Copyright (C) 1999-2002, Medical Research Council, Laboratory of Molecular Biology.
convert_trace -- Converts trace file formats
convert_trace converts between the various DNA sequence chromatogram
formats, optionally performing trace processing actions too. It can read ABI
(raw or processed), ALF, CTF, SCF and ZTR formats. It can write CTF, EXP, PLN,
SCF and ZTR formats. (Note that EXP (Experiment File) and PLN formats are
text sequences rather than a binary trace.)
There are two main modes of operation; either with a file of filenames
specified using the
-fofn filename option, or acting as a filter
to process one single file. In this case the input and output file format may
be specified as the last two options on the command line.
DATAchannel numbers to use. For sequencing files this defaults to "9,10,11,12" which corresponds to the processed data. To read the raw data use "1,2,3,4".
convert_traceis operating as a filter (and so requires use of the
-fofnoption). Valid values for mode are compress, bzip, bzip2, gzip, pack and szip. Note that for ZTR, ZTR2 and ZTR3 format files specifying compression modes will not reduce the file size as this format already contains internal compression algorithms. The ZTR1 format does not internally compress and so
-compresswill have an effect.
file\ a.scf file\ a.ztr fileb.scf fileb.ztr
IDline. Without this option default Experiment File ID line is the output filename, or if this is stdout it is the input filename.
To convert several files to ZTR format using the same example file of
filenames listed in the
-fofn option above:
convert_trace -out_format ZTR -fofn filename
To subtract the background from a raw ABI file and save this as an SCF file:
convert_trace -abi_data 1,2,3,4 -subtract_background ABI SCF < a.abi > a.scf
If ABI files are manually edited before input to convert_trace then the internal formats of these files may differ to the format expected by convert_trace.
See section scf(4).See section ztr(4).See section makeSCF(1).