gt-convertseq(1) Parse and convert sequence file formats (FASTA/FASTQ, GenBank, EMBL).


gt convertseq [options] file [...]


-v [yes|no]

be verbose (default: no)

-r [yes|no]

reverse complement sequences (default: no)

-showfilelengthvalues [yes|no]

show filelengths (default: no)

-noseq [yes|no]

do not show sequences (default: no)

-fastawidth [value]

FASTA output line width, 0 for unlimited (default: 60)

-contractdnawc [yes|no]

replace stretches of DNA wildcards with a single N (default: no)

-contractproteinwc [yes|no]

replace stretches of protein wildcards with a single X (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)


display help and exit


display version information and exit


Report bugs to <[email protected]>.