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Top Forums Shell Programming and Scripting Challenging Awk array problem Post 302423685 by polsum on Friday 21st of May 2010 05:29:46 PM
Old 05-21-2010
Challenging Awk array problem

Hi,

I rather have a very complicated awk problem here, at least to me. I have two files.

File 1:

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:
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 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

If field 6 of file 1 is same as field 4 of file 2, then see if field 5 of file 2 lies within the range specified by the fields 7 and 8 of file 1. If yes, extract the line from file 2 and add the fields 11, 12 and 13 of file 1 in to a separate file. Whew!

Ok for example - field 4 of file 2 i.e. chr1 is same as field 6 of file 1. Then see if field 5 of file 2 i.e.3000072 (which is always a number) lies in the range of fields 7 and 8 (3000001 3000156) of file 1. So, I need the output (the line from file 2 plus fields 11,12 and 13 of file 1) in a separate file as

Code:
4|17999 - gi|149361523|ref|NC_000074.5|NC_000074  chr1  3000072 TTTATCGTCATCGTC L1_Mur2    LINE    L1

Thank you very much in advance

Last edited by Scott; 05-21-2010 at 06:44 PM.. Reason: Please use code tags
 

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GIT-SYMBOLIC-REF(1)						    Git Manual						       GIT-SYMBOLIC-REF(1)

NAME
git-symbolic-ref - Read, modify and delete symbolic refs SYNOPSIS
git symbolic-ref [-m <reason>] <name> <ref> git symbolic-ref [-q] [--short] <name> git symbolic-ref --delete [-q] <name> DESCRIPTION
Given one argument, reads which branch head the given symbolic ref refers to and outputs its path, relative to the .git/ directory. Typically you would give HEAD as the <name> argument to see which branch your working tree is on. Given two arguments, creates or updates a symbolic ref <name> to point at the given branch <ref>. Given --delete and an additional argument, deletes the given symbolic ref. A symbolic ref is a regular file that stores a string that begins with ref: refs/. For example, your .git/HEAD is a regular file whose contents is ref: refs/heads/master. OPTIONS
-d, --delete Delete the symbolic ref <name>. -q, --quiet Do not issue an error message if the <name> is not a symbolic ref but a detached HEAD; instead exit with non-zero status silently. --short When showing the value of <name> as a symbolic ref, try to shorten the value, e.g. from refs/heads/master to master. -m Update the reflog for <name> with <reason>. This is valid only when creating or updating a symbolic ref. NOTES
In the past, .git/HEAD was a symbolic link pointing at refs/heads/master. When we wanted to switch to another branch, we did ln -sf refs/heads/newbranch .git/HEAD, and when we wanted to find out which branch we are on, we did readlink .git/HEAD. But symbolic links are not entirely portable, so they are now deprecated and symbolic refs (as described above) are used by default. git symbolic-ref will exit with status 0 if the contents of the symbolic ref were printed correctly, with status 1 if the requested name is not a symbolic ref, or 128 if another error occurs. GIT
Part of the git(1) suite Git 1.8.3.1 06/10/2014 GIT-SYMBOLIC-REF(1)
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