Scroll to navigation

GT-SEQ(1) GenomeTools Manual GT-SEQ(1)

NAME

gt-seq - Parse the given sequence file(s) and construct the corresponding index files.

SYNOPSIS

gt seq [option ...] sequence_file [...]

DESCRIPTION

-recreate [yes|no]
recreate index files, even if they exist already (default: no)
-showfasta [yes|no]
show all sequences (in FASTA format) (default: no)
-showseqnum [value]
show sequence with given number (sequences are counted from 1 unless -seqnum_from_0 is specified) (default: undefined)
-showseqlength [value]
show length of sequence with given number (sequences are counted from 1 unless -seqnum_from_0 is specified) (default: undefined)
-showseqnum_inputfile [filename]
show sequence with given numbers specified line by line in given file (sequences are counted from 1 unless -seqnum_from_0 is specified) (default: undefined)
-seqnum_from_0 [yes|no]
for options -showseqnum and -showseqnum_inputfile: count sequence numbers from 0 instead of 1 (default: no)
-gc-content [yes|no]
print GC-content (for DNA files) (default: no)
-stat [yes|no]
show sequence statistics (default: no)
-seqlengthdistri [yes|no]
show sequence length distribution (default: no)
-width [value]
set output width for FASTA sequence printing (0 disables formatting) (default: 0)
-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

REPORTING BUGS

Report bugs to <gt-users@genometools.org>.
07/29/2016 GenomeTools 1.5.9