seqret.txt

emboss的linux版本的源代码

   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

   Extract an entry from a database and write it to a file:


% seqret 
Reads and writes (returns) sequences
Input (gapped) sequence(s): tembl:hsfau
output sequence(s) [hsfau.fasta]: 

   Go to the input files for this example
   Go to the output files for this example

   Example 2

   Read all entries in the database 'tembl' that start with 'hs' and
   write 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 tembl:hs\*  hsall.seq 
Reads and writes (returns) sequences

   Go to the output files for this example

   Example 3

   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. N.B. use embl format for the output file as the default
   format 'fasta' reports the features in gff (file "<seqname>.gff")


% seqret -feature 
Reads and writes (returns) sequences
Input (gapped) sequence(s): tembl:hsfau
output sequence(s) [hsfau.fasta]: embl::hsfau.embl

   Go to the output files for this example

   Example 4

   Display the contents of the sequence on the screen:


% seqret 
Reads and writes (returns) sequences
Input (gapped) sequence(s): tembl:hsfau
output sequence(s) [hsfau.fasta]: stdout

>HSFAU X65923.1 H.sapiens fau mRNA
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttcagtcaaaaaaaaaa

   Example 5

   Write the result in GCG format by using the qualifier '-osformat'.


% seqret -osf gcg 
Reads and writes (returns) sequences
Input (gapped) sequence(s): tembl:hsfau
output sequence(s) [hsfau.gcg]: 

   Go to the output files for this example

   Example 6

   Write the result in GCG format by specifying the format in the output
   USA on the command line.


% seqret -outseq gcg::hsfau.gcg 
Reads and writes (returns) sequences
Input (gapped) sequence(s): tembl:hsfau

   Example 7

   Write the result in GCG format by specifying the format in the output
   USA at the prompt.


% seqret 
Reads and writes (returns) sequences
Input (gapped) sequence(s): tembl:hsfau
output sequence(s) [hsfau.fasta]: gcg::hsfau.gcg

   Example 8

   Write the reverse-complement of a sequence:


% seqret -srev 
Reads and writes (returns) sequences
Input (gapped) sequence(s): tembl:hsfau
output sequence(s) [hsfau.fasta]: 

   Go to the output files for this example

   Example 9

   Extract the bases between the positions starting at 5 and ending at
   25:


% seqret -sbegin 5 -send 25 
Reads and writes (returns) sequences
Input (gapped) sequence(s): tembl:hsfau
output sequence(s) [hsfau.fasta]: 

   Go to the output files for this example

   Example 10

   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 (gapped) sequence(s): tembl:hsfau
output sequence(s) [hsfau.fasta]: 

   Go to the output files for this example

   Example 11

   Read all entries in the database 'tembl' that start with 'hs' and
   write them to a file:


% seqret 
Reads and writes (returns) sequences
Input (gapped) sequence(s): tembl:hs*
output sequence(s) [hs989235.fasta]: hsall.seq

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     (Gapped) sequence(s) filename and optional
                                  format, or reference (input USA)
  [-outseq]            seqoutall  [.] Sequence set(s)
                                  filename and optional format (output USA)

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

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outseq" associated qualifiers
   -osformat2          string     Output seq format
   -osextension2       string     File name extension
   -osname2            string     Base file name
   -osdirectory2       string     Output directory
   -osdbname2          string     Database name to add
   -ossingle2          boolean    Separate file for each entry
   -oufo2              string     UFO features
   -offormat2          string     Features format
   -ofname2            string     Features file name
   -ofdirectory2       string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Input file format

   seqret reads one or more sequence USAs.

  Input files for usage example

   'tembl:hsfau' is a sequence entry in the example nucleic acid database
   'tembl'

  Database entry: tembl:hsfau

ID   HSFAU      standard; RNA; HUM; 518 BP.
XX
AC   X65923;
XX
SV   X65923.1
XX
DT   13-MAY-1992 (Rel. 31, Created)
DT   23-SEP-1993 (Rel. 37, Last updated, Version 10)
XX
DE   H.sapiens fau mRNA
XX
KW   fau gene.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-518
RA   Michiels L.M.R.;
RT   ;
RL   Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases.
RL   L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL   Universiteisplein 1, 2610 Wilrijk, BELGIUM
XX
RN   [2]
RP   1-518
RX   MEDLINE; 93368957.
RA   Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT   " fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT   an antisense sequences in the Finkel-Biskis-Reilly murine sarcoma virus";
RL   Oncogene 8:2537-2546(1993).
XX
DR   SWISS-PROT; P35544; UBIM_HUMAN.
DR   SWISS-PROT; Q05472; RS30_HUMAN.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..518
FT                   /chromosome="11q"
FT                   /db_xref="taxon:9606"
FT                   /organism="Homo sapiens"
FT                   /tissue_type="placenta"
FT                   /clone_lib="cDNA"
FT                   /clone="pUIA 631"
FT                   /map="13"
FT   misc_feature    57..278
FT                   /note="ubiquitin like part"
FT   CDS             57..458
FT                   /db_xref="SWISS-PROT:P35544"
FT                   /db_xref="SWISS-PROT:Q05472"
FT                   /gene="fau"
FT                   /protein_id="CAA46716.1"
FT                   /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLA
G
FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKT
G
FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT   misc_feature    98..102
FT                   /note="nucleolar localization signal"
FT   misc_feature    279..458
FT                   /note="S30 part"
FT   polyA_signal    484..489
FT   polyA_site      509
XX
SQ   Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
     ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc        6
0
     agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       12
0
     cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       18
0
     tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       24
0
     tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       30
0
     gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       36
0
     agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       42
0
     cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       48
0
     tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               51
8
//