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Top Forums Shell Programming and Scripting Challenging Awk array problem Post 302423715 by alister on Friday 21st of May 2010 09:43:28 PM
Old 05-21-2010
Hi, curleb:

I'm not sure I understand what you mean by iterate over the lines of the file. Every line in both files is read by that solution; the paste merges them:

file1 line1
file2 line1
file1 line2
file2 line2
file1 line3
file2 line3
...etc

There just happens to be only one line that meets the requirements.

If I misundersood your question, please elaborate.

Cheers,
Alister

P.S. The last line in your output seems garbled. Perhaps a terminal hiccup? Or a carriage return somehwere? Here's a sample run from my system:
Code:
$ cat file1
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
$ cat file2
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 file1 file2 |
> awk '{
>     chr=$6; min=$7; max=$8; s=$11" "$12" "$13;
>     getline;
>     if (chr==$4 && $5>=min && $5<=max)
>         print $0, s;
> }'
4|17999 - gi|149361523|ref|NC_000074.5|NC_000074 chr1  3000072  TTTATCGTCATCGTC L1_Mur2 LINE L1

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PASTE(1)							   User Commands							  PASTE(1)

NAME
paste - merge lines of files SYNOPSIS
paste [OPTION]... [FILE]... DESCRIPTION
Write lines consisting of the sequentially corresponding lines from each FILE, separated by TABs, to standard output. With no FILE, or when FILE is -, read standard input. Mandatory arguments to long options are mandatory for short options too. -d, --delimiters=LIST reuse characters from LIST instead of TABs -s, --serial paste one file at a time instead of in parallel --help display this help and exit --version output version information and exit AUTHOR
Written by David M. Ihnat and David MacKenzie. REPORTING BUGS
Report paste bugs to bug-coreutils@gnu.org GNU coreutils home page: <http://www.gnu.org/software/coreutils/> General help using GNU software: <http://www.gnu.org/gethelp/> COPYRIGHT
Copyright (C) 2009 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. SEE ALSO
The full documentation for paste is maintained as a Texinfo manual. If the info and paste programs are properly installed at your site, the command info coreutils 'paste invocation' should give you access to the complete manual. GNU coreutils 7.1 July 2010 PASTE(1)
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