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Compare fasta file with text file in bash script

Hi everyone ! I have some problems with my bash script. I have a text file( filt80more.txt) that contain my best alignments and I want to compare the alignments in that text file(filt80more.txt) with directory that contain all alignments(Tcoffee_outputs/E.aa.fa.aln) and take out that best alignments from directory(Tcoffee_outputs/E.aa.fa.aln) to my new folder (Filtrerad). I will be very grateful for your help :) 

  for FILE1 in Tcoffee_outputs/E*.aa.fa.aln;
   do
    for FILE2 in `cat filt80more.txt`;
      do
       if [ $( diff "${FILE1}" "${FILE2}" ) == 0 ];
        then
mv Tcoffee_outputs/$FILE1~/Users/vazgengevorgyan/Desktop/perl_krill/merged_min_4_species_filtered/Filtrerad/$FILE1
       break
       fi
    done
   done
alignment bash script fast file text file
• 2,059 views • link
updated by lieven.sterck lieven.sterck • written by ArusjakGevorgyan • ArusjakGevorgyan

and what exactly is the problem with the script? (I'm not saying it's correct otherwise!). do you get any errors/warnings? or is it just not doing what you expect?

L.

• 0 views • link
written by lieven.sterck lieven.sterck

Hi :) I get this error: diff: EOG090Y02RG: No such file or directory getfiles.sh: line 105: [: ==: unary operator expected

• 0 views • link
written by ArusjakGevorgyan • ArusjakGevorgyan

1 answer

Try this in the if statement :

if [ $( diff "${FILE1}" "${FILE2}" | wc -l ) == 0 ];

so add " | wc -l " to the if statement. this will check if there are differences reported (= line count will be > 0 )

• 0 views • link
written by lieven.sterck lieven.sterck

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

• 0 views • link
written by GenoMax GenoMax

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