EMBOSS: seqret

| ## EMBOSS: seqret

# Program seqret

## Function

Reads and writes (returns) sequences

## Description

The simplicity of the above description of this program greatly understates the rich functionality of this program.

Because EMBOSS programs can take a wide range of qualifiers that slightly change the behaviour of the program when reading or writing a sequence, this program can do many more things than simply "read and write a sequence".

seqret can read a sequence or many sequences from databases, files, files of sequence names, the command-line or the output of other programs and then can write them to files, the screen or pass them to other programs. Because it can read in a sequence from a database and write it to a file, seqret is a program for extracting sequences from databases. Because it can write the sequence to the screen, seqret is a program for displaying sequences.

seqret can read sequences in any of a wide range of standard sequence formats. You can specify the input and output formats being used. If you don't specify the input format, seqret will try a set of possible formats until it reads it in successfully. Because you can specify the output sequence format, seqret is a program to reformat a sequence.

seqret can read in the reverse complement of a nucleic acid sequence. It therefore is a program for producing the reverse complement of a sequence.

seqret can read in a sequence whose begin and end positions you have specified and write out that fragment. It is therefore a utility for doing simple extraction of a region of a sequence.

seqret can change the case of the sequence being read in to upper or to lower case. It is therefore a simple sequence beautification utility.

seqret can do any combination of the above functions.

The sequence input and output specification of this (and many other EMBOSS programs) is described as being a Uniform Sequence Address.

The Uniform Sequence Address, or USA, is a somewhat tongue-in-cheek reference to a URL-style sequence naming used by all EMBOSS applications.

The USA is a very flexible way of specifying one or more sequences from a variety of sources and includes sequence files, database queries and external applications.

The basic USA syntax is one of:

- "file"
- "file:entry"
- "format::file"
- "format::file:entry"
- "database:entry"
- "database"
- "@file"

Note that ':' separates the name of a file containing many possible entries from the specific name of a sequence entry in that file. It also separates the name of a database from an entry in that database

Note also that '::' separates the specified format of a file from the name of the file. Normally the format can be omitted, in which case the program will attempt to identify the correct format when reading the sequence in and will default to using FASTA format when writing the sequence out.

Valid names of the databases set up in your local implementation of EMBOSS can be seen by using the program 'showdb'.

Database queries, and individual entries in files that have more than one sequence entry, use wildcards of "?" for any character and "*" for any string of characters. There are some problems with the Unix shell catching these characters so they do need to be hidden in quotes or preceded by a backslash on the Unix command line, (for example "embl:hs\*")

The output USA name 'stdout' is special. It makes the output go to the device 'standard output'. This is the screen, by default.

### Example USAs

The following are valid USAs for sequences:

USA | Description
--- | ---
xxx.seq | A sequence file "xxx.seq" in any format
fasta::xxx.seq | A sequence file "xxx.seq" in fasta format
gcg::egmsmg.gcg | A sequence file "egmsmg.gcg" in GCG 9 format
egmsmg.gcg -sformat=gcg | A sequence file "egmsmg.gcg" in GCG 9 format
embl::paamir.em | A sequence file "paamir.em" in EMBL format
embl:paamir | EMBL entry PAAMIR, using whatever access method is defined locally for the EMBL database
embl:X13776 | EMBL entry X13776, using whatever access method is defined locally for the EMBL database and searching by accession number and entry name (X13776 is the accession number in this case)
embl-acc:X13776 | EMBL entry X13776, using whatever access method is defined locally for the EMBL database and searching by accession number only
embl-id:paamir | EMBL entry PAAMIR, using whatever access method is defined locally for the EMBL database, and searching by ID only
embl:paami* | EMBL entries PAAMIB, PAAMIE and so on, usually in alphabetical order, using whatever access method is defined locally for the EMBL database
embl or EMBL:* | All sequences in the EMBL database
@mylist | Reads file mylist and uses each line as a separate USA. This is standard VMS list file syntax, also used in SRS 4.0 but missing in SRS 5.0. The list file is a list of USAs (one per line). List files can contain references to other lists files or any other standard USA.
list::mylist | Same as "@mylist" above
'getz -e [embl-id:paamir] |' | The pipe character "|" causes EMBOSS to fire up getz (SRS 5.1) to extract entry PAAMIR from EMBL in EMBL format. Any application or script which writes one or more sequences to stdout can be used in this way.
asis::atacgcagttatctgaccat | So far the shortest USA we could invent. In 'asis' format the name is the sequence so no file needs to be opened. This is a special case. It was intended as a joke, but could be quite useful for generating command lines.

### Input sequence formats

To date, the following sequence formats are accepted as input.

By default, (i.e. if no format is explicitly specified) EMBOSS tries each format in turn until one succeeds.

Input Format | Comments
--- | ---
gcg | GCG 9.x and 10.x format with the format and sequence type identified on the first line of the file
gcg8 | GCG 8.x format where anything up to the first line containing ".." is considered as heading, and the remainder is sequence data. This format is complicated by the header appearing to be in other formats such as EMBL, and by the possibility of reading a large amount of data in the wrong format before discovering that there is no ".." line because it is not GCG format after all.
embl em | EMBL entry format, or at least a minimal subset of the fields. The Staden package and others use EMBL or similar formats for sequence data.
swiss sw | SWISSPROT entry format, or at least a minimal subset of the fields.
fasta pearson | FASTA format with an optional accession number after the sequence identifier, eg: >name description or >name accession description and with an optional database name in GCG style fasta format included as part of the sequence identifier, eg: >database:name accession description
ncbi | FASTA format with optional accession number and database name in NCBI style included as part of the sequence identifier. eg >database|accession|id description (and other variants on this theme!)
genbank gb | GENBANK entry format, or at least a minimal subset of the fields.
nbrf pir | NBRF (PIR) format, as used in the PIR database sequence files.
codata | CODATA format.
strider | DNA strider format
clustal aln | ClustalW ALN (multiple alignment) format.
phylip | PHYLIP non-interleaved multiple alignment format.
acedb | ACeDB format
msf | Wisconsin Package GCG's MSF multiple sequence format.
hennig86 | Hennig86 format
jackknifer | Jackknifer format
jackknifernon | Jackknifernon format
nexus paup | Nexus/PAUP format
nexusnon paupnon | Nexusnon/PAUPnon format
treecon | Treecon format
mega | Mega format
meganon | Meganon format
ig | IntelliGenetics format.
staden experiment | The experiment file format used by the "gap" program in the Staden package, where the sequence identifier is optional and the remainer is plain text. Some alternative nucleotide ambiguity codes are used and must be converted.
unknown text plain | Plain text. This is the format with no format. The whole of the file is read in as a sequence. No attempt is made to parse the file contents in any way. Anything is acceptable in this format.
raw | Like unknown/text/plain format except that it accepts only alphanumeric and whitespace characters and rejects anything else.
asis | This is not so much a sequence format as a quick way of entering a sequence on the command line, but it is included here for completeness. Where a filename would normally be given, in asis format there is the sequence itself. An example would be: asis::atacgcagttatctgaccat In 'asis' format the name is the sequence so no file needs to be opened. This is a special case. It was intended as a joke, but could be quite useful for generating command lines.

### Output sequence formats

To date, the following sequence formats are available as output.

Some sequence formats can hold multiple sequences in one file, these are marked as multiple in the following table. The details of how many sequences are held in one file differs between formats, but they either allow many sequences to be concatenated one after the other, or they hold the sequences together in some sort of aligned set of sequences.

Other formats, such as GCG, plain and staden formats can only hold one sequence per file, these are marked as single. An attempt to concatenate several sequences in one file leaves the results as a mess that makes it impossible to decide where the sequences start and end or what is annotation and what is sequence.

These single formats therefore cause problems when there are multiple sequences to write out because a single file containing multiple sequences in that format is invalid. When these formats are specified for output, an EMBOSS program will allow you to write many sequences to one file, but EMBOSS programs will not be able to reliably read in the resulting mess.

N.B This behaviour changed in EMBOSS version 1.7.0. (31 Oct 2000) Previously, EMBOSS programs that were asked to write multiple sequences in a single format whould ignore the requested output file name and would write each sequence into a separate file whose name was constructed from the sequence name and the name of the format. This resulted in ouput to files whose names could not be reliably controlled. A decision was taken that EMBOSS users were intelligent people who could live with the consequences of their actions and who could learn not to write out multiple sequences to a file in formats that could not cope with multiple sequences.

It you really wish to write multiple sequences out in formats that can not cope with multiple sequences, you are advised to add the global qualifier -ossingle on the command line. This will force the EMBOSS program to ignore the given output file name and will generate its own file names. One sequence will be written to each such file. These file names are made from the sequence ID name, with the name of the format as the extension (e.g. hsfau.gcg).

This is not ideal. Preferably, you should stay away from formats that can't cope with multiple sequences in a file.

Output Format | Single/ Multiple | Comments
--- | --- | ---
gcg | single | Wisconsin Package GCG 9.x and 10.x format with the sequence type on the first line of the file.
gcg8 | single | GCG 8.x format where anything up to the first line containing ".." is considered as heading, and the remainder is sequence data.
embl em | multiple | EMBL entry format with available fields filled in and others with no infomation omitted. The EMBOSS command line allows missing data such as accession numbers to be provided if they are not obtainable from the input sequence.
swiss sw | multiple | SwisProt entry format with available fields filled in and others with no infomation omitted. The EMBOSS command line allows missing data such as accession numbers to be provided if they are not obtainable from the input sequence.
fasta | multiple | Standard Pearson FASTA format, but with the accession number included after the identifier if available.
pearson | multiple | Simple Pearson FASTA format, an alias for "fasta" format.
ncbi | multiple | NCBI style FASTA format with the database name, entry name and accession number separated by pipe ("|") characters.
nbrf pir | multiple | NBRF (PIR) format, as used in the PIR database sequence files.
genbank gb | multiple | GENBANK entry format with available fields filled in and others with no infomation omitted. The EMBOSS command line allows missing data such as accession numbers to be provided if they are not obtainable from the input sequence.
ig | multiple | Intelligenetics format, as used by the Intelligenetics package
codata | multiple | CODATA format.
strider | multiple | DNA strider format
acedb | multiple | ACeDB format
staden experiment | single | The experiment file format used by the "gap" program in the Staden package. Some alternative nucleotide ambiguity codes are used and are converted.
text plain raw | single | Plain sequence, no annotation or heading.
fitch | multiple | Fitch format
msf | multiple | Wisconsin Package GCG's MSF multiple sequence format.
clustal aln | multiple | Clustal multiple sequence format.
phylip | multiple | PHYLIP non-interleaved format.
phylip3 | multiple | PHYLIP interleaved format.
asn1 | multiple | A subset of ASN.1 containing entry name, accession number, description and sequence, similar to the current ASN.1 output of readseq
hennig86 | multiple | Hennig86 format
mega | multiple | Mega format
meganon | multiple | Meganon format
nexus paup | multiple | Nexus/PAUP format
nexusnon paupnon | multiple | Nexusnon/PAUPnon format
jackknifer | multiple | Jackknifer format
jackknifernon | multiple | Jackknifernon format
treecon | multiple | Treecon format
debug | multiple | EMBOSS sequence object report for debugging showing all available fields. Not all fields will contain data - this depends very much on the input format used.

### Future directions

More formats, both for input and for output, can be easily added, so suggestions are always welcome.

### Associated qualifiers

As noted previously there are many 'associated' qualifiers that alter the behaviour of seqret when it reads in or writes out a sequence. As these are used in all EMBOSS programs that read in or write out sequences, they are not reported by the '-help' qualifier. They are however reported by the pair of qualifiers: '-help -verbose':

Some of the more useful associated qualifiers are:

Qualifier | Description
--- | ---
-sbegin | The first position to be used in the sequence
-send | The last position to be used in the sequence
-sreverse | Use the reverse complement of a nucleic acid sequence
-sask | Ask the user for begin/end/reverse information
-slower | Convert the sequence to lower case
-supper | Convert the sequence to upper case
-sformat | Specify the input sequence format
-osformat | Specify the output sequence format
-ossingle | Write each entry into a separate file
-auto | Turn off prompts and don't report the one-line description
-stdout | Write the results to 'standard output' (the screen)
-filter | Read input from another program, write to the screen
-options | Prompt for optional qualifiers
-help | Display a table of the command-line options

The set of associated qualifiers for sequences behave in different ways depending on where they appear.

If these qualifiers immediately follow a parameter they apply only to that parameter and not to all cases. If they occur before any parameters, they apply to all following sequence parameters.

If there are no two parameters of equal type, the order of parameters and their qualifiers is irrelevant.

Where a qualifier is defined more than once, for example "-sformat" for 2 input sequences to be aligned, the qualifier name can have a number to indicate which sequence is meant. "-sbegin2=25" will apply only to the second sequence, no matter where it appears on the command line.

The -sbegin and -send qualifiers take an integer number specifying the position to begin or end reading a sequence. If the number is positive, the number is the position counting from the first base or residue of the sequence. If the number is negative the position is counted from the end of the sequence, so position -1 is the last base or residue of the sequence. (If -sbegin 0 is used, it is assumed to be the same as -sbegin 1 and -send 0 is the same as -send -1.)

The filter qualifier makes the program behave like a filter, reading its (first) input 'file' from the standard input, and writing its (first) output 'file' to the standard output. The -filter qualifier will also invoke the -auto qualifier, so the user is never prompted for any missing values.

Example:

    % cat sequence.seq | seqret -filter | lpr

The example shows the application seqret being run with the -filter qualifier. The input file is 'piped' into the program using the unix command cat and the output is 'piped' directly to the unix program lpr, which will print it on the printer.

When the -options qualifier is used and not all the parameters are given on the command line, it will query the user for those parameters. It will not only query the user for the required parameters as it would do without the -options qualifier, but it will also query the user for the optional parameters.

When the -stdout qualifier is used, the user will still be prompted for all the info that is required, but will write to standard output by default. The user will also still be prompted for an output filename, in case the user wants to save the output to a file.

## Usage

Here is a sample session with seqret. It is used to extract an entry from a database and write it to a file:

    % seqret
    Input sequence: embl:paamir
    Output sequence [paamir.fasta]:

Here seqret is used to display the contents of the sequence on the screen:

    % seqret
    Reads and writes (returns) sequences
    Input sequence: embl:paamir
    Output sequence [paamir.fasta]: stdout

Here it is used in three different ways to write the result to a file in GCG format. Once by using the qualifier '-osformat', once by using the format in the output USA on the command line and once by specifying the format in the USA at the prompt.

    % seqret -osf gcg
    Reads and writes (returns) sequences
    Input sequence: embl:paamir
    Output sequence [paamir.gcg]:

    % seqret -outseq gcg::paamir.gcg
    Reads and writes (returns) sequences
    Input sequence: embl:paamir

    % seqret
    Reads and writes (returns) sequences
    Input sequence: embl:paamir
    Output sequence [paamir.fasta]: gcg::paamir.gcg

Here seqret is used to produce the reverse-complement of a sequence:

    % seqret -srev
    Reads and writes (returns) sequences
    Input sequence: embl:paamir
    Output sequence [paamir.fasta]:

Here seqret is used to extract the bases between the positions starting at 5 and ending at 25:

    % seqret -sbegin 5 -send 25
    Reads and writes (returns) sequences
    Input sequence: embl:paamir
    Output sequence [paamir.fasta]:

Here seqret is used to extract the bases between the positions starting at 5 and ending at 5 bases before the end of the sequence:

    % seqret -sbegin 5 -send -5
    Reads and writes (returns) sequences
    Input sequence: embl:paamir
    Output sequence [paamir.fasta]:

Here seqret is used to read all entries in the database 'tembl' that start with 'hs' and writes them to a file:

    % seqret
    Reads and writes (returns) sequences
    Input sequence(s): embl:hs*
    Output sequence [hs989235.fasta]:

Here seqret is used to read all entries in the database 'tembl' that start with 'hs' and writes them to a file. In this example the specification is all done in the command line and to stop Unix getting confused by the '*' character, it has to have a backslash ('\') before it:

    % seqret embl:hs\*  hs989235.fasta
    Reads and writes (returns) sequences

Here seqret is used to read only the entry 'hsfau' from the file 'hs989235.fasta' which contains many entries:

    % seqret
    Reads and writes (returns) sequences
    Input sequence(s): hs989235.fasta:hsfau
    Output sequence [hsfau.fasta]:

Here seqret is used to read all entries in the file 'hs989235.fasta', but only writes the first one of these entries out to a file:

    % seqret -firstonly
    Reads and writes (returns) sequences
    Input sequence(s): hs989235.fasta
    Output sequence [hs989235.fasta]: first.fasta

Here seqret is used to display on the screen the short sequence "actgatcgtg" in uppercase in EMBL format:

    % seqret -supper -osf embl asis::actgatcgtg stdout
    Reads and writes (returns) sequences
    ID              standard; DNA; UNC; 10 BP.
    SQ   Sequence 10 BP; 2 A; 2 C; 3 G; 3 T; 0 other;
         ACTGATCGTG                                10
    //

To force seqret to both read in and write out features, use the command-line qualifier '-feature'.

seqret does not read in features by default because this results in slightly faster performance. If however you wish to read in features with your sequence and write them out on output, using '-feature' will change the default behaviour to use any features present in the sequence.

    % seqret -feature
    Reads and writes (returns) sequences
    Input sequence(s): em:hs989235
    Output sequence [hs989235.fasta]: embl::hs989235.embl

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
      [-outseq]            seqoutall  Output sequence(s) USA

       Optional qualifiers: (none)
       Advanced qualifiers:
       -feature            bool       Use feature information
       -firstonly          bool       Read one sequence and stop

       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
[-outseq] (Parameter 2) | Output sequence(s) USA | Writeable sequence(s) | <sequence>.format
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
-feature | Use feature information | Yes/No | No
-firstonly | Read one sequence and stop | Yes/No | No

## Input file format

The USA of one or more sequences.

## Output file format

An output USA.

The output from seqret is one or more sequences, and by default will be written in FASTA format.

If the '-firstonly' qualifier is used then only the first sequence of the input USA specification will be written out.

In some cases the output filename will be the same as the input filename, but as seqret reads only the first sequence before opening the output file it may try to overwrite the input. Note that this is not true of seqretset which reads all sequences into memory at startup, but which can need a large amount of memory for many sequences..

## Data files

None.

## Notes

This description of what you can do when reading or writing files is not specific to the program seqret. All EMBOSS programs that read or write sequences can do the same.

seqret is often one of the first programs taught in EMBOSS training courses. This is because it is versatile, it is extremely powerful for its size (17 lines of code) it illustrates many aspects of EMBOSS programs and it was one of the first EMBOSS programs to be written, so it has a special place in the hearts of EMBOSS developers.

The name 'seqret' derives both from its function ("sequence return") and from the fact that immense amounts of functionality can come from so few lines of source code - most of the work is done by the EMBOSS libraries which the program calls and whose complexity is hidden, or "secret".

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with a status of 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
biosed | Replace or delete sequence sections
cutseq | Removes a specified section from a sequence
degapseq | Removes gap characters from sequences
descseq | Alter the name or description of a sequence
entret | Reads and writes (returns) flatfile entries
extractfeat | Extract features from a sequence
extractseq | Extract regions from a sequence
listor | Writes a list file of the logical OR of two sets of sequences
maskfeat | Mask off features of a sequence
maskseq | Mask off regions of a sequence
newseq | Type in a short new sequence
noreturn | Removes carriage return from ASCII files
notseq | Excludes a set of sequences and writes out the remaining ones
nthseq | Writes one sequence from a multiple set of sequences
pasteseq | Insert one sequence into another
revseq | Reverse and complement a sequence
seqretsplit | Reads and writes (returns) sequences in individual files
splitter | Split a sequence into (overlapping) smaller sequences
swissparse | Retrieves sequences from swissprot using keyword search
trimest | Trim poly-A tails off EST sequences
trimseq | Trim ambiguous bits off the ends of sequences
union | Reads sequence fragments and builds one sequence
vectorstrip | Strips out DNA between a pair of vector sequences
yank | Reads a sequence range, appends the full USA to a list file

Valid names of the databases set up in your local implementation of EMBOSS can be seen by using the program 'showdb'.

## Author(s)

This application was written by Peter Rice (pmr@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

## History

1999 - Written by Peter Rice
Feb 2002 - '-feature' qualifier added by Peter Rice

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments

### Fasta output format

#### Question

When i tried to convert the EMBL format file into fasta format using the program "seqret", I found that the Access.no appears twice...

    >AF102796 AF102796 Homo sapiens alphaE-catenin (CTNNA1) gene, exon 11.

#### Answer

"It is not a bug ... it is a feature"

There are many "FASTA formats". EMBOSS uses the format that ACEDB and the Sanger Centre genome projects use. The first field after the ID is the accession number, so that accession numbers can be kept when sequences are converted to FASTA format, without using the NCBI format (with '|' characters in the IDs).

Your EMBL format file has IDs that look like accession numbers, so EMBOSS fills in the accession number for each sequence, and reports it in the FASTA format.