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Top Forums UNIX for Beginners Questions & Answers awk script to extract transcript information from gff3 file Post 303043918 by Maduranga on Tuesday 11th of February 2020 07:04:06 AM
Old 02-11-2020
I came up with this question but that is not correct.
Code:
awk '{if(g3=="mRNA"){split($9,a,"=");split(a[2],b,";");split(g9,ga,"=");split(ga[2],gb,";");print b[1]"\t"gb[1]"\tDesc\t"$1"\t"$7"\t"g4"\t"g5"\tPAC\tPEP\t"$4"\t"$5};g3=$3;g1=$1;g2=$2;g4=$4;g5=$5;g9=$9}'

 

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bup-meta(1)						      General Commands Manual						       bup-meta(1)

NAME
bup-meta - create or extract a metadata archive SYNOPSIS
bup meta --create [-R] [-v] [-q] [--no-symlinks] [--no-paths] [-f file] <paths...> bup meta --list [-v] [-q] [-f file] bup meta --extract [-v] [-q] [--numeric-ids] [--no-symlinks] [-f file] bup meta --start-extract [-v] [-q] [--numeric-ids] [--no-symlinks] [-f file] bup meta --finish-extract [-v] [-q] [--numeric-ids] [-f file] DESCRIPTION
bup meta either creates or extracts a metadata archive. A metadata archive contains the metadata information (timestamps, ownership, access permissions, etc.) for a set of filesystem paths. OPTIONS
-c, --create Create a metadata archive for the specified paths. Write the archive to standard output unless --file is specified. -t, --list Display information about the metadata in an archive. Read the archive from standard output unless --file is specified. -x, --extract Extract a metadata archive. Conceptually, perform --start-extract followed by --finish-extract. Read the archive from standard input unless --file is specified. --start-extract Build a filesystem tree matching the paths stored in a metadata archive. By itself, this command does not produce a full restora- tion of the metadata. For a full restoration, this command must be followed by a call to --finish-extract. Once this command has finished, all of the normal files described by the metadata will exist and be empty. Restoring the data in those files, and then calling --finish-extract should restore the original tree. The archive will be read from standard input unless --file is specified. --finish-extract Finish applying the metadata stored in an archive to the filesystem. Normally, this command should follow a call to --start- extract. The archive will be read from standard input unless --file is specified. -f, --file=filename Read the metadata archive from filename or write it to filename as appropriate. If filename is "-", then read from standard input or write to standard output. -R, --recurse Recursively descend into subdirectories during --create. --numeric-ids Apply numeric user and group IDs (rather than text IDs) during --extract or --finish-extract. --symlinks Record symbolic link targets when creating an archive, or restore symbolic links when extracting an archive (during --extract or --start-extract). This option is enabled by default. Specify --no-symlinks to disable it. --paths Record pathnames when creating an archive. This option is enabled by default. Specify --no-paths to disable it. -v, --verbose Be more verbose (can be used more than once). -q, --quiet Be quiet. EXAMPLES
# Create a metadata archive for /etc. $ bup meta -cRf etc.meta /etc bup: removing leading "/" from "/etc" # Extract the etc.meta archive (files will be empty). $ mkdir tmp && cd tmp $ bup meta -xf ../etc.meta $ ls etc # Restore /etc completely. $ mkdir tmp && cd tmp $ bup meta --start-extract -f ../etc.meta ...fill in all regular file contents using some other tool... $ bup meta --finish-extract -f ../etc.meta BUGS
Hard links are not handled yet. BUP
Part of the bup(1) suite. AUTHORS
Rob Browning <rlb@defaultvalue.org>. Bup unknown- bup-meta(1)
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