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Top Forums Shell Programming and Scripting Help with merge data with a reference sequence Post 302978378 by cpp_beginner on Friday 29th of July 2016 12:38:12 PM
Old 07-29-2016
Help with merge data with a reference sequence

I have two input file.:

File 1 is a large reference sequence (A large Fasta sequence);

File 1 (is a file which first line is the header description and line other ">" is its corresponding word and counting from 1 till end of file);
Code:
>Data_1
ASWDADAQTWQQGSAAAAASDAFAFA
.
.

File 2 is list of data that I interested to replace specific word at specific location in File 1;
File 2 (3 column in File 2 and is tab-delimited format);
Code:
Data_1 2 Z
Data_1 3 T
Data_1 10 A
Data_1 11 T
.
.

Desired Output File
Code:
>Data_1
AZTDADAQTATQGSAAAAASDAFAFA
.
.

File 1 is a long record Fasta file (Include a first line of header description and line after ">" is its corresponding word).
File 2 is a file got 3 column (Tab-delimited).
First column is the header description (without ">") of File 1;
Second column is the position of word that I wanna to replace in File 1 based on Third column data;
Third column is the word that I wanna to replace it which specific word/specific position of File 1;

Awk code try
Code:
awk -F "\t" '(FNR==1){x++} (x==1){a[$1][$2]=$3;next} (x==2){if($0~/>/){h=$0;sub(/^.*Data/,"",h);sub(/ .*/,"",h)} else{seq[h]=seq[h]$0}} END{for(i in a){s=0; for(j in a[i]){m=m substr(seq[i],s,j-1) a[i][j];s=j+1} m=m substr(seq[i],s); print ">Data"i"\n"m}}' File 2 File 1

I would like to replace specific word (exclude header >Data_1) at specific location in File 1 if it is list on File 2 data.
My main objective is hope to replace specific word at specific location in File 1 based on the record provided in File 2 (specific position and replace with new word based on File 2).

Thanks for any advice.

Last edited by cpp_beginner; 07-31-2016 at 12:04 PM.. Reason: Corrected code tags.
 

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PR(1)							      General Commands Manual							     PR(1)

NAME
pr - print file SYNOPSIS
pr [ option ... ] [ file ... ] DESCRIPTION
Pr produces a printed listing of one or more files on its standard output. The output is separated into pages headed by a date, the name of the file or a specified header, and the page number. With no file arguments, pr prints its standard input. Options apply to all following files but may be reset between files: -n Produce n-column output. +n Begin printing with page n. -b Balance columns on last page, in case of multi-column output. -d Double space. -en Set the tab stops for input text every n spaces. -h Take the next argument as a page header (file by default). -in Replace sequences of blanks in the output by tabs, using tab stops set every n spaces. -f Use formfeeds to separate pages. -ln Take the length of the page to be n lines instead of the default 66. -m Print all files simultaneously, each in one column. -n Number the lines of each file. -on Offset the left margin n character positions. -sc Separate columns by the single character c instead of aligning them with white space. A missing c is taken to be a tab. -t Do not print the 5-line header or the 5-line trailer normally supplied for each page. -wn For multi-column output, take the width of the page to be n characters instead of the default 72. SOURCE
/sys/src/cmd/pr.c SEE ALSO
cat(1), lp(1) PR(1)
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