bash - why diff utility show the similar text in result file? -

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i using diff find differences between 2 text file. working great but, when change order of lines in text files, show similar text in result file.

here file1.txt:

>gi17 aaaaaa >gi30 bbbbbb >gi40 cccccc >gi92 dddddd >gi50 eeeeee >gi81 ffffff

file2.txt

>gi40 cccccc >gi01 bbbbbb >gi02 aaaaaa >gi30 bbbbbb

result.txt:

>gi17 aaaaaa >gi30        ??? bbbbbb       ??? >gi92 dddddd >gi01 bbbbbb >gi50 eeeeee >gi81 ffffff >gi02 aaaaaa >gi30        ??? bbbbbb       ???

diff statement:

$ diff c:/users/user/desktop/file1.txt c:/users/user/desktop/file2.txt > c:/users/user/desktop/result.txt

why displays

>gi30 bbbbbb

as defferent?

edit 1: want search occurrence of each line in file 1 in whole file 2 because 2 files not ordered , cannot touch them (genetic data).

edit 2: want execute join command php code. run in cygwin cmd application but, did not run php

shell_exec("c:\\cygwin64\\bin\\bash.exe --login -c 'join -v 1 <(sort $olddatabasefile.txt) <(sort $newdatabasefile.txt) > $text_files_path/delseqgi.txt 2>&1'");

thanks.

to difference between files use bash join util below:-

description      join utility performs ``equality join'' on specified files ,      writes result standard output.  ``join field''      field in each file files compared.  first field in      each line used default.  there 1 line in output each      pair of lines in file1 , file2 have identical join fields.  each      output line consists of join field, remaining fields file1      , remaining fields file2.   -v file_number          not display default output, display line each          unpairable line in file file_number.  options -v 1 , -v 2          may specified @ same time.   -1 field          join on field'th field of file1.   -2 field          join on field'th field of file2.  join -v 1 <(sort file1.txt) <(sort file2.txt)     # lines in file file1.txt file file2.txt not have join -v 2 <(sort file1.txt) <(sort file2.txt)     # vice versa of above

original answer/credits:- https://stackoverflow.com/a/4544780/5291015


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