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Top Forums Shell Programming and Scripting Join lines from two files based on match Post 302844326 by pathunkathunk on Sunday 18th of August 2013 01:46:36 PM
Old 08-18-2013
Join lines from two files based on match

I have two files.
File1
Code:
>gi|11320906|gb|AF197889.1|_Buchnera_aphidicola
ATGAAATTTAAGATAAAAAATAGTATTTT
>gi|11320898|gb|AF197885.1|_Buchnera_aphidicola
ATGAAATTTAATATAAACAATAAAA
>gi|11320894|gb|AF197883.1|_Buchnera_aphidicola
ATGAAATTTAATATAAACAATAAAATTTTT

File2
Code:
AF197885	Uroleucon aeneum
AF197886	Uroleucon jaceae
AF197889	Uroleucon obscurum
AF197883	Uroleucon astronomus
AF197893	Uroleucon erigeronense

For all lines in file1, I want to match the term bracked by "gb|" and "." (i.e. AF197889 in the first line) to a line in file2. In this example of file1, all terms of interest start with "AF" but this isn't always the case.

If there's a match, I'd like to append the species name in file2, preceded by "_host_" to the matching line in file1, using underscores and no spaces. Desired output:
Code:
>gi|11320906|gb|AF197889.1|_Buchnera_aphidicola_host_Uroleucon_obscurum
ATGAAATTTAAGATAAAAAATAGTATTTT
>gi|11320898|gb|AF197885.1|_Buchnera_aphidicola_host_Uroleucon_aeneum
ATGAAATTTAATATAAACAATAAAA
>gi|11320894|gb|AF197883.1|_Buchnera_aphidicola_host_Uroleucon_astronomus
ATGAAATTTAATATAAACAATAAAATTTTT

With the meager skills I have, I could use "|" as a filed separator for file 1 and use awk to fill an array to find matches. But I'm not sure how to to append the file2 data, or how to accomplish it in one step. Can anyone help?

Last edited by Don Cragun; 08-18-2013 at 02:56 PM.. Reason: CODE tags; not QUOTE tags for input, output, and code samples.
 

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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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