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FromTrace converts one or more ABI or SCF trace files into GCG single sequence files.
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.
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
%
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
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.
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.
The sequences in the trace files should not be longer than 350,000 bases long.
None.
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
None.
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.
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.
writes your output file in RSF format instead of the default single sequence file format.
excludes trace information from the RSF output file. You cannot view traces from RSF files that were created with the -NOTRACEinfo parameter.
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