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GT-SPLICESITEINFO(1) | GenomeTools Manual | GT-SPLICESITEINFO(1) |
NAME¶
gt-splicesiteinfo - Show information about splice sites given in GFF3 files.SYNOPSIS¶
gt splicesiteinfo [option ...] [GFF3_file ...]DESCRIPTION¶
-seqfile [filename]set the sequence file from which to take the sequences
(default: undefined)
-encseq [filename]
set the encoded sequence indexname from which to take the
sequences (default: undefined)
-seqfiles
set the sequence files from which to extract the features
use -- to terminate the list of sequence files
-matchdesc [yes|no]
search the sequence descriptions from the input files for
the desired sequence IDs (in GFF3), reporting the first match (default:
no)
-matchdescstart [yes|no]
exactly match the sequence descriptions from the input
files for the desired sequence IDs (in GFF3) from the beginning to the first
whitespace (default: no)
-usedesc [yes|no]
use sequence descriptions to map the sequence IDs (in
GFF3) to actual sequence entries. If a description contains a sequence range
(e.g., III:1000001..2000000), the first part is used as sequence ID (
III) and the first range position as offset ( 1000001) (default:
no)
-regionmapping [string]
set file containing sequence-region to sequence file
mapping (default: undefined)
-addintrons [yes|no]
add intron features between existing exon features
(before computing the information to be shown) (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 -regionmapping:
The file supplied to option -regionmapping defines a “mapping”. A
mapping maps the sequence-region entries given in the GFF3_file to a
sequence file containing the corresponding sequence. Mappings can be defined
in one of the following two forms:
mapping = { chr1 = "hs_ref_chr1.fa.gz", chr2 = "hs_ref_chr2.fa.gz" }
function mapping(sequence_region) return "hs_ref_"..sequence_region..".fa.gz" end
REPORTING BUGS¶
Report bugs to <gt-users@genometools.org>.07/29/2016 | GenomeTools 1.5.9 |