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Top Forums Shell Programming and Scripting Challenging Awk array problem Post 302423714 by curleb on Friday 21st of May 2010 09:30:13 PM
Old 05-21-2010
Alister, another quick and dirty masterpiece! Works great, for me...

But I must ask: what if they wanted to iterate over the lines in the file? Or would you just wrap it into a while read...?
Code:
$ tr -s ' ' <Edit1
607 687 174 0 0 chr1 3000001 3000156 -194195276 - L1_Mur2 LINE L1 -4310 1567 1413 1
607 917 214 114 45 chr1 3000237 3000733 -194194699 - L1_Mur2 LINE L1 -4488 1389 913 1
607 215 31 0 30 chr1 3000733 3000766 -194194666 + (TTTG)n Simple_repeat Simple_repeat 2 33 0 2
607 845 233 76 114 chr1 3000766 3000792 -194194640 - L1_Mur2 LINE L1 -6816 912 887 1
607 621 250 65 37 chr1 3001287 3001583 -194193849 - Lx9 LINE L1 -1596 6048 5742 3
607 1320 197 332 7 chr1 3001722 3002005 -194193427 - RLTR25A LTR ERVK 0 1028 625 4

$ tr -s ' ' <Edit2
4|17999 - gi|149361523|ref|NC_000074.5|NC_000074 chr1 3000072 TTTATCGTCATCGTC
28|3721 + gi|149352351|ref|NC_000069.5|NC_000069 chr3 154935392 GAGTTTTACAGTCCA
28|3721 + gi|149288852|ref|NC_000067.5|NC_000067 chr1 152633707 GAGTTTTACAGTCCA
28|3721 + gi|149361432|ref|NC_000073.5|NC_000073 chr7 86595415 GAGTTTTACAGTCCA
34|3145 - gi|149321426|ref|NC_000084.5|NC_000084 chr18 43464724 ACGGCTTACGA
34|3145 - gi|149354224|ref|NC_000071.5|NC_000071 chr5 37676290 ACGGCTTACGA

$ paste -d\\n Edit1 Edit2 |
> awk '{
>     chr=$6; min=$7; max=$8; s=$11" "$12" "$13;
>     getline;
>     if (chr==$4 && $5>=min && $5<=max)
>         print $0, s;
> }'
 L1_Mur2 LINE L1361523|ref|NC_000074.5|NC_000074 chr1  3000072  TTTATCGTCATCGTC


Last edited by curleb; 05-21-2010 at 10:43 PM.. Reason: spoke too soon...
This User Gave Thanks to curleb For This Post:
 

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WRAP-AND-SORT(1)                                              General Commands Manual                                             WRAP-AND-SORT(1)

NAME
wrap-and-sort - wrap long lines and sort items in Debian packaging files SYNOPSIS
wrap-and-sort [options] DESCRIPTION
wrap-and-sort wraps the package lists in Debian control files. By default the lists will only split into multiple lines if the entries are longer than 80 characters. wrap-and-sort sorts the package lists in Debian control files and all .install files. Beside that wrap-and-sort removes trailing spaces in these files. This script should be run in the root of a Debian package tree. It searches for control, control.in, copyright, copyright.in, install, and *.install in the debian directory. OPTIONS
-h, --help Show this help message and exit. -a, --wrap-always Wrap all package lists in the Debian control file even if the entries are shorter than 80 characters and could fit in one line line. -s, --short-indent Only indent wrapped lines by one space (default is in-line with the field name). -b, --sort-binary-packages Sort binary package paragraphs by name. -k, --keep-first When sorting binary package paragraphs, leave the first one at the top. Unqualified debhelper(7) configuration files are applied to the first package. -n, --no-cleanup Do not remove trailing whitespaces. -d path, --debian-directory=path Location of the debian directory (default: ./debian). -f file, --file=file Wrap and sort only the specified file. You can specify this parameter multiple times. All supported files will be processed if no files are specified. -v, --verbose Print all files that are touched. AUTHORS
wrap-and-sort and this manpage have been written by Benjamin Drung <bdrung@debian.org>. Both are released under the ISC license. DEBIAN Debian Utilities WRAP-AND-SORT(1)
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