| Qualifier |
Type |
Description |
Allowed values |
Default |
| Standard (Mandatory) qualifiers |
[-seqall]
(Parameter 1) |
seqall |
Nucleotide sequence(s) filename and optional format, or reference (input USA) |
Readable sequence(s) |
Required |
[-outfile]
(Parameter 2) |
outfile |
Output file name |
Output file |
<*>.coderet |
[-cdsoutseq]
(Parameter 3) |
seqoutall |
Coding nucleotide output sequence(s) (optional) |
Writeable sequence(s) |
<*>.format |
[-mrnaoutseq]
(Parameter 4) |
seqoutall |
Messenger RNA nucleotide output sequence(s) (optional) |
Writeable sequence(s) |
<*>.format |
[-translationoutseq]
(Parameter 5) |
seqoutall |
Translated coding protein output sequence(s) (optional) |
Writeable sequence(s) |
<*>.format |
[-restoutseq]
(Parameter 6) |
seqoutall |
Non-coding nucleotide output sequence(s) (optional) |
Writeable sequence(s) |
<*>.format |
| Additional (Optional) qualifiers |
| (none) |
| Advanced (Unprompted) qualifiers |
| (none) |
| Associated qualifiers |
| "-seqall" associated seqall qualifiers
|
-sbegin1
-sbegin_seqall |
integer |
Start of each sequence to be used |
Any integer value |
0 |
-send1
-send_seqall |
integer |
End of each sequence to be used |
Any integer value |
0 |
-sreverse1
-sreverse_seqall |
boolean |
Reverse (if DNA) |
Boolean value Yes/No |
N |
-sask1
-sask_seqall |
boolean |
Ask for begin/end/reverse |
Boolean value Yes/No |
N |
-snucleotide1
-snucleotide_seqall |
boolean |
Sequence is nucleotide |
Boolean value Yes/No |
N |
-sprotein1
-sprotein_seqall |
boolean |
Sequence is protein |
Boolean value Yes/No |
N |
-slower1
-slower_seqall |
boolean |
Make lower case |
Boolean value Yes/No |
N |
-supper1
-supper_seqall |
boolean |
Make upper case |
Boolean value Yes/No |
N |
-scircular1
-scircular_seqall |
boolean |
Sequence is circular |
Boolean value Yes/No |
N |
-squick1
-squick_seqall |
boolean |
Read id and sequence only |
Boolean value Yes/No |
N |
-sformat1
-sformat_seqall |
string |
Input sequence format |
Any string |
|
-iquery1
-iquery_seqall |
string |
Input query fields or ID list |
Any string |
|
-ioffset1
-ioffset_seqall |
integer |
Input start position offset |
Any integer value |
0 |
-sdbname1
-sdbname_seqall |
string |
Database name |
Any string |
|
-sid1
-sid_seqall |
string |
Entryname |
Any string |
|
-ufo1
-ufo_seqall |
string |
UFO features |
Any string |
|
-fformat1
-fformat_seqall |
string |
Features format |
Any string |
|
-fopenfile1
-fopenfile_seqall |
string |
Features file name |
Any string |
|
| "-outfile" associated outfile qualifiers
|
-odirectory2
-odirectory_outfile |
string |
Output directory |
Any string |
|
| "-cdsoutseq" associated seqoutall qualifiers
|
-osformat3
-osformat_cdsoutseq |
string |
Output seq format |
Any string |
|
-osextension3
-osextension_cdsoutseq |
string |
File name extension |
Any string |
cds |
-osname3
-osname_cdsoutseq |
string |
Base file name |
Any string |
|
-osdirectory3
-osdirectory_cdsoutseq |
string |
Output directory |
Any string |
|
-osdbname3
-osdbname_cdsoutseq |
string |
Database name to add |
Any string |
|
-ossingle3
-ossingle_cdsoutseq |
boolean |
Separate file for each entry |
Boolean value Yes/No |
N |
-oufo3
-oufo_cdsoutseq |
string |
UFO features |
Any string |
|
-offormat3
-offormat_cdsoutseq |
string |
Features format |
Any string |
|
-ofname3
-ofname_cdsoutseq |
string |
Features file name |
Any string |
|
-ofdirectory3
-ofdirectory_cdsoutseq |
string |
Output directory |
Any string |
|
| "-mrnaoutseq" associated seqoutall qualifiers
|
-osformat4
-osformat_mrnaoutseq |
string |
Output seq format |
Any string |
|
-osextension4
-osextension_mrnaoutseq |
string |
File name extension |
Any string |
mrna |
-osname4
-osname_mrnaoutseq |
string |
Base file name |
Any string |
|
-osdirectory4
-osdirectory_mrnaoutseq |
string |
Output directory |
Any string |
|
-osdbname4
-osdbname_mrnaoutseq |
string |
Database name to add |
Any string |
|
-ossingle4
-ossingle_mrnaoutseq |
boolean |
Separate file for each entry |
Boolean value Yes/No |
N |
-oufo4
-oufo_mrnaoutseq |
string |
UFO features |
Any string |
|
-offormat4
-offormat_mrnaoutseq |
string |
Features format |
Any string |
|
-ofname4
-ofname_mrnaoutseq |
string |
Features file name |
Any string |
|
-ofdirectory4
-ofdirectory_mrnaoutseq |
string |
Output directory |
Any string |
|
| "-translationoutseq" associated seqoutall qualifiers
|
-osformat5
-osformat_translationoutseq |
string |
Output seq format |
Any string |
|
-osextension5
-osextension_translationoutseq |
string |
File name extension |
Any string |
prot |
-osname5
-osname_translationoutseq |
string |
Base file name |
Any string |
|
-osdirectory5
-osdirectory_translationoutseq |
string |
Output directory |
Any string |
|
-osdbname5
-osdbname_translationoutseq |
string |
Database name to add |
Any string |
|
-ossingle5
-ossingle_translationoutseq |
boolean |
Separate file for each entry |
Boolean value Yes/No |
N |
-oufo5
-oufo_translationoutseq |
string |
UFO features |
Any string |
|
-offormat5
-offormat_translationoutseq |
string |
Features format |
Any string |
|
-ofname5
-ofname_translationoutseq |
string |
Features file name |
Any string |
|
-ofdirectory5
-ofdirectory_translationoutseq |
string |
Output directory |
Any string |
|
| "-restoutseq" associated seqoutall qualifiers
|
-osformat6
-osformat_restoutseq |
string |
Output seq format |
Any string |
|
-osextension6
-osextension_restoutseq |
string |
File name extension |
Any string |
noncoding |
-osname6
-osname_restoutseq |
string |
Base file name |
Any string |
|
-osdirectory6
-osdirectory_restoutseq |
string |
Output directory |
Any string |
|
-osdbname6
-osdbname_restoutseq |
string |
Database name to add |
Any string |
|
-ossingle6
-ossingle_restoutseq |
boolean |
Separate file for each entry |
Boolean value Yes/No |
N |
-oufo6
-oufo_restoutseq |
string |
UFO features |
Any string |
|
-offormat6
-offormat_restoutseq |
string |
Features format |
Any string |
|
-ofname6
-ofname_restoutseq |
string |
Features file name |
Any string |
|
-ofdirectory6
-ofdirectory_restoutseq |
string |
Output directory |
Any string |
|
| General qualifiers |
| -auto |
boolean |
Turn off prompts |
Boolean value Yes/No |
N |
| -stdout |
boolean |
Write first file to standard output |
Boolean value Yes/No |
N |
| -filter |
boolean |
Read first file from standard input, write first file to standard output |
Boolean value Yes/No |
N |
| -options |
boolean |
Prompt for standard and additional values |
Boolean value Yes/No |
N |
| -debug |
boolean |
Write debug output to program.dbg |
Boolean value Yes/No |
N |
| -verbose |
boolean |
Report some/full command line options |
Boolean value Yes/No |
Y |
| -help |
boolean |
Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose |
Boolean value Yes/No |
N |
| -warning |
boolean |
Report warnings |
Boolean value Yes/No |
Y |
| -error |
boolean |
Report errors |
Boolean value Yes/No |
Y |
| -fatal |
boolean |
Report fatal errors |
Boolean value Yes/No |
Y |
| -die |
boolean |
Report dying program messages |
Boolean value Yes/No |
Y |
| -version |
boolean |
Report version number and exit |
Boolean value Yes/No |
N |