08-21-2002
Perderabo, you da the man!! (of course, making a gender assumption there). That worked beautifully!! Question for you as this is the 1st time I've come accross file descriptor 3 - 1 is STDOUT, 2 is STDERR but 3? And, if you don't mind - what is the last redirection "3>&-" doing?
Thanks Perderabo!!
Asifraj - I can't use just "2> error" because then it won't also go to the screen. I want the user to know there was an error but I don't want to have to rely on them to know what the error is.
Optimus_P - while that would work for getting the errors to the screen and a file, it would also send STDOUT to the same file, which I don't want (I have a debug log that I want to contain only debug and error messages).
Thanks everyone!
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LEARN ABOUT DEBIAN
fastx_clipper
FASTX_CLIPPER(1) User Commands FASTX_CLIPPER(1)
NAME
fastx_clipper - FASTA/Q Clipper
DESCRIPTION
usage: fastx_clipper [-h] [-a ADAPTER] [-D] [-l N] [-n] [-d N] [-c] [-C] [-o] [-v] [-z] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit
0.0.13.2 by A. Gordon (gordon@cshl.edu)
[-h] = This helpful help screen.
[-a ADAPTER] = ADAPTER string. default is CCTTAAGG (dummy adapter). [-l N] = discard sequences shorter than N nucleotides.
default is 5. [-d N] = Keep the adapter and N bases after it.
(using '-d 0' is the same as not using '-d' at all. which is the default).
[-c] = Discard non-clipped sequences (i.e. - keep only sequences which contained the adapter).
[-C] = Discard clipped sequences (i.e. - keep only sequences which did not contained the adapter).
[-k] = Report Adapter-Only sequences.
[-n] = keep sequences with unknown (N) nucleotides. default is to discard such sequences.
[-v] = Verbose - report number of sequences.
If [-o] is specified,
report will be printed to STDOUT.
If [-o] is not specified (and output goes to STDOUT), report will be printed to STDERR.
[-z] = Compress output with GZIP.
[-D] = DEBUG output.
[-M N] = require minimum adapter alignment length of N.
If less than N nucleotides aligned with the adapter - don't clip it.
[-i INFILE] = FASTA/Q input file. default is STDIN.
[-o OUTFILE] = FASTA/Q output file. default is STDOUT.
SEE ALSO
The quality of this automatically generated manpage might be insufficient. It is suggested to visit
http://hannonlab.cshl.edu/fastx_toolkit/commandline.html
to get a better layout as well as an overview about connected FASTX tools.
fastx_clipper 0.0.13.2 May 2012 FASTX_CLIPPER(1)