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
GNU coreutils online help: <http://www.gnu.org/software/coreutils/> Report paste translation bugs to <http://translationproject.org/team/>
AUTHOR
Written by David M. Ihnat and David MacKenzie.
COPYRIGHT
Copyright (C) 2013 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 8.22 June 2014 PASTE(1)