If it is a "fixed width file" as you said, then you can identify the broken ones by the deviating number of characters in it.
The regexp:
matches exactly a single character. So you just have to repeat this the number of times you expect the line to be wide to find all non-broken lines:
where "n" is the number of characters. Now you just reverse the search by using i.e "grep -v":
But you probably want to correct this circumstance, so "grep" is not the right tool - but "sed" is, and it works with the same syntax:
First every line has line feeds deleted. Then every line NOT consisting of n characters (the "!") - that is: the broken ones - will cause the next line to be read in and added to the line before. Then control branches to the beginning of the script again. If the line still is too short, even the next line will be read in, etc.., until the correct line length is reached. Then the line is printed in the last statement.
In the perl one-liner below I am identifying the runs of 6a or 6A in each line starting with >. The code seems close but it prints each > line no matter if it has 6a or 6A in it. Only the line with the 6a or 6A needs to be printed.
So using the input file, only the >hg19_refGene_NM_001918_3... (10 Replies)
Gurus,
I have a data file which has a certain number of columns say 101. It has one description column which contains foreign characters and due to this some times, those special characters are translated to new line character and resulting in failing the process.
I am using the following awk... (4 Replies)
Hi - I have req to join broken lines and remove empty lines but should NOT be in one line. It has to be as is line by line. The challenge here is there is no end of line/start of line char.
thanks in advance
Source:-
2003-04-34024|04-10-2003|Claims|Claim|01-13-2003|Air Bag:Driver;... (7 Replies)
Hi,
I am running my pipeline and capturing all stout from multiple programs to a .txt file. I want to go into that .txt file and search for specific lines, and finally print those lines in a second .txt file.
I can do this using grep, awk, or sed for each line, but have not been able to get... (2 Replies)
Hi,
I have a huge file with sql broken statements like:
PP3697HB @@@@0
<<<<<<Record has been deleted as per PP3697HB>>>>>>
FROM sys.xtab_ref rc,sys.xtab_sys f,sys.domp ur WHE
RE rc.milf = ur.milf AND rc.molf = f.molf AND ur.dept = 'SWIT'AND ur
.department = 'IND' AND share = '2' AND... (4 Replies)
i have a file of this type:
SEAT-RES¦$D0317.PBOUC32A.GURD3591 ¦00000100¦201203161000¦B¦32 ¦2WN¦EUS-¦MAN¦VAS¦4827¦TTL011 ¦
SEAT-RES¦$D0317.PBOUC32A.GURD3591 ¦00000101¦201203161000¦B¦25 ¦2WN¦EUS-¦MAN¦VAS¦4827¦TTL011 ¦ ... (22 Replies)
Hi everybody,
i have this biological situation to fix:
> Id.1
ACGTACANNNNNNNNNNNACGTGCNNNNNNNACTGTGGT
>Id.2
ACGGGT
>Id.3
ACGTNNNNNNNNNNNNACTGGGGG
>Id.4
ACGTGCGNNNNNNNNGGTCANNNNNNNNCGTGCAAANNNNN
........
....
These are nucleotidic sequences with some "NNNN..." always of the same... (4 Replies)
I have a plain test file with a delimeter ''. In this file some lines are broken into two. The first part of these broken line will have 6 columns and the second part will have 4. These broken lines will be consicutive.
I want to join the two consicutive lines which are having 6 fields and 4... (8 Replies)
Gurus,
I am struggling with a issue and thought I could use some of your expertise.
Need Help with this
I have a flat file that has millions of records
24|john|account ~ info |56|
25|kuo|account ~ journal |58|
27|kim|account ~ journal |59|
28|San|account ~
journal |60|... (3 Replies)