coderet.txt

emboss的linux版本的源代码

                                  coderet 



Function

   Extract CDS, mRNA and translations from feature tables

Description

   The feature table of sequence database entries often have sections
   like this:

   This specifies that the coding sequence for the gene is constructed by
   joining several sections of code, many of which are in other entries
   in this database.
     _________________________________________________________________

FT   CDS             join(U21925.1:818..987,U21926.1:258..420,
FT                   U21927.1:428..520,U21928.1:196..336,U21929.1:279..415,
FT                   U21930.1:895..1014,516..708)
     _________________________________________________________________

   or:

   This specifies that the messenger RNA sequence for the gene is
   constructed by joining several sections of code, many of which are in
   other entries in this database.
     _________________________________________________________________

FT   mRNA            join(M88628.1:1006..1318,M88629.1:221..342,
FT                   M88630.1:101..223,M88631.1:46..258,M88632.1:104..172,
FT                   M88633.1:387..503,M88634.1:51..272,M88635.1:303..564,
FT                   M88635.1:849..1020,M88636.1:282..375,M88637.1:39..253,
FT                   M88638.1:91..241,M88639.1:168..377,M88640.1:627..3732,
FT                   M88641.1:158..311,M88642.1:1051..1263,M88642.1:1550..1778,
FT                   M88642.1:1986..2168,M88642.1:3904..4020,
FT                   M88642.1:4627..4698,M88643.1:39..124,M88644.1:42..197,
FT                   M88645.1:542..686,M88646.1:75..223,M88647.1:109..285,
FT                   253..2211)
     _________________________________________________________________

   or:

   This specifies that the translation of the coding region is as
   follows.
     _________________________________________________________________

FT                   /translation="MAQDSVDLSCDYQFWMQKLSVWDQASTLETQQDTCLHVAQFQEF
L
FT                   RKMYEALKEMDSNTVIERFPTIGQLLAKACWNPFILAYDESQKILIWCLCCLINKEPQ
N
FT                   SGQSKLNSWIQGVLSHILSALRFDKEVALFTQGLGYAPIDYYPGLLKNMVLSLASELR
E
FT                   NHLNGFNTQRRMAPERVASLSRVCVPLITLTDVDPLVEALLICHGREPQEILQPEFFE
A
FT                   VNEAILLKKISLPMSAVVCLWLRHLPSLEKAMLHLFEKLISSERNCLRRIECFIKDSS
L
FT                   PQAACHPAIFRVDEMFRCALLETDGALEIIATIQVFTQCFVEALEKASKQLRFALKTY
F
FT                   PYTSPSLAMVLLQDPQDIPRGHWLQTLKHISELLREAVEDQTHGSCGGPFESWFLFIH
F
FT                   GGWAEMVAEQLLMSAAEPPTALLWLLAFYYGPRDGRQQRAQTMVQVKAVLGHLLAMSR
S
FT                   SSLSAQDLQTVAGQGTDTDLRAPAQQLIRHLLLNFLLWAPGGHTIAWDVITLMAHTAE
I
FT                   THEIIGFLDQTLYRWNRLGIESPRSEKLARELLKELRTQV"
     _________________________________________________________________

   It is often a tedious and error-prone job to extract the several
   sections of these sequences from the database entries and to join them
   together to construct the indicated finished sequence.

   coderet does this job for you.

   You specify the sequence containing the feature table and it extracts
   the required CDS, mRNA and/or protein sequences specified by this
   feature table. If any sequences are in other entries of that database,
   they are automatically fetched and incorporated correctly into the
   final sequence.

   The translations are not made from the coding sequence, they are
   extracted directly from the translation sequence held in the feature
   table.

Usage

   Here is a sample session with coderet

   To extract all of the CDS, mRNA, non-coding and the protein
   translations:


% coderet 
Extract CDS, mRNA and translations from feature tables
Input nucleotide sequence(s): tembl:X03487
Output file [hsferg1.coderet]: 
Coding nucleotide output sequence(s) (optional) [hsferg1.cds]: 
Messenger RNA nucleotide output sequence(s) (optional) [hsferg1.mrna]: 
Translated coding protein output sequence(s) (optional) [hsferg1.prot]: 
Non-coding nucleotide output sequence(s) (optional) [hsferg1.noncoding]: 

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

   Example 2

   To only extract the mRNA sequence:


% coderet -nocds -notranslation -norest 
Extract CDS, mRNA and translations from feature tables
Input nucleotide sequence(s): tembl:X03487
Output file [hsferg1.coderet]: 
Messenger RNA nucleotide output sequence(s) (optional) [hsferg1.mrna]: 

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-seqall]            seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
  [-outfile]           outfile    [*.coderet] Output file name
  [-cdsoutseq]         seqoutall  [.] Coding nucleotide
                                  output sequence(s) (optional)
  [-mrnaoutseq]        seqoutall  [.] Messenger RNA
                                  nucleotide output sequence(s) (optional)
  [-translationoutseq] seqoutall  [.] Translated coding
                                  protein output sequence(s) (optional)
  [-restoutseq]        seqoutall  [.] Non-coding nucleotide
                                  output sequence(s) (optional)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-seqall" 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

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   "-cdsoutseq" associated qualifiers
   -osformat3          string     Output seq format
   -osextension3       string     File name extension
   -osname3            string     Base file name
   -osdirectory3       string     Output directory
   -osdbname3          string     Database name to add
   -ossingle3          boolean    Separate file for each entry
   -oufo3              string     UFO features
   -offormat3          string     Features format
   -ofname3            string     Features file name
   -ofdirectory3       string     Output directory

   "-mrnaoutseq" associated qualifiers
   -osformat4          string     Output seq format
   -osextension4       string     File name extension
   -osname4            string     Base file name
   -osdirectory4       string     Output directory
   -osdbname4          string     Database name to add
   -ossingle4          boolean    Separate file for each entry
   -oufo4              string     UFO features
   -offormat4          string     Features format
   -ofname4            string     Features file name
   -ofdirectory4       string     Output directory

   "-translationoutseq" associated qualifiers
   -osformat5          string     Output seq format
   -osextension5       string     File name extension
   -osname5            string     Base file name
   -osdirectory5       string     Output directory
   -osdbname5          string     Database name to add
   -ossingle5          boolean    Separate file for each entry
   -oufo5              string     UFO features
   -offormat5          string     Features format
   -ofname5            string     Features file name
   -ofdirectory5       string     Output directory

   "-restoutseq" associated qualifiers
   -osformat6          string     Output seq format
   -osextension6       string     File name extension
   -osname6            string     Base file name
   -osdirectory6       string     Output directory
   -osdbname6          string     Database name to add
   -ossingle6          boolean    Separate file for each entry
   -oufo6              string     UFO features
   -offormat6          string     Features format
   -ofname6            string     Features file name
   -ofdirectory6       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