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>.