This works like a charm, except that it takes a tab-delimited file and returns a space-delimited file. My fault for not mentioning it in the original post.
Hi :)
I have some problems with "FOR"...
I have a text file in this format:
name1
www.link1/random_number
name2
www.link2/random_number
name3
www.link3/random_number
...
(Names and info changes)
Now, I need: (4 Replies)
Hi this is my first time posting ever. I'm relatively new in using AWK/SED, I've been trying many a solution. I'm trying to replace the 59th column in a file where if I encounter '' then I would like to replace it with the word NULL.
example
0 , '' , '' , 0 , 195.538462
change it to
0... (5 Replies)
hi,
i have file say email.temp looks like
Bell_BB 17
Bell_MONTHLY 888
SOLO_UNBEATABLE 721
and another file r3
Bell BB,Bell_BB
Bell,Bell_MONTHLY
SOLO,SOLO_UNBEATABLE
i want email.temp files $1 say Bell_BB should be replaced by r3 Bell BB and Bell_MONTHLY by... (2 Replies)
How would I do this? How could i use <> symbols for numbers in the find/replace code below?
perl -pi -e 's/test/tst/'
OR is there a better way?
100 5000 2 432 4 2 33 4 5 6 65 300 301
needs to be:
100 300 2 300 4 2 33 4 5 6 65 300 300
also it might not always need spaces... i... (12 Replies)
Dear board,
(I am trying to post this the 3rd time, seems there's some conflicts with my firefox with this forum, now use IE)
------
yes, I have searched the forum, but seems my ? is too complicated.
------------origianl file ---------------
\storage\qweq\ertert\ertert\3452\&234\test.rec... (4 Replies)
I have looked around and there are several examples of how to use sed, but I don't think any of them help me very much with what I am trying to do.
I have a text file like this....
1! SRCNAM = 00001 !
1! X = 50.0000, 0.0000,... (10 Replies)
Hello all. I am a beginner UNIX user who is using UNIX to work on a bioinformatics project for my university.
I have a bit of a complicated issue in trying to use sed (or awk) to "find and replace" bases (letters) in a genetics data spreadsheet (converted to a text file, can be either... (3 Replies)
All,
I have thousands of lines in a file with following format
DATA=_ONE_XXX_YYY_CCC_HHHG_
DATA1=_GGG_JJJJ_HHH_UUU_JJJJ_HHHH_LLL_
DATA3=_MMM_GG_NN_QQQQ_FFF_III_
I want to replace _ with . by ignoring the first (=_) and last (_)
So that out put should looks like... (4 Replies)
i Have a file as following
view pz19a0c0/1000T_J_3MoDw9DSLh1ZsCubdua-LKOQmbtiVgkIsiMbSiwF467?sessionId=15451401994597121249
view pz19a0c0/100086X67pR0MwzWnhhSO6sAEoxeFMyhh-IIbUCCdxicaQM4FC9?sessionId=154514019945971212494898
view/cart ... (5 Replies)
Discussion started by: Raghuram717
5 Replies
LEARN ABOUT DEBIAN
vcf-isec
VCF-ISEC(1) User Commands VCF-ISEC(1)NAME
vcf-isec - create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files
SYNOPSIS
vcf-isec [OPTIONS] file1.vcf file2.vcf ...
DESCRIPTION
About: Create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files.
Note that lines from all files can be intermixed together on the output, which can yield unexpected results.
OPTIONS -C, --chromosomes <list|file>
Process the given chromosomes (comma-separated list or one chromosome per line in a file).
-c, --complement
Output positions present in the first file but missing from the other files.
-d, --debug
Debugging information
-f, --force
Continue even if the script complains about differing columns.
-o, --one-file-only
Print only entries from the left-most file. Without -o, all unique positions will be printed.
-n, --nfiles [+-=]<int>
Output positions present in this many (=), this many or more (+), or this many or fewer (-) files.
-p, --prefix <path>
If present, multiple files will be created with all possible isec combinations. (Suitable for Venn Diagram analysis.)
-t, --tab <chr:pos:file>
Tab-delimited file with indexes of chromosome and position columns. (1-based indexes)
-w, --win <int>
In repetitive sequences, the same indel can be called at different positions. Consider records this far apart as matching (be it a
SNP or an indel).
-h, -?, --help
This help message.
EXAMPLES
bgzip file.vcf; tabix -p vcf file.vcf.gz bgzip file.tab; tabix -s 1 -b 2 -e 2 file.tab.gz
vcf-isec 0.1.5 July 2011 VCF-ISEC(1)