Copyright (C) 1999-2002, Medical Research Council, Laboratory of Molecular Biology.

Convert_trace

NAME

convert_trace -- Converts trace file formats

SYNOPSIS

convert_trace [-in_format format] [-out_format format] [-fofn file_of_filenames] [-passed fofn] [-failed fofn] [-name id] [-subtract_background] [-normalise] [-scale range] [-compress mode] [-abi_data counts] [informat outformat]

DESCRIPTION

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.

OPTIONS

-abi_data counts

Only of use when processing ABI files. This indicates which ABI DATA channel 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".

-compress mode

Specifies the name of a program to use to compress the trace data prior to writing. Due to limitations in the current implementation this option does not work when convert_trace is operating as a filter (and so requires use of the -fofn option). 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 -compress will have an effect.

-failed fofn

Produces a file listing the filenames which have failed to be converted. This only makes sense when also using -fofn.

-fofn file_of_filenames

Processes several files instead of one, with the filenames to read from and written to being listed in file_of_filenames with one pair (input and output filenames) being listed per line, separated by spaces. If the filenames contain spaces then these may be "escaped" using backslashes. Similarly backslashes should be escaped using a double backslash. For example to convert "file a.scf" and "fileb.scf" to "file a.ztr" and "fileb.ztr" respectively we would use a file_of_filenames containing:

file\ a.scf    file\ a.ztr
fileb.scf      fileb.ztr

-in_format format

Specifies the format for the input data. Typically the input format is automatically determined so this may not be required. format should be one of ABI, ALF, CTF, EXP, PLN, SCF, ZTR, ZTR1, ZTR2 or ZTR3. The ZTR formats all conform to the ZTR specification, but this indicates the compression level to be used.

-name id

When producing an Experiment File this specifies the value of the ID line. Without this option default Experiment File ID line is the output filename, or if this is stdout it is the input filename.

-normalise

Attempts to normalise the trace amplitudes to produce more even height peaks. This may be useful to compensate for large spikes at either the start or end of the trace.

-out_format format

Specifies the output format for all files, whether read from a file of filenames or via a filter. format should be one of ABI, ALF, CTF, EXP, PLN, SCF, ZTR, ZTR1, ZTR2 or ZTR3. The ZTR formats all conform to the ZTR specification, but this indicates the compression level to be used.

-passed fofn

Produces a file listing the filenames which have been successfully converted. This only makes sense when also using -fofn.

-scale range

Scales all trace amplitudes so that they fit within the range of 0 to range inclusive. Any integer value of range may be used between 1 and 65535, but this option is designed for down-scaling traces in order to reduce file size.

-subtract_background

Attempts to remove background trace levels by analysing each trace channel independently to determine the baseline. This option is mainly used when processing raw data.

EXAMPLES

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

NOTES

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 ALSO

See section scf(4).See section ztr(4).See section makeSCF(1).