gthgetseq - get FASTA sequences from GenomeThreader files
gthgetseq -getcdna | -getprotein | -getgenomic [option ...]
[file ...]
Get FASTA sequences from GenomeThreader files containing
intermediate results. The sequences are shown on stdout.
-getcdna
get cDNA/EST sequences default: no
-getcdnacomp
get complement of cDNA/EST sequences default: no
-getprotein
get protein sequences default: no
-getproteincomp
get complement of protein sequences default: no
-getgenomic
get genomic sequences default: no
-getgenomiccomp
get complement of genomic sequences default: no
-minalignmentscore
set the minimum alignment score for spliced alignments to
be included into the set of spliced alignments default: 0.00
-maxalignmentscore
set the maximum alignment score for spliced alignments to
be included into the set of spliced alignments default: 1.00
-mincoverage
set the minimum coverage for spliced alignments to be
included into the set of spliced alignments default: 0.00
-maxcoverage
set the maximum coverage for spliced alignments to be
included into the set of spliced alignments default: 9999.99
-gzip
gzip compressed input file(s) default: no
-bzip2
bzip2 compressed input file(s) default: no
-help
display help and exit
-version
display version information and exit