Hi all, 

I have these two .dat files (I only show the first 20 lines for both):

    GO:0005509	PDCD6
    GO:0004672	CDK1
    GO:0005524	CDK1
    GO:0005634	CDK1
    GO:0005737	CDK1
    GO:0006468	CDK1
    GO:0005615	SERPINB6
    GO:0006629	APOC2
    GO:0006869	APOC2
    GO:0008047	APOC2
    GO:0042627	APOC2
    GO:0043085	APOC2
    GO:0001932	TADA2L
    GO:0003677	TADA2L
    GO:0005671	TADA2L
    GO:0006357	TADA2L
    GO:0007067	TADA2L
    GO:0008270	TADA2L
    GO:0016573	TADA2L

And

    GO:0000001	mitochondrion inheritance
    GO:0000002	mitochondrial genome maintenance
    GO:0000003	reproduction
    GO:0000005	ribosomal chaperone activity
    GO:0000006	high affinity zinc uptake transmembrane transporter activity
    GO:0000007	low-affinity zinc ion transmembrane transporter activity
    GO:0000008	thioredoxin
    GO:0000009	alpha-1,6-mannosyltransferase activity
    GO:0000010	trans-hexaprenyltranstransferase activity
    GO:0000011	vacuole inheritance
    GO:0000012	single strand break repair
    GO:0000014	single-stranded DNA specific endodeoxyribonuclease activity
    GO:0000015	phosphopyruvate hydratase complex
    GO:0000016	lactase activity
    GO:0000017	alpha-glucoside transport
    GO:0000018	regulation of DNA recombination
    GO:0000019	regulation of mitotic recombination
    GO:0000020	negative regulation of recombination within rDNA repeats
    (...)


When I try to make a join for both files, I only get a few results (exactly 10). The complete code is:

    ls *gene_association* | while read file;
    do
    echo;
    echo @@@ File: $file;
    echo;
    
    # New file "assoc_specie.txt"
    IFS='_' read -r -a array <<< "$file"
    SPECIE=${array[2]}
    
    #Filtering comments (!comment...)
    cat $file | grep -v '!' > assoc_$SPECIE.txt;
    gawk 'BEGIN{OFS="\t";FS="\t"}{print $5, $3}' assoc_$ESPECIE.txt > goTerms_$ESPECIE.dat;
    join goTerms_$SPECIE.dat gene_ontology.dat > join.dat
    
    echo
    done;

I don't know what I am doing wrong, but it's obvious that join is not showing all the results.

Thanks in advance

PS: assoc_specie.txt file has this format (only showing first line):

    UniProtKB	A0A024QZ42	PDCD6		GO:0005509	GO_REF:0000002	IEA	InterPro:IPR002048	F	HCG1985580, isoform CRA_c	A0A024QZ42_HUMAN|PDCD6|hCG_1985580	protein	taxon:9606	20160312	InterPro
    (...)
Hi all,

I just saw the mistake. I forgot to sort the file:

    (...)
        gawk 'BEGIN{OFS="\t";FS="\t"}{print $5, $3}' assoc_$ESPECIE.txt | sort | uniq > goTerms_$ESPECIE.dat;
    (...)