Awk- Indexing a list of numbers in file2 to print certain rows in file1
Hi
Does anyone know of an efficient way to index a column of data in file2 to print the coresponding row in file1 which corresponds to the data in file2 AND 30 rows preceding and after the row in file1.
For example suppose you have a list of numbers in file2 (single column) as follows:
Code:
rs25678
rs25679
rs25680
rs25681
rs25682
rs25683
file1:
Code:
2 9658 rs25681 G G GT1=0.20;GT2=0.65;GT3=0.75
2 4258 rs25679 A G GT1=0.20;GT2=0.65;GT3=0.76
2 4258 rs25680 T T GT1=0.20;GT2=0.65;GT3=0.77
I would like all rows in file1 corresponding to the file2 numbers indexed printed AND 30 rows before and after also printed.
Desired output:
Code:
. . . . . .
2 9658 rs25681 G G GT1=0.20;GT2=0.65;GT3=0.75
. . . . . .
. . . . . .
2 4258 rs25679 A G GT1=0.20;GT2=0.65;GT3=0.76
. . . . . .
. . . . . .
2 4258 rs25680 T T GT1=0.20;GT2=0.65;GT3=0.77
. . . . . .
. . . . . .
Dots signify 30 rows of data preceding and after the targeted rows being printed along with targeted rows indexed in file2
Thanks...
Last edited by Geneanalyst; 10-30-2018 at 01:59 PM..
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Please your help with this.
I have 2 files,
File_1-->contains a column of N numbers
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Also file 2 will either start with A, B or C.
And 3rd column in file 2 is always F2.
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Here is an example.
file 1:
100
103
104
108
file 2:
... (6 Replies)
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I hope somebody could help me with this:
I have this File1 (real has 5 million of lines):
Number Category
--------------- --------------------------------------
8734060355 3
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file1:
EN_comp12952_c0_seq3:367-1668
ES_comp17168_c1_seq6:1-864
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I have 2 file, file1 and file2. file1 has some keys and file2 has keys+some other data. I want to remove the lines from file2,if the key for that line exists in file1.
file1:
key1
key2
flie2:
key1,moredata
key2,moredata
key3,moredata
Required output:
key3,moredata
Thanks
EDIT:... (6 Replies)
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file1
file2
desired output:
I'm getting the lines to match
awk 'FNR==NR {a++}; FNR!=NR && a' file1 file2
but they are in sorted order, which is not what I want:
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Discussion started by: cmccabe
6 Replies
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xzcmp
XZDIFF(1) XZ Utils XZDIFF(1)NAME
xzcmp, xzdiff, lzcmp, lzdiff - compare compressed files
SYNOPSIS
xzcmp [cmp_options] file1 [file2]
xzdiff [diff_options] file1 [file2]
lzcmp [cmp_options] file1 [file2]
lzdiff [diff_options] file1 [file2]
DESCRIPTION
xzcmp and xdiff invoke cmp(1) or diff(1) on files compressed with xz(1), lzma(1), gzip(1), or bzip2(1). All options specified are passed
directly to cmp or diff. If only one file is specified, then the files compared are file1 (which must have a suffix of a supported com-
pression format) and file1 from which the compression format suffix has been stripped. If two files are specified, then they are uncom-
pressed if necessary and fed to cmp(1) or diff(1). The exit status from cmp or diff is preserved.
The names lzcmp and lzdiff are provided for backward compatibility with LZMA Utils.
SEE ALSO cmp(1), diff(1), xz(1), gzip(1), bzip2(1), zdiff(1)BUGS
Messages from the cmp(1) or diff(1) programs refer to temporary filenames instead of those specified.
Tukaani 2009-07-05 XZDIFF(1)