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Full Discussion: extract multiple cloumns from multiple files; skip rows and include filenames; awk
Top Forums Shell Programming and Scripting extract multiple cloumns from multiple files; skip rows and include filenames; awk Post 302345229 by manishabh on Tuesday 18th of August 2009 05:47:51 PM
Old 08-18-2009
extract multiple cloumns from multiple files; skip rows and include filenames; awk
Hello,

I am trying to write a bash shell script that does the following:

1.Finds all *.txt files within my directory of interest
2. reads each of the files (25 files) one by one (tab-delimited format and have the same data format)
3. skips the first 10 rows of the file
4. extracts and prints out columns 2,14 , 15 into one output file
5. adds a new column to the final output file with the name of the txt file from where the data was extracted.

I have written a shell script which is not working properly and doesnot have the code for the part to skip 10 rows.

Below I have pasted a sample input file, output file and my code


Input file format:

TYPEtexttexttexttextintegerfloatfloattexttexttextintegerintegerintegerintegerFEPARAMSProtocol_NamePr otocol_dateScan_DateScan_ScannerNameScan_NumChannelsScan_MicronsPerPixelXScan_MicronsPerPixelYScan_O riginalGUIDGrid_NameGrid_DateGrid_NumSubGridRowsGrid_NumSubGridColsGrid_NumRowsGrid_NumColsDATAmiRNA-v1_95_May07 (Read Only)####################Agilent Technologies Scanner G2505B US45102930155a18d8bd4-628a-4054-b2ba-45c7a66de583016436_D_20070426############1119282* TYPEfloatfloatfloatintegerintegerfloatintegerfloatfloatfloatintegerfloatfloatintegerSTATSgDarkOffset AveragegDarkOffsetMediangDarkOffsetStdDevgDarkOffsetNumPtsgSaturationValuegAvgSig2BkgNegCtrlgNumSatF eatgLocalBGInlierNetAvegLocalBGInlierAvegLocalBGInlierSDevgLocalBGInlierNumgGlobalBGInlierAvegGlobal BGInlierSDevgGlobalBGInlierNumDATA26.709275.44777100012031791.11899038.717365.42632.954291202965.426 32.9542912029* TYPEintegerintegerintegertextintegertextintegerintegertexttexttexttextfloatfloatFEATURESFeatureNumRo wColchr_coordSubTypeMaskSubTypeNameProbeUIDControlTypeProbeNameGeneNameSystematicNameDescriptionPosi tionXPositionYDATA111 0 01miRNABrightCorner30miRNABrightCorner30miRNABrightCorner30 6774.29228.723DATA212 66Structural21DarkCornerDarkCornerDarkCorner 6800.2229.421DATA313chr14:100595916-1005958970 30A_25_P00010115hsa-miR-154*hsa-miR-154*NA6826.51228.385DATA414chr8:135881995-1358820100 50A_25_P00010390hsa-miR-30bhsa-miR-30bNA6850.48228.853DATA515chr14:100558179-1005581610 70A_25_P00010956hsa-miR-379hsa-miR-379NA6875.37228.408DATA616chr19:058916206-0589161860 80A_25_P00011941hsa-miR-517bhsa-miR-517bNA6900.98229.321

Output format: tab delimited file. The last column shows the filename from which the data was extracted

16774.29228.723ABC.txt26800.2229.421ABC.txt36826.51228.385DEF.txt46850.48228.853DEF.txt56875.37228.4 08XYZ.txt66900.98229.321XYZ.txt


My incomplete code:
Code:
find -name '*.txt' |
while read filename
do
awk -F"\t" -v name="$file"'
BEGIN {OFS="|"}
{print $2,$14,$15,name}
' $filename > output.txt
done

thanks in advance for your help.
Last edited by Yogesh Sawant; 06-01-2010 at 10:48 AM.. Reason: added code tags
 

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LEARN ABOUT REDHAT

unix2dos

unix2dos(1)						      General Commands Manual						       unix2dos(1)

NAME

       unix2dos - UNIX to DOS text file format converter

SYNOPSYS

       unix2dos [options] [-c convmode] [-o file ...] [-n infile outfile ...]

       Options:

       [-hkqV] [--help] [--keepdate] [--quiet] [--version]

DESCRIPTION

       This manual page documents unix2dos, the program that converts text files in UNIX format to DOS format.

OPTIONS

       The following options are available:

       -h --help
	      Print online help.

       -k --keepdate
	      Keep the date stamp of output file same as input file.

       -q --quiet
	      Quiet mode. Suppress all warning and messages.

       -V --version
	      Prints version information.

       -c --convmode convmode
	      Sets conversion mode. Simulates unix2dos under SunOS.

       -o --oldfile file ...
	      Old file mode. Convert the file and write output to it. The program default to run in this mode. Wildcard names may be used.

       -n --newfile infile outfile ...
	      New  file  mode.	Convert the infile and write output to outfile. File names must be given in pairs and wildcard names should NOT be
	      used or you WILL lost your files.

EXAMPLES

       Get input from stdin and write output to stdout.

	      unix2dos

       Convert and replace a.txt. Convert and replace b.txt.

	      unix2dos a.txt b.txt

	      unix2dos -o a.txt b.txt

       Convert and replace a.txt in ASCII conversion mode.  Convert and replace b.txt in ISO conversion mode.

	      unix2dos a.txt -c iso b.txt

	      unix2dos -c ascii a.txt -c iso b.txt

       Convert and replace a.txt while keeping original date stamp.

	      unix2dos -k a.txt

	      unix2dos -k -o a.txt

       Convert a.txt and write to e.txt.

	      unix2dos -n a.txt e.txt

       Convert a.txt and write to e.txt, keep date stamp of e.txt same as a.txt.

	      unix2dos -k -n a.txt e.txt

       Convert and replace a.txt. Convert b.txt and write to e.txt.

	      unix2dos a.txt -n b.txt e.txt

	      unix2dos -o a.txt -n b.txt e.txt

       Convert c.txt and write to e.txt. Convert and replace a.txt.  Convert and replace b.txt. Convert d.txt and write to f.txt.

	      unix2dos -n c.txt e.txt -o a.txt b.txt -n d.txt f.txt

DIAGNOSTICS

BUGS

       The program does not work properly under MSDOS in stdio processing mode.  If you know why is that so, please tell me.

AUTHOR

       Benjamin Lin - ( blin@socs.uts.edu.au )

MISCELLANY

       Tested environment:

	      Linux 1.2.0 with GNU C 2.5.8

	      SunOS 4.1.3 with GNU C 2.6.3

	      MS-DOS 6.20 with Borland C++ 4.02

       Suggestions and bug reports are welcome.

SEE ALSO

       dos2unix(1)

1995.03.31							   unix2dos v2.2						       unix2dos(1)
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