12-20-2010
No, they do not work. I am getting error with the code echo "${LINE:86:3}". It says "${LINE:89:3}": The specified substitution is not valid for this command.
However the awk is working and giving me wrong result. There is no tab character - all spaces.
Thanks
Asutoshch
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LEARN ABOUT DEBIAN
tigr-extract
TIGR-GLIMMER(1) General Commands Manual TIGR-GLIMMER(1)
NAME
tigr-glimmer -- Fine start/stop positions of genes in genome sequence
SYNOPSIS
tigr-extract [genome-file options]
DESCRIPTION
Program extract takes a FASTA format sequence file and a file with a list of start/stop positions in that file (e.g., as produced by the
long-orfs program) and extracts and outputs the specified sequences.
The first command-line argument is the name of the sequence file, which must be in FASTA format.
The second command-line argument is the name of the coordinate file. It must contain a list of pairs of positions in the first file, one
per line. The format of each entry is:
<IDstring>> <start position> <stop position>
This file should contain no other information, so if you're using the output of glimmer or long-orfs , you'll have to cut off header
lines.
The output of the program goes to the standard output and has one line for each line in the coordinate file. Each line contains the
IDstring , followed by white space, followed by the substring of the sequence file specified by the coordinate pair. Specifically, the
substring starts at the first position of the pair and ends at the second position (inclusive). If the first position is bigger than the
second, then the DNA reverse complement of each position is generated. Start/stop pairs that "wrap around" the end of the genome are
allowed.
OPTIONS
-skip makes the output omit the first 3 characters of each sequence, i.e., it skips over the start codon. This was the behaviour of
the previous version of the program.
-l makes the output omit an sequences shorter than n characters. n includes the 3 skipped characters if the -skip switch is
one.
SEE ALSO
tigr-glimmer3 (1), tigr-long-orfs (1), tigr-adjust (1), tigr-anomaly (1), tigr-build-icm (1), tigr-check (1), tigr-codon-usage (1), tigr-
compare-lists (1), tigr-extract (1), tigr-generate (1), tigr-get-len (1), tigr-get-putative (1),
http://www.tigr.org/software/glimmer/
Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.
AUTHOR
This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@debian.org for the Debian system.
TIGR-GLIMMER(1)