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Full Discussion: Attach filename to wc results on massive number of files
Top Forums Shell Programming and Scripting Attach filename to wc results on massive number of files Post 303032276 by yifangt on Thursday 14th of March 2019 01:22:04 PM
Old 03-14-2019
Attach filename to wc results on massive number of files
Hello,
I have massive number of big files that needed to be counted for the total number of lines (> 100x millions) each. I want the file name attached to the count results so that they are aligned nicely matching name and counts.
I could do each file at a time, which will take hours to finish, so that the jobs were sent to background as I have multiple cores available to get the job done quickly. The problem with my script is the "echo -n $f" "; always accomplishes first, and the ${f}_R1.fq.gz | wc -l part is behind too much and the result was not aligned as expected.

Here is my code:
Code:
for f in $(cat ${LIST1}); do 
echo -n $f" "  >> raw_reads_count.table1; 
zcat ${f}_R1.fq.gz | wc -l >> raw_reads_count.table1 &      #This is the part
 done
------------------------------------------------------------------------------------------------------
messed-up output:
a      
bb    
ccc   
xyz 
267234214
777234211
937214233
1027254258
------------------------------------------------------------------------------------------------------
 Expected output:
a    267234214
bb   937214233
ccc  777234211
xyz 1027254258

How should I improve my script to get what is expected? Thanks a lot!
 

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LEARN ABOUT MOJAVE

quot

quot(1M)                                                  System Administration Commands                                                  quot(1M)

NAME

       quot - summarize file system ownership

SYNOPSIS

       quot [-acfhnv] filesystem...

       quot -a [-cfhnv]

DESCRIPTION

       quot  displays  the  number  of blocks (1024 bytes) in the named filesystem (one or more) currently owned by each user. There is a limit of
       2048 blocks. Files larger than this will be counted as a 2048 block file, but the total block count will be correct.

OPTIONS

       The following options are supported:

       -a       Generate a report for all mounted file systems.

       -c       Display three columns giving a file size in blocks, the number of files of that size, and a cumulative total of blocks  containing
                files of that size or a smaller size.

       -f       Display  three  columns  giving,  for each user, the number of blocks owned, the count of number of files, and the user name. This
                option is incompatible with the -c and -v options.

       -h       Estimate the number of blocks in the file. This does not account for files with holes in them.

       -n       Attach names to the list of files read from standard input. quot -n cannot be used alone, because it expects  data  from  standard
                input. For example, the pipeline

                ncheck myfilesystem | sort +0n | quot -n myfilesystem

                will produce a list of all files and their owners. This option is incompatible with all other options.

       -v       In  addition  to the default output, display three columns containing the number of blocks not accessed in the last 30, 60, and 90
                days.

OPERANDS

       filesystem      mount-point of the filesystem(s) being checked

USAGE

       See largefile(5) for the description of the behavior of quot when encountering files greater than or equal to 2 Gbyte ( 2**31 bytes).

EXIT STATUS

       0        Successful operation.

       32       Error condition (bad or missing argument, bad path, or other error).

FILES

       /etc/mnttab     Lists mounted file systems.

       /etc/passwd     Used to obtain user names

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE         |      ATTRIBUTE VALUE        |
       +-----------------------------+-----------------------------+
       |Availability                 |SUNWcsu                      |
       +-----------------------------+-----------------------------+

SEE ALSO

       du(1), mnttab(4), passwd(4), attributes(5), largefile(5)

NOTES

       This command can only be used by the super-user.

SunOS 5.10                                                          30 May 2001                                                           quot(1M)
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