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LIPID Metabolites And Pathways Strategy |
LMStrGen.pl - Generate arbitrary LIPID MAPS structures
LMStrGen.pl LMAbbrev|LMAbbrevFileName ...
LMStrGen.pl [-h, --help] [-o, --overwrite] [-r, --root rootname] [-w, --workingdir dirname] <arguments>...
Generate arbitrary LIPID MAPS (LM) structures using compound abbreviations specified on a command line or in a CSV/TSV Text file. All the command line arguments represent either compound abbreviations or file name containing abbreviations. Use mode option to control the type of command line arguments.
A SD file, containing structures for all LM abbreviations along with ontological information, is generated as an output.
Current support for LM structure generation include these headgroups and acyl chains:
Print this help message
Controls interpretation of command line arguments. Two different methods are provided: specify compound abbreviations or a file name containing compound abbreviations. Possible values: Abbrev or AbbrevFileName. Default: Abbrev
In AbbrevFileName mode, a single line in CSV/TSV files can contain multiple compound abbreviations. The file extension determines delimiter used to process data lines: comma for CSV and tab for TSV. For files with TXT extension, only one compound abbreviation per line is allowed.
Wild card character, *, is not supported in compound abbreviations.
Examples:
Overwrite existing files
New file name is generated using the root: <Root>.sdf. Default for new file names: LMAbbrev.sdf, <AbbrevFilenName>.sdf, or <FirstAbbrevFileName>1To<Count>.sdf.
Location of working directory. Default: current directory
On some systems, command line scripts may need to be invoked using perl -s LMStrGen.pl; however, all the examples assume direct invocation of command line script works.
To generate a LMStructures.sdf file containing a structure specified by a command line LM abbreviation, type:
To generate a LMStructures.sdf file containing structures specified by a command line LM abbreviations, type:
CLStrGen.pl, FAStrGen.pl, GLStrGen.pl, SPStrGen.pl, STStrGen.pl
Copyright (C) 2006-2012. The Regents of the University of California. All Rights Reserved.
Modified BSD License