The format of your input sequence can be specified by adding -sformat Format on the command line, where Format is the name of a supported sequence format (Section A.1, “Supported Sequence Formats”). For example:

The format may also be specified in the USA of the input filename. For example:

The behaviour of -sformat and Format:: in a USA are identical. The format is not required, however. When reading in a sequence, EMBOSS will work out the sequence format by trying all known formats until one succeeds. Very few formats (only those that can be misinterpreted) are unsuitable for autodetection.

Here the input sequence is specified in the USA:

% seqret embl::L07770.embl -outseq L07770.fasta

% more L07770.fasta
>L07770 L07770.1 Xenopus laevis rhodopsin mRNA, complete cds.
ggtagaacagcttcagttgggatcacaggcttctagggatcctttgggcaaaaaagaaac
acagaaggcattctttctatacaagaaaggactttatagagctgctaccatgaacggaac
.......

In the example below, a sequence is read from GCG format and written in FASTA (default) format:

% cat L07770.gcg
!!NA_SEQUENCE 1.0

Xenopus laevis rhodopsin mRNA, complete cds.

L07770  Length: 1684  Type: N  Check: 9453 ..

    1 ggtagaacag cttcagttgg gatcacaggc ttctagggat cctttgggca

   51 aaaaagaaac acagaaggca ttctttctat acaagaaagg actttataga

  101 gctgctacca tgaacggaac agaaggtcca aatttttatg tccccatgtc
  .........................

% seqret L07770.gcg
Reads and writes (returns) sequences
output sequence(s) [L07770.fasta]: L077703.fasta

% cat L07770.fasta
>L07770
ggtagaacagcttcagttgggatcacaggcttctagggatcctttgggcaaaaaagaaac
acagaaggcattctttctatacaagaaaggactttatagagctgctaccatgaacggaac
.........

To read sequence(s) from a database, the database name and sequence id or accession number must be specified in the USA:

The database name must be already defined. The application showdb lists all known database definitions.

In the example below, entry P10932 is retrieved from the UniProt database via its accession number.

% seqret
Reads and writes (returns) sequences
Input sequence(s): uniprot:p10932
Output sequence [amir_pseae.fasta]: 

% more amir_pseae.fasta
>AMIR_PSEAE P10932 Aliphatic amidase regulator;
MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSI
FQNRHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLV
SARRISEEMAKLKQKTEQLQERIAGQARINQAKALLMQRHGWDEREAHQYLSREAMKRRE
PILKIAQELLGNEPSA
........

Here the same entry is retrieved by its database ID:

% seqret
Reads and writes (returns) sequences
Input sequence(s): uniprot:amir_pseae
Output sequence [amir_pseae.fasta]: p10932.fasta

%  more p10932.fasta 
>AMIR_PSEAE P10932 Aliphatic amidase regulator;
MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSI
FQNRHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLV
SARRISEEMAKLKQKTEQLQERIAGQARINQAKALLMQRHGWDEREAHQYLSREAMKRRE
PILKIAQELLGNEPSA
.......

To read sequence(s) from an input file, use FileName where FileName is the name of the source file. For example:

If the file contains more than one sequence, you can specify the sequence identifier or accession number in the same way as for databases:

If the file has no sequence identifier, or you need to specify a new sequence identifier, use the -sid qualifier. Note that this is also used for the default output file name.

EMBOSS determines whether a sequence is nucleotide or protein by the proportion of possible nucleotide characters in the sequence. It is usually correct, but might make a mistake with an unusually short and ambiguous sequence. You can force EMBOSS to accept that the sequence is nucleotide or protein using -snucleotide or -sprotein. These are boolean qualifiers and are set on if they are given on the command line. For example:

To specify a subsequence, use -sbegin Start and -send End, where Start and End are the start and end respectively of the region of interest. For example:

Or via the USA:

In practice, various styles of command line are supported (see Section 6.1, “Introduction to the EMBOSS Command Line”) and the qualifier names can be abbreviated so long as they remain unambiguous. The following command lines all tell seqret to read sequence P10932 in FASTA format, starting at base 25:

This may seem rather confusing, but only because there is no enforcement of a single way for users to specify the command lines. For general use, the first style above is strongly recommended.

The format of your output sequence can be specified with -osformat Format on the command line, where Format is the name of a supported sequence format (Section A.1, “Supported Sequence Formats”). In the following examples, -outseq is used to refer explicitly to the output parameter of seqret, which is the second parameter in the ACD file:

The format may also be specified in the USA of the output filename:

The behaviour of -osformat and Format:: in a USA is identical. It is not necessary to specify the output format however because EMBOSS will use FASTA format by default.

The following example reads sequence L07770 from the EMBL database and writes it to a file in GCG format:

%  seqret embl:L07770 -outseq gcg::L07770.gcg
Reads and writes (returns) sequences

%  cat L07770.gcg
!!NA_SEQUENCE 1.0

Xenopus laevis rhodopsin mRNA, complete cds.

L07770  Length: 1684  Type: N  Check: 9453 ..

    1 ggtagaacag cttcagttgg gatcacaggc ttctagggat cctttgggca

   51 aaaaagaaac acagaaggca ttctttctat acaagaaagg actttataga

  101 gctgctacca tgaacggaac agaaggtcca aatttttatg tccccatgtc

.........................

This example reads entry L07770 from EMBL and writes it to L07770.ncbi in NCBI format.

%  seqret embl:L07770 L07770.ncbi -osformat ncbi
Reads and writes (returns) sequences

%  cat L077704.ncbi
>gnl|embl|L07770 (L07770.1) Xenopus laevis rhodopsin mRNA, complete cds.
ggtagaacagcttcagttgggatcacaggcttctagggatcctttgggcaaaaaagaaac
acagaaggcattctttctatacaagaaaggactttatagagctgctaccatgaacggaac

Command lines to write sequences in the file myfile.seq to the output file myfile.seqout in the format EMBL are:

The output file name defaults to the sequence identifier in lower case as the base name, and the sequence output format as the extension. These can be overridden with -osname FileBaseName and -osextension FileExtension, where FileBaseName is the base name of the output file and FileExtension is the filename extension. For example:

Or to do this via the USA:

In some output sequence formats (e.g. NCBI) the output includes the sequence identifier and a database name. NCBI format defaults to 'unk' for an unknown database, or uses the database name of the input sequence. The database name can be specified or replaced using -osdbname DatabaseName where DatabaseName is the name of the database to be used in the output file. For example:

Similarly, the output sequence identifier can be specified or replaced with the -sid input qualifier:

It is also possible to specify the database name with the -sdbname input qualifier, but only if the sequence is read from a file as any input database name takes precedence.

Not all of the sequence formats can hold multiple sequences. Some formats, such as gcg, plain, raw and staden have no indication of where the sequence ends and the next sequence starts. They cannot, therefore, hold more than one sequence.

To write multiple sequences to a new file per sequence, you can use the -ossingle qualifier. Any output file name specified will be ignored and names of output files will be assigned automatically from the sequence ID name, with the format name used as the extension. So a sequence with the ID name IXI_567 being written in gcg format would be written to the file ixi_567.gcg. For example:

One output file would be created for each file in myfile.seq. Even though the output file (myfile.seqout) was specified, this would be ignored and files with names of EntryName.gcg would be generated.

Sequence output can be printed to the screen rather than a file or database. This is useful if you want to see the output immediately after running the program, for example, when testing an application. It is also useful to pipe output to another application on UNIX. To do this you specify stdout in place of the file name. stdout is the standard UNIX filename for the screen. For example:

Or to do this via the USA:

The format of your input features can be specified by adding -fformat Format on the command line, where Format is the name of a supported feature format (Section A.2, “Supported Feature Formats”). For example:

The name of a raw features file can be set directly by adding -fopenfile FileName where FileName is the name of the raw features file. For example:

The file name and format may also be specified in the UFO of the input filename. For example:

The behaviour of -fformat and Format:: in a UFO is identical. The format is not required, however. When reading in features, EMBOSS will guess the sequence feature format by trying all known formats until one succeeds.

In this example, showfeat is used to extract features from the EMBL entry U23808:

%  showfeat embl:U23808
Show features of a sequence.
Output file [U23808.showfeat]: 

%  cat U23808.showfeat 
U23808
Xenopus laevis rhodopsin gene, complete cds.
|==========================================================| 4734
|----------------------------------------------------------> source
             |----->                                         mRNA
               |--->                                         CDS
                       |->                                   CDS
                       |->                                   mRNA
                                |->                          CDS
                                |->                          mRNA
                                      |-->                   CDS
                                      |-->                   mRNA
                                                  |>         CDS
                                                  |------->  mRNA

The -feature option of seqret is used extract the sequence with its features from the EMBL entry U23808:

%  seqret -feature embl:U23808
Reads and writes (returns) sequences
Output sequence [U23808.fasta]: 

%  cat U23808.gff
##gff-version 3
#!sequence-region U23808 1 8914
#!date 2008-03-10
#!Type DNA
#!Source-version EMBOSS 6.1.0
U23808 EMBL databank_entry 1    8194 0.000 + . ID="U23808.1";
          organism="Xenopus laevis";mol_type="genomic DNA";db_xref="taxon:8355"
U23808 EMBL promoter 5128 5360 0.000 + . ID="U23808.2"
U23808 EMBL sequence_feature 5128 5158 0.000 + . ID="U23808.3";
          note="XOP4 cis element"
U23808 EMBL sequence_feature 5191 5215 0.000 + . ID="U23808.4";
          note="XOP3 cis element"
U23808 EMBL sequence_feature 5225 5239 0.000 + . ID="U23808.5";
          note="Ret1 cis element"
U23808 EMBL sequence_feature 5254 5270 0.000 + . ID="U23808.6";
          note="Bat1 cis element"
U23808 EMBL sequence_feature 5277 5302 0.000 + . ID="U23808.7";
          note="NRE cis element"
U23808 EMBL sequence_feature 5309 5318 0.000 + . ID="U23808.8";
          note="Ret4 cis element"
U23808 EMBL mRNA 5361 5830 0.000 + . ID="U23808.9";featflags="0x100";
          product="rhodopsin"
U23808 EMBL mRNA 6079 6247 0.000 + . ID="U23808.9";featflags="0x104"
U23808 EMBL mRNA 6849 7014 0.000 + . ID="U23808.9";featflags="0x104"
U23808 EMBL mRNA 7265 7504 0.000 + . ID="U23808.9";featflags="0x104"
U23808 EMBL mRNA 8210 8867 0.000 + . ID="U23808.9";featflags="0x104"
U23808 EMBL CDS 5470 5830 0.000 + 0 ID="U23808.10";featflags="0x100";
         codon_start=1;product="rhodopsin";
         note="cDNA sequence deposited under GenBank Accession Number L07770";
         db_xref="GOA:P29403";db_xref="HSSP:1F88";db_xref="InterPro:IPR017452";
         db_xref="UniProtKB/Swiss-Prot:P29403";protein_id="AAC59901.1";
         translation="MNGTEGPN...SQVSPA"
U23808 EMBL CDS 6079 6247 0.000 + 0 ID="U23808.10";featflags="0x104"
U23808 EMBL CDS 6849 7014 0.000 + 0 ID="U23808.10";featflags="0x104"
U23808 EMBL CDS 7265 7504 0.000 + 0 ID="U23808.10";featflags="0x104"
U23808 EMBL CDS 8210 8338 0.000 + 0 ID="U23808.10";featflags="0x104"

To read a raw feature table from file, you must either name it explicitly using -fopenfile as shown above, or specify the -ufo on the command line; this is specific to the sequence datatypes (see Section 6.4.2, “Sequences”). For example:

This behaviour cannot be set in the sequence USA directly: -ufo must be used for separate feature input with any sequence. For example:

In the example below, seqret is used to read features (-feature) from the file U23808.gff which is specified as containing a feature table (-ufo) with automatically detected format, and to write the features out in EMBL format to the file U23808.embl:

%  seqret -feature myfile.seq -ufo U23808.gff embl::U23808.embl
Reads and writes (returns) sequences

%  cat U23808.embl
ID   U23808    standard; DNA; UNC; 4734 BP.
AC   U23808;
SV   U23808.1
DE   Xenopus laevis rhodopsin gene, complete cds.
FH   Key             Location/Qualifiers
FH
FT   source          1..4734
FT                   /db_xref="taxon:8355"
FT                   /mol_type="genomic DNA"
FT                   /organism="Xenopus laevis"
FT   mRNA            join(1181..1650,1899..2067,2669..2834,3085..3324,
FT                   4030..4687)
FT                   /product="rhodopsin"
FT   CDS             join(1290..1650,1899..2067,2669..2834,3085..3324,
FT                   4030..4158)
FT                   /codon_start=1
FT                   /db_xref="GOA:P29403"
FT                   /db_xref="HSSP:1F88"
FT                   /db_xref="UniProt/Swiss-Prot:P29403"
FT                   /note="cDNA sequence deposited under GenBank Accession
FT                   Number L07770"
FT                   /product="rhodopsin"
FT                   /protein_id="AAC59901.1"
FT                   /translation="MNGTEGPNFYVPMSNKTGVVRSPFDYPQYYLAEPWQYSALAAYMF
FT                   LLILLGLPINFMTLFVTIQHKKLRTPLNYILLNLVFANHFMVLCGFTVTMYTSMHGYFI
FT                   FGQTGCYIEGFFATLGGEVALWSLVVLAVERYMVVCKPMANFRFGENHAIMGVAFTWIM
FT                   ALSCAAPPLFGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFIVHFTIPLIVIFFC
FT                   YGRLLCTVKEAAAQQQESATTQKAEKEVTRMVVIMVVFFLICWVPYAYVAFYIFTHQGS
FT                   NFGPVFMTVPAFFAKSSAIYNPVIYIVLNKQFRNCLITTLCCGKNPFGDEDGSSAATSK
FT                   TEASSVSSSQVSPA"
SQ   Sequence 4734 BP; 1315 A; 1046 C; 985 G; 1388 T; 0 other;
     cgtaactagg accccaggtc gacacgacac cttccctttc ccagttattt cccctgtaga        60
     cgttagaagg ggaaggggtg tacttatgtc acgacgaact acgtccttga ctacttaggg       120

On input, a region of features can be specified by using -fbegin and -fend. You can force a program to prompt for these values, and also the sense in a nucleotide sequence, by specifying -fask on the command line.

All the common feature formats (Section A.2, “Supported Feature Formats”) are supported for output. If a program is capable of writing out sequences with features (for example seqret -feature), then the feature table will be written out as part of the output sequence file, if the format of the sequence file was designed to hold a feature table, i.e. is one of:

If the specified output sequence format cannot hold a feature table (e.g. FASTA format), then a file with the extension .gff is written with the feature table in GFF format.

The -ofname and -offormat options enable you to specify a name and format for separate output to a feature table file, even for formats that are capable of holding the feature table with its sequence.

The format of your output features can be specified by adding -offormat Format on the command line, where Format is the name of a supported output feature format (Section A.2, “Supported Feature Formats”). In the following examples, the output parameter is named explicitly (-outseq) because seqret has two parameters but only the second parameter in the ACD file is specified on the command line:

The file name can be set directly with -ofname FileName where FileName is the name of the features file. For example:

The file name and format may also be specified together in a UFO string. For example:

The output directory (-ofdirectory) and file name -ofname may be set for the feature output files. If these are not set then the output files will be assigned names automatically from the sequence ID name, with the format name used as the extension, and written to the current directory. So a sequence with the ID name IXI_567 being written in gcg format would be written to the file ixi_567.gcg with features in the file ixi_567.gff.

The behaviour of -offormat and Format:: in a UFO is identical. The output format is not required, however. When writing features, EMBOSS will use GFF by default.