LIPID MAPS® Lipidomics Gateway

NAME

LMStrGen.pl - Generate arbitrary LIPID MAPS structures

SYNOPSIS

LMStrGen.pl LMAbbrev|LMAbbrevFileName ...

LMStrGen.pl [-h, --help] [-o, --overwrite] [-r, --root rootname] [-w, --workingdir dirname] <arguments>...

DESCRIPTION

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.

SUPPORTED ABBREVIATIONS

Current support for LM structure generation include these headgroups and acyl chains:

o DIMAXX - sn1, sn2 and sn3 o DIMA20 - sn1 and sn2 o DIMA22 - sn1 and sn2 o DIMA20Me - sn1 and sn2 o DIMA22Me - sn1 and sn2 o DIMB20 - sn1 and sn2 o DIMB22 - sn1 and sn2 o DIB20Me - sn1 and sn2 o DIB22Me - sn1 and sn2 o PIM1 - sn1 and sn2 o PIM2 - sn1 and sn2 o PIM3 - sn1 and sn2 o PIM4 - sn1 and sn2 o PIM5 - sn1 and sn2 o PIM6 - sn1 and sn2 o DAT - sn1 and sn2 o CoA - sn1

OPTIONS

-h, --help

Print this help message

-m, --mode Abbrev|AbbrevFileName

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:

Specific structures: DIMA20(12:0/13:0) DIMB20(17:1(9Z)/18:0) CoA(16:0) PIM1(21:0/22:0)

-o, --overwrite

Overwrite existing files

-r, --root rootname

New file name is generated using the root: <Root>.sdf. Default for new file names: LMAbbrev.sdf, <AbbrevFilenName>.sdf, or <FirstAbbrevFileName>1To<Count>.sdf.

-w, --workingdir dirname

Location of working directory. Default: current directory

EXAMPLES

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:

% LMStrGen.pl -r LMStructures -o "DIMA20(12:0/13:0)"

To generate a LMStructures.sdf file containing structures specified by a command line LM abbreviations, type:

% LMStrGen.pl -r LMStructures -o "DIMA22(16:0/18:0)" "DIMA22Me(18:1(11E)/16:0)"

AUTHOR

Manish Sud

CONTRIBUTOR

Eoin Fahy

COPYRIGHT

LICENSE

Modified BSD License