
-onlysickSpecifies that only affected children should be included in the output.
-pos m[-n]For families meeting the other criteria, this selects based on family order in the input file. Either a single family number or a range of family numbers can be specified.
-sib m[-,]nFor families meeting the other criteria, this selects specific siblings from each family. Sibs are numbered starting at 1 in their order in the input file. Either ranges (``m-n'') or specific pairs (``m,n'') can be selected.
-keep id...]Only include families with the specified ID's. The ID list may be space- or comma-delimited; if space-delimited, it should be enclosed in quotes. An ID can either be just a family ID, or a family ID and person ID separated by a period.
-remove id...]Remove individuals with the specified ID's, with the same format rules
as -keep.
UNIX command syntax:
list_untyped
[blank_allele]
[< marker_data]
DOS command syntax:
perl list_unt
[blank_allele]
[< marker_data]
This filter scans a file of marker data in sib_ibd format, and
extracts any individual that has an untyped or partially typed marker.
It accepts one argument:
Specifies the allele that indicates missing data. The default is '0'.
UNIX command syntax:
list_incompat
[-c cmd]
[-f file]
[< marker_data]
DOS command syntax:
perl list_inc
[-c cmd]
[-f file]
[< marker_data]
The list_incompat filter has exactly the same syntax as the
sib_ibd program, except that the -v option is not used. It
runs the sib_ibd program, and filters the allele inheritance data
to produce a listing of all siblings whose genotypes are incompatible
with their parents.
UNIX command syntax:
rec_dist
[-v]
[-c cmd]
[-f file]
[< marker_data]
The rec_dist filter has the same syntax as sib_ibd. It
processes the output of sib_ibd and derives estimates of the
recombination fractions between all pairs of markers. For
compactness, the default output is a matrix showing the recombination
fraction multiplied by 1000.
If -v is specified, then a table is generated showing, for each
marker pair, the number of times the IBD state was known to be the
same at those two positions, and the number of times it differed, with
the corresponding recombination fraction.
UNIX command syntax:
xmgr_map file
DOS command syntax:
perl xmgr_map file
The xmgr_map script is used with the xmgr plotting program
to generate nicely formatted multipoint exclusion maps. It reads a
sib_ibd parameter file, and outputs a set of xmgr commands
to label the X axis with the marker names at the appropriate
positions. The output of xmgr_map should be appended to the
output of sib_ibd to create a complete xmgr input file.
The xmgr program is a completely separate public domain graphing
program for Unix systems. Current information about xmgr can be
found at
http://plasma-gate.weizmann.ac.il/Xmgr/.