Converting text files to xls through awk script for specific data format Post: 302882605

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Top Forums Shell Programming and Scripting Converting text files to xls through awk script for specific data format Post 302882605 by Amit1 on Wednesday 8th of January 2014 04:46:17 AM

01-08-2014

Registered User

Converting text files to xls through awk script for specific data format

Dear Friends,
I am in urgent need for awk/sed/sh script for converting a specific data format (.txt) to .xls.
The input is as follows:

Code:

>gi|1234|ref|
  
 Query = 1 - 65, Target = 1677 - 1733
 Score = 8.38, E = 0.6529, P = 0.0001513, GC =  46
  fd sdfsdfsdfsdf
fsdfdsfdfdfdfdfdf
dfdfdfdfedfsdfsdfdsf
dfdfdfsdfsdfsdfsdfdsf
sdfdsfdfdfdfdsfdfdfdfd
  
>gi|54367|ref|


  fd sdfsdfsdfsdf
fsdfdsfdfdfdfdfdf
dfdfdfdfedfsdfsdfdsf
dfdfdfsdfsdfsdfsdfdsf
sdfdsfdfdfdfdsfdfdfdfd

 Query = 1 - 65, Target = 6780 - 6812
 Score = 8.13, E = 0.7692, P = 0.0001782, GC =  36

//
................EOF................................

The desired output EXCEL table will the contain the headers and data in the following order:

Code:

            Serial   Query start    Query End   target start   target end   Score   E   P   GC
       >gi|1234|ref|   1   65   1677   1733   8.38   0.6529   0.000151   46
       >gi|54367|ref|   1   65   6780   6812   8.13   0.7692   0.000178   36

I have to iteratively perform this conversion in several (1000+ ) .txt files.

Code:

awk '/gi/ {print ;}'
awk '/Query/{print $3,$5,$8,$10;}'
awk '/Score/ {print $3, $6, $9, $12;}'

I was trying with the preliminary awk one-liners and trying to use "CAT" for concatenating all 3 .xls output which did not fulfiling the purpose.
I need urgent help!!!!!!!!!, looking forward for your responses (new script/ modified version of the one-liners).
P.S: Input file and output file is attached for more clarity.
Best regards,
Amit

Moderator's Comments:

Although attaching files sometimes helps, using CODE tags (as required by forum rules) makes it much easier for those of us trying to help you see spacing between fields and to be able to see field alignments. Please use CODE tags when including sample code, sample input file data, and sample output file data.

Input file.txt (437 Bytes)

InputOutput.zip (6.1 KB)

Last edited by Don Cragun; 01-10-2014 at 05:37 AM..

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