gt-seq1
Parse the given sequence file(s) and construct the corresponding index files.
Usage
gt seq
[option ...]
sequence_file
[]
Overview
-
-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
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.
-seqnum_from_0 since Debian 9 (Stretch);
-showseqlength since Debian 9 (Stretch);
-showseqnum_inputfile since Debian 9 (Stretch).