coderet problems

Wiepert, Mathieu Wiepert.Mathieu at
Wed Apr 23 16:08:52 UTC 2003


Have you tried the coderet -help -verbose options?  That should give you all the possible parameters available.  I couldn't tell you what they all do though, sorry...

~ $ coderet -help -verbose
   Mandatory qualifiers:
  [-seqall]            seqall     Sequence database USA
  [-seqout]            seqout     Output sequence USA

   Optional qualifiers: (none)
   Advanced qualifiers:
   -[no]cds            boolean    Extract CDS sequences
   -[no]mrna           boolean    Extract mrna sequences
   -[no]translation    boolean    Extract translated sequences

   Associated qualifiers:
  "-seqall" related qualifiers
  -sbegin1             integer    First base used
  -send1               integer    Last base used, def=seq length
  -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
  -sopenfile1          string     Input filename
  -sdbname1            string     Database name
  -sid1                string     Entryname
  -ufo1                string     UFO features
  -fformat1            string     Features format
  -fopenfile1          string     Features file name
  "-seqout" related qualifiers
  -osformat2           string     Output seq format
  -osextension2        string     File name extension
  -osname2             string     Base file name
  -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

   General qualifiers:
  -auto                boolean    Turn off prompts
  -stdout              boolean    Write standard output
  -filter              boolean    Read standard input, write standard output
  -options             boolean    Prompt for required and optional values
  -debug               boolean    Write debug output to program.dbg
  -acdlog              boolean    Write ACD processing log to program.acdlog
  -acdpretty           boolean    Rewrite ACD file as program.acdpretty
  -acdtable            boolean    Write HTML table of options
  -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 deaths

-----Original Message-----
From: Joerg Schaber [mailto:Joerg.Schaber at]
Sent: Wednesday, April 23, 2003 10:47 AM
To: emboss at
Subject: coderet problems


i am having problems extracting CDS from NCBI flat files using coderet. 
I keep getting the error 'Unable to read sequence'.
I guess the problem could be solved if I used the appropriate command 
line arguments like -sformat1, for instance. However, in the docs is is 
not stated what options I have for the associated qualifiers.
Any idea what could be the problem or what options there are for the 


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