apt-dmet-translation is a part of the DMET Console (DC) responsible for translating CHP file gene experiment data into the allele translation lingua franca of biologists. As a convience this tool can be run from the command line independent of the GUI. However, the results will identical unless the command line only options are used.
The translation tool always requires the following three options.
Translation Table ("-t" or "--translate-file")
Annotation File ("-a" or "--annotate-file" )
CHP file[s] ("-e" or "--experiment-list", "-E" or "--experiment-list-file" )
apt-dmet-translation -a /path/to/DMET_Plus.v1.20110329.dc_annot.csv \ -t /path/to/DMET_Plus.v1.20110329.translation \ -e /path/to/experiment1.CHP:/path/to/experiment2.CHP
OR
apt-dmet-translation -a /path/to/DMET_Plus.v1.20110329.dc_annot.csv \\ -t /path/to/DMET_Plus.v1.20110329.translation \\ -E /path/to/experiment-files-CHP.txt
WHERE
experiment-files-CHP.txt is a TsvFile with header "file":
chp_files /path/to/experiment1.CHP /path/to/experiment2.CHP #/path/to/commented/out/experimentN.CHP
Allele translatione engine for the generation of allele translation reports.
options:
Common Options (not used by all programs)
-h, --help Display program options and extra
documentation about possible analyses. See
-explain for information about a specific
operation. [default 'false']
-v, --verbose How verbose to be with status messages 0 -
quiet, 1 - usual messages, 2 - more
messages. [default '1']
--console-off Turn off the default messages to the
console but not logging or sockets.
[default 'false']
--use-socket Host and port to print messages over in
localhost:port format [default '']
--version Display version information. [default
'false']
-f, --force Disable various checks including chip
types. Consider using --chip-type option
rather than --force. [default 'false']
--throw-exception Throw an exception rather than calling
exit() on error. Useful for debugging. This
option is intended for command line use
only. If you are wrapping an Engine and
want exceptions thrown, then you should
call Err::setThrowStatus(true) to ensure
that all Err::errAbort() calls result in an
exception. [default 'false']
--analysis-files-path Search path for analysis library files.
Will override AFFX_ANALYSIS_FILES_PATH
environment variable. [default '']
--xml-file Input parameters in XML format (Will
override command line settings). [default
'']
--temp-dir Directory for temporary files when working
off disk. Using network mounted drives is
not advised. When not set, the output
folder will be used. The defaut is
typically the output directory or the
current working directory. [default '']
-o, --out-dir Directory for output files. Defaults to
current working directory. [default '.']
--log-file The name of the log file. Generally
defaults to the program name in the out-dir
folder. [default '']
Engine Options (Not used on command line)
--command-line The command line executed. [default '']
--exec-guid The GUID for the process. [default '']
--program-name The name of the program [default '']
--program-company The company providing the program [default
'']
--program-version The version of the program [default '']
--program-cvs-id The CVS version of the program [default '']
--version-to-report The version to report in the output files.
[default '']
--free-mem-at-start How much physical memory was available when
the engine run started. [default '0']
--meta-data-info Meta data in key=value pair that will be
output in headers. [default '']
Program Control
--dmet2-calling => use DMET2 logic for making allele calls.
[default 'false']
--enforce-complete-haplotypes => Enforce that experiment data has a
complete set of markers for any haplotype
set and abort when incomplete haplotype
sets are detected. [default 'false']
--ignore-unknown-alleles => Ignore unknown alleles for a
multi-allelic marker where the allele is
not specified in the translation file.
[default 'false']
--ignore-report-allele => Use the alleles from the translation
file for reporting and not the report
allele in the annotation file. [default
'false']
--audit => Audit various components of translation,
don't translate.
Available audit types are:
* annotation - audit annotation file probe
sets against the translation file. [default
'']
--use-first-dup-allele-def => If marker list filtering removes markers
needed to differntiate among multiple
possible haplotypes then report only the
first named haplotype in the Translation
file. [default 'false']
Input Options
-a, --annotation-file => file.csv (probe set annotation file,
CSV) [default '']
-c, --copy-dmet2-number-file (DMET2: 2 of 2 experiment files) =>
YYYYMMDD_*_DMET[23]_cn_*.txt [default '']
-e, --experiment-list => file1.chp;file2.chp;... OR
file1.chp:file2.chp:.. [default '']
-E, --experiment-list-file => file with listing of CHP files.
(Commented out lines starting with '#' are
allowed). [default '']
-g, --geno-dmet2-type-file (DMET2: 1 of 2 experiment files) =>
YYYYMMDD_*_DMET[23]_Genotypes*.txt [default
'']
-i, --input-dir => Directory to read input files from when
file is not specified (-c, -g, -t_). The
current directory is assumed when not
specified. [default '']
-m, --marker-list-file => marker-list-file.*.txt file is a simple
list of probe sets, one per line, to be
used for translation. [default '']
-n, --genotype-override-file => file with genotype override base calls
in TSV format. [default '']
-s, --sample-file => file.txt (sample info file, TSV)
[default '']
-t, --translate-file => DMET3_TTTable_vYYYYMMDD_*.txt
(DMET2_TTTable_vYYYYMMDD_*.txt for DMET2
testing) [default '']
Output Options
-b, --base-name-prefix => Base name prefix of all output reports.
[default '']
Reporting Options
-p, --profile => Profile reporting. [default 'false']
-r, --regression => Regression log level. [default '0']
--marker-report => Output DMET2 Marker Report. [default
'false']
--summary-report-sort => Sort the summary report rather than use
the default translation table order.
[default 'true']
-u, --uncalled-report-all-markers => Report all markers in the uncalled
report, not just the uncalled markers.
[default 'false']
--experiment-list-vector => Not a command line option. [default '']
--marker-list-vector => Not a command line option. [default '']
--sample-table => Not a command line option. [default '0']
Internal Use Only
--prototype-chp-files => For internal use only. [default 'false']
--time-start The time the engine run was started
[default '']
--time-end The time the engine run ended [default '']
--time-run-minutes The run time in minutes. [default '']
--analysis-guid The GUID for the analysis run. [default '']
Override file
apt-dmet-translation -a /path/to/DMET3b.GT_plus_CN_annotation.csv \ -t /path/to/DMETplusTTable20080902.translation.txt \ -E /path/to/experiment-files-CHP.txt -n /ath/to/report_uncalled.rpt
Sample Info
apt-dmet-translation -a /path/to/DMET3b.GT_plus_CN_annotation.csv \ -t /path/to/DMETplusTTable20080902.translation.txt \ -E /path/to/experiment-files-CHP.txt -n /ath/to/sample-info.txt
Marker List
apt-dmet-translation -a /path/to/DMET3b.GT_plus_CN_annotation.csv \ -t /path/to/DMETplusTTable20080902.translation.txt \ -E /path/to/experiment-files-CHP.txt -m /ath/to/marker-list-file.txt
1.7.1