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NAME

SPStrGen.pl - Generate structures for Sphingophospholipids (SP)

SYNOPSIS

SPStrGen.pl SPAbbrev|SPAbbrevFileName ...

SPStrGen.pl [-c, --ChainAbbrevMode MostLikely | Arbitrary] [-h, --help] [-m, --mode Abbrev | AbbrevFileName] [-p, --ProcessMode WriteSDFile | CountOnly] [-o, --overwrite] [-r, --root rootname] [-w, --workingdir dirname] <arguments>...

DESCRIPTION

Generate Sphingophospholipids (SP) 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 SP abbreviations along with ontological information, is generated as an output.

SUPPORTED ABBREVIATIONS

Current support for SP structure generation include these main classes and sub classes:

o Sphingoid bases

. Sphing-4-enines (Sphingosines)
. Sphinganines
. 4-Hydroxysphinganines (Phytosphingosines)
. Sphingoid base homologs and variants
. Sphingoid base 1-phosphates
. Lysosphingomyelins and lysoglycosphingolipids

o Sphingoid bases

. Sphing-4-enines (Sphingosines)
. Sphinganines
. 4-Hydroxysphinganines (Phytosphingosines)
. Sphingoid base homologs and variants
. Sphingoid base 1-phosphates
. Lysosphingomyelins and lysoglycosphingolipids
. Sphingoid base analogs

o Ceramides

. N-acylsphingosines (ceramides)
. N-acylsphinganines (dihydroceramides)
. N-acyl-4-hydroxysphinganines (phytoceramides)
. Ceramide 1-phosphates

o Phosphosphingolipids

. Ceramide phosphocholines (sphingomyelins)
. Ceramide phosphoethanolamines
. Ceramide phosphoinositols

o Neutral glycosphingolipids

. Simple Glc series (GlcCer, LacCer, etc)
. GalNAcb1-3Gala1-4Galb1-4Glc- (Globo series)
. GalNAcb1-4Galb1-4Glc- (Ganglio series)
. Galb1-3GlcNAcb1-3Galb1-4Glc- (Lacto series)
. Galb1-4GlcNAcb1-3Galb1-4Glc- (Neolacto series)
. GalNAcb1-3Gala1-3Galb1-4Glc- (Isoglobo series)
. GlcNAcb1-2Mana1-3Manb1-4Glc- (Mollu series)
. GalNAcb1-4GlcNAcb1-3Manb1-4Glc- (Arthro series)
. Gal- (Gala series)

o Acidic glycosphingolipids

. Gangliosides

OPTIONS

-c, --ChainAbbrevMode MostLikely|Arbitrary

Specify what types of acyl chain abbreviations are allowed during processing of complete abbreviations: allow most likely chain abbreviations containing specific double bond geometry specifications; allow any acyl chain abbreviation with valid chain length and double bond geometry specificatios. Possible values: MostLikely or Arbitrary. Default value: MostLikely.

Arbitrary value of -c, --ChainAbbrevMode option is not allowed during processing of abbreviations containing wild cards.

During MostLikely value of -c, --ChainAbbrevMode option, only the most likely acyl chain abbreviations specified in ChainAbbrev.pm module are allowed. However, during Arbitrary value of -c, --ChainAbbrevMode option, any acyl chain abbreviations with valid chain length and double bond geometry can be specified. The current release of lipidmapstools support chain lengths from 2 to 50 as specified in ChainAbbev.pm module.

In addition to double bond geometry specifications, valid substituents can be specified for in the acyl chain abbreviations.

-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 also supported in compound abbreviations.

Examples:

Specific structures: Cer(d18:0/0:0) Cer(d18:1(4E)/0:0) Cer(d19:1(4E)/24:4(5Z,8Z,11Z,14Z))
Specific structures: SM(d18:0/16:0) SM(d19:0/24:1(15Z))
Specific possibilities: Cer(*/0:0) Cer(d18:1(4E)/*)
All possibilites: *(*:*/*:*) or *(*/*)

With wild card character, +/- can also be used for chain lengths to indicate even and odd lengths at sn1/sn2/sn3 positions; additionally > and < qualifiers are also allowed to specify length requirements. Examples:

Odd and even number chains at sn1 and sn2: *(*-:*/*+:*)
Odd and even number chains at sn1 and sn2 with length longer than 18 and 22: *(*->18:*/*+>22:*)
-p, --ProcessMode WriteSDFile|CountOnly

Specify how abbreviations are processed: generate structures for specified abbreviations along with generating a SD file or just count the number of structures corresponding to specified abbreviations without generating any SD file. Possible values: WriteSDFile or CountOnly. Default: WriteSDFile.

It can take substantial amount of time for generating all the structures and writing out a SD file for abbreviations containing wild cards. CountOnly value of --ProcessMode option can be used to get a quick count of number of structures to be generated without writing out any SD file.

-o, --overwrite

Overwrite existing files

-r, --root rootname

New file name is generated using the root: <Root>.sdf. Default for new file names: SPAbbrev.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 SPStrGen.pl; however, all the examples assume direct invocation of command line script works.

To generate a SPStructures.sdf file containing a structure specified by a command line SP abbreviation, type:

% SPStrGen.pl -r SPStructures -o "Cer(d18:0/0:0)"

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

% SPStrGen.pl -r SPStructures -o "SM(d18:0/16:0)" "SM(d19:0/24:1(15Z))"

To enumerate all possible SP structures and generate a SPStructures.sdf file, type:

% SPStrGen.pl -r SPStructures -o "*(*/*)"

or

% SPStrGen.pl -r SPStructures -o "*(*:*/*:*)"

AUTHOR

Manish Sud

CONTRIBUTOR

Eoin Fahy

SEE ALSO

CLStrGen.plFAStrGen.plGLStrGen.plGPStrGen.plSTStrGen.pl

COPYRIGHT

Copyright (C) 2006-2012. The Regents of the University of California. All Rights Reserved.

LICENSE

Modified BSD License

 

logo LIPID MAPS is funded by a Wellcome Trust.