seqret

seqret

seqret reads and writes (returns) sequences.

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 write 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. To avoid confusing Unix with the * character, put 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 the short sequence actgatcgtg in uppercase EMBL format on the screen:

% 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, resulting in slightly faster performance. If you want to read features with your sequence and write them out on output, using -feature will change the default behavior so that any features present in the sequence are used:

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

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA.

[-outseq] (seqoutall)

Output sequence(s) USA.

Advanced qualifiers:

-feature (boolean)

Use feature information.

-firstonly (boolean)

Read one sequence and stop .



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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