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gt-select - Online in the Cloud

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This is the command gt-select that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


gt-select - Select certain features (specified by the used options) from given GFF3
file(s).

SYNOPSIS


gt select [option ...] [GFF3_file ...]

DESCRIPTION


-retainids [yes|no]
when available, use the original IDs provided in the source file (memory consumption
is proportional to the input file size(s)) (default: no)

-seqid [string]
select feature with the given sequence ID (all comments are selected). (default:
undefined)

-source [string]
select feature with the given source (the source is column 2 in regular GFF3 lines)
(default: undefined)

-contain [start end]
select all features which are contained in the given range (default: undefined)

-overlap [start end]
select all features which do overlap with the given range (default: undefined)

-strand [string]
select all top-level features(i.e., features without parents) whose strand equals the
given one (must be one of +-.?) (default: undefined)

-targetstrand [string]
select all top-level features (i.e., features without parents) which have exactly one
target attribute whose strand equals the given one (must be one of +-.?) (default:
undefined)

-targetbest [yes|no]
if multiple top-level features (i.e., features without parents) with exactly one
target attribute have the same target_id, keep only the feature with the best score.
If -targetstrand is used at the same time, this option is applied after -targetstrand.
Memory consumption is proportional to the input file size(s). (default: no)

-hascds [yes|no]
select all top-level features which do have a CDS child (default: no)

-maxgenelength [value]
select genes up to the given maximum length (default: undefined)

-maxgenenum [value]
select the first genes up to the given maximum number (default: undefined)

-mingenescore [value]
select genes with the given minimum score (default: undefined)

-maxgenescore [value]
select genes with the given maximum score (default: undefined)

-minaveragessp [value]
set the minimum average splice site probability (default: undefined)

-rule_files
specify Lua filter rule files to be used for selection (terminate list with --)

-rule_logic [...]
select how multiple Lua files should be combined choose from AND|OR (default: AND)

-dropped_file [filename]
save non-selected features to file (default: undefined)

-v [yes|no]
be verbose (default: no)

-o [filename]
redirect output to specified file (default: undefined)

-gzip [yes|no]
write gzip compressed output file (default: no)

-bzip2 [yes|no]
write bzip2 compressed output file (default: no)

-force [yes|no]
force writing to output file (default: no)

-help
display help and exit

-version
display version information and exit

File format for option -rule_files:

The files supplied to option -rule_files define a function for filtering by user given
criteria (see example below):

function filter(gn)
target = "exon"
for curnode in gn:children() do
if (curnode:get_type() == target) then
return false
end
end
return true
end

The above function iterates over all children of gn and checks whether there is a node of
type exon. If there is such a node the function returns false, indicating that the parent
node gn will not be sorted out.

NOTE: The function must be named filter and must return false, indicating that the node
survived the filtering process.

REPORTING BUGS


Report bugs to <[email protected]>.

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