FROMTRACE*

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Table of Contents
FUNCTION
DESCRIPTION
EXAMPLE
OUTPUT
INPUT FILES
RELATED PROGRAMS
RESTRICTIONS
CONSIDERATIONS
COMMAND-LINE SUMMARY
LOCAL DATA FILES
PARAMETER REFERENCE

FUNCTION

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FromTrace converts one or more ABI or SCF trace files into GCG single sequence files.

DESCRIPTION

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Use FromTrace when you want to convert ABI or SCF trace files into a format suitable for use with the Wisonsin Package(TM). By default, the format of the output files are GCG single sequence files; use option -RSF to create RSF file output. The resulting files are always nucleotide sequence files.

EXAMPLE

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Here is a session using FromTrace to convert the trace file ci0207sa.scf into a GCG single sequence file:


% fromtrace

  Convert what trace file ?  ci0207sa.scf

     ci0207sa.seq    348 bp
%

OUTPUT

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Here is the complete output file called ci0207sa.seq:


!!NA_SEQUENCE 1.0
  FROMTRACE of: /gcg/users/traces/ci0207sa.scf  check: 7375  from: 1  to: 348

ci0207sa.seq  Length: 348  January 21, 2000 17:02  Type: N  Check: 7375  ..

       1  GGGTGGTCTC CCCGGGCGGG GGCCGcTCnG GcGACGGGGC ACGGGGCTGG

      51  GGCGCGCGGC CGGGCGGGGC GCGAGGCGGG GTGCGCGCTT AGAGGCGGTC

     101  AGCGCAGGGC CCCCGGGcGC GGcGGCGcGG CGcTGCCCGG cCGGGCAACC

     151  GnGGGGCTGG CGGCCCGcGG CGGGCGTTCC TCTCGTACTG GCCCGCCGTG

     201  CTCTGGCCCC GGGGCCAGTA GGGTAAAACT AACCTGTCTC ACGACGGTCT

     251  AAACCCAGCT CACGATCCCT TGAACGGGTG AACAATCCGA CGnTTnCGnG

     301  cCGGTGCGGC GGnACGGTAG GAAGAGCCGA CATCGAAGGA TCAAAAAG

INPUT FILES

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FromTrace accepts multiple (one or more) binary trace files in ABI- or SCF-format generated by an automated sequencer. You can specify multiple input files by using a file specification with an asterisk (*) wildcard, for example traces*.SCF.

RELATED PROGRAMS

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The following programs convert sequences between other formats and GCG format: FromEMBL, FromGenBank, FromIG, FromPIR, FromStaden, FromFastA, ToIG, ToPIR, ToStaden and ToFastA.

DataSet creates a GCG data library from any set of sequences in GCG format. GCGToBLAST creates a database that can be searched by the BLAST program from any set of sequences in GCG format.

RESTRICTIONS

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The sequences in the trace files should not be longer than 350,000 bases long.

CONSIDERATIONS

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None.

COMMAND-LINE SUMMARY

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All parameters for this program may be added to the command line. Use -CHEck to view the summary below and to specify parameters before the program executes. In the summary below, the capitalized letters in the parameter names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.


Minimal Syntax:       % fromtrace [-INfile1=]ci0207sa.scf -Default

Prompted Parameters:  None

Local Data Files:     None

Optional Parameters:

-NOMONitor            suppresses the screen output

-RSF[=fromtrace.rsf] changes output file format to RSF format

-NOTRACEinfo suppresses writing of trace information to the RSF output file

LOCAL DATA FILES

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None.

PARAMETER REFERENCE

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You can set the parameters listed below from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.

-MONitor

This program normally monitors its progress on your screen. However, when you use -Default to suppress all program interaction, you also suppress the monitor. You can turn it back on with this parameter. If you are running the program in batch, the monitor will appear in the log file.

-RSF=fromtrace.rsf

writes your output file in RSF format instead of the default single sequence file format.

-NOTRACEinfo

excludes trace information from the RSF output file. You cannot view traces from RSF files that were created with the -NOTRACEinfo parameter.

Printed: April 27, 2000 17:51 (1162)

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