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Top Forums Shell Programming and Scripting Challenging Awk array problem Post 302424195 by polsum on Monday 24th of May 2010 01:19:20 PM
Old 05-24-2010
Ok - Now I am in to another problem (life is tough!). May be I did not explain this properly and I am apologize for it. The code here seems to assume line to line matching of file 1 and file 2. But my actual files (which are very big) do not match line by line. For example let me re-frame the original files.

file 1 (THIS IS SAME AS ORIGINAL)
HTML Code:
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
file 2

HTML Code:
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 chr1  3000073 GAGTTTTACAGTCCA
34|3145  - gi|149321426|ref|NC_000084.5|NC_000084 chr1 3000767 ACGGCTTACGA
34|3145  - gi|149354224|ref|NC_000071.5|NC_000071 chr5  37676290 ACGGCTTACGA
So the output should be,

HTML Code:
4|17999 - gi|149361523|ref|NC_000074.5|NC_000074  chr1  3000072 TTTATCGTCATCGTC L1_Mur2    LINE    L1
28|3721  + gi|149361432|ref|NC_000073.5|NC_000073 chr1  3000073  GAGTTTTACAGTCCA     L1_Mur2    LINE    L1
34|3145  - gi|149321426|ref|NC_000084.5|NC_000084 chr1 3000767 ACGGCTTACGA     (TTTG)n    Simple_repeat    Simple_repeat
The code here seems to be matching the two files line to line. I tried editing the code to this purpose but of no avail. Please help me. thanks.
 

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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/> Report paste translation bugs to <http://translationproject.org/team/> COPYRIGHT
Copyright (C) 2011 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 8.12.197-032bb September 2011 PASTE(1)
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