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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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IPSEC_RANBITS(8)						  [FIXME: manual]						  IPSEC_RANBITS(8)

NAME
ipsec_ranbits - generate random bits in ASCII form SYNOPSIS
ipsec ranbits [--quick] [--continuous] [--bytes] nbits DESCRIPTION
Ranbits obtains nbits (rounded up to the nearest byte) high-quality random bits from random(4), and emits them on standard output as an ASCII string. The default output format is datatot(3) h format: lowercase hexadecimal with a 0x prefix and an underscore every 32 bits. The --quick option produces quick-and-dirty random bits: instead of using the high-quality random bits from /dev/random, which may take some time to supply the necessary bits if nbits is large, ranbits uses /dev/urandom, which yields prompt results but lower-quality randomness. The --continuous option uses datatot(3) x output format, like h but without the underscores. The --bytes option causes nbits to be interpreted as a byte count rather than a bit count. FILES
/dev/random, /dev/urandom SEE ALSO
ipsec_datatot(3), random(4) HISTORY
Written for the Linux FreeS/WAN project <http://www.freeswan.org> by Henry Spencer. BUGS
There is an internal limit on nbits, currently 20000. Without --quick, ranbits's run time is difficult to predict. A request for a large number of bits, at a time when the system's entropy pool is low on randomness, may take quite a while to satisfy. Though not a bug of ranbits, the direct use of /dev/hw_random, the Linux hardware random number generator is not supported because it can produce very non-random data. To properly use /dev/hw_random, the rngd daemon should be used to read from /dev/hw_random and write to /dev/random, while performing a FIPS test on the hardware random read. No changes to Openswan are required for this support - just a running rngd. [FIXME: source] 10/06/2010 IPSEC_RANBITS(8)
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