mapping = {
chr1 = "hs_ref_chr1.fa.gz",
chr2 = "hs_ref_chr2.fa.gz"
}
NAME
gt-id_to_md5 - Change sequence IDs in given GFF3 files to MD5 fingerprints of the corresponding sequences.
SYNOPSIS
gt id_to_md5 [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)
- -subtargetids [yes|no]
-
substitute the target IDs with MD5 sums (default: yes)
- -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 -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:
or
function mapping(sequence_region) return "hs_ref_"..sequence_region..".fa.gz" end
The first form defines a Lua (http://www.lua.org) table named “mapping” which maps each sequence region to the corresponding sequence file. The second one defines a Lua function “mapping”, which has to return the sequence file name when it is called with the sequence_region as argument.
REPORTING BUGS
Report bugs to https://github.com/genometools/genometools/issues.