gt-select - Online in the Cloud

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]>.

Use gt-select online using onworks.net services