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Full Discussion: A find and replace script
Operating Systems Linux A find and replace script Post 302659943 by herasj01 on Thursday 21st of June 2012 04:49:03 PM
Old 06-21-2012
A find and replace script

Hello everyone,
I am trying to do a simple script (shell or perl) for a bioinformatic problem, where I want to use a list from file2 and append this information to file1 (output).

Example:
File1
Code:
>Apple1 
GAGACGATTTATATATAGAAGAGAG
>Banana2 
CAGAGAGAGAGACCCCCCCCCCCC

File2
Code:
>Apple1      20     100
>Banana2    30     300

Ouput (new File1)
Code:
>Apple1   20     100
GAGACGATTTATATATAGAAGAGAG
>Banana2  30     300
CAGAGAGAGAGACCCCCCCCCCCC


If anyone has any feedback that would be greatly appreciated.


Cheers

herasj

Last edited by Scrutinizer; 06-21-2012 at 05:49 PM.. Reason: code tags
 

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JOIN(1) 						      General Commands Manual							   JOIN(1)

NAME
join - relational database operator SYNOPSIS
join [ options ] file1 file2 DESCRIPTION
Join forms, on the standard output, a join of the two relations specified by the lines of file1 and file2. If file1 is `-', the standard input is used. File1 and file2 must be sorted in increasing ASCII collating sequence on the fields on which they are to be joined, normally the first in each line. There is one line in the output for each pair of lines in file1 and file2 that have identical join fields. The output line normally con- sists of the common field, then the rest of the line from file1, then the rest of the line from file2. Fields are normally separated by blank, tab or newline. In this case, multiple separators count as one, and leading separators are dis- carded. These options are recognized: -an In addition to the normal output, produce a line for each unpairable line in file n, where n is 1 or 2. -e s Replace empty output fields by string s. -jn m Join on the mth field of file n. If n is missing, use the mth field in each file. -o list Each output line comprises the fields specified in list, each element of which has the form n.m, where n is a file number and m is a field number. -tc Use character c as a separator (tab character). Every appearance of c in a line is significant. SEE ALSO
sort(1), comm(1), awk(1) BUGS
With default field separation, the collating sequence is that of sort -b; with -t, the sequence is that of a plain sort. The conventions of join, sort, comm, uniq, look and awk(1) are wildly incongruous. 7th Edition April 29, 1985 JOIN(1)
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