Sort bash array following an ordered array pattern

Question

I have an array, let's call it ensembldb that has the following lines:

rs2799070   ENST00000379389 ENSG00000187608 ISG15   inframe_insertion   NA  NA  protein_coding  ISG15   ubiquitin-like  modifier    [Source:HGNC    Symbol;Acc:HGNC:4053]NM_005101.3    NP_005092
rs2799070   ENST00000458555 ENSG00000224969 AL645608.2  missense_variant    NA  NA  antisense   NA  NULL    NULL
rs2799070   ENST00000624652 ENSG00000187608 ISG15   inframe_deletion    NA  NA  protein_coding  ISG15   ubiquitin-like  modifier    [Source:HGNC    Symbol;Acc:HGNC:4053]NULL   NULL
rs2799070   ENST00000624697 ENSG00000187608 ISG15   frameshift_variant  NA  NA  protein_coding  ISG15   ubiquitin-like  modifier    [Source:HGNC    Symbol;Acc:HGNC:4053]NULL   NULL

and another ordered array, let's call it ordered_array:

frameshift_variant
missense_variant
inframe_insertion
inframe_deletion

I would like to order my array ensembldb to match the orders in array ordered_array. The output expected is the following:

rs2799070   ENST00000624697 ENSG00000187608 ISG15   frameshift_variant  NA  NA  protein_coding  ISG15   ubiquitin-like  modifier    [Source:HGNC    Symbol;Acc:HGNC:4053]NULL   NULL
rs2799070   ENST00000458555 ENSG00000224969 AL645608.2  missense_variant    NA  NA  antisense   NA  NULL    NULL
rs2799070   ENST00000379389 ENSG00000187608 ISG15   inframe_insertion   NA  NA  protein_coding  ISG15   ubiquitin-like  modifier    [Source:HGNC    Symbol;Acc:HGNC:4053]NM_005101.3    NP_005092
rs2799070   ENST00000624652 ENSG00000187608 ISG15   inframe_deletion    NA  NA  protein_coding  ISG15   ubiquitin-like  modifier    [Source:HGNC    Symbol;Acc:HGNC:4053]NULL   NULL

I checked this question but it doesn't answer my question as it is a multidimensional array. How can I order my array ensembldb according to the ordered array ordered_array ?

Thank you.

Edit 1: Adding code as requested by @anubhava

declare -A ordered_array
ordered_array[0]="frameshift_variant"
ordered_array[1]="missense_variant"
ordered_array[2]="inframe_insertion"
ordered_array[3]="inframe_deletion"

while read -r LINE; do
    chrom=$(echo -e "$LINE" | cut -f1 -d$'\t' | sed 's/^chr//g')
    pos=$(echo -e "$LINE" | cut -f2 -d$'\t')
    ref=$(echo -e "$LINE" | cut -f3 -d$'\t')
    alt=$(echo -e "$LINE" | cut -f4 -d$'\t')
    LINE=$(echo -e "$LINE" | sed 's/^chr//g')
    ensembldb=$(echo "PREPARE stmt1 FROM 'SELECT Annotated_ID, Transcript, Gene_ID, Gene_name, Consequence, Swissprot_ID, AA_change, Biotype, Gene_description, RefSeq_mRNA, RefSeq_peptide FROM SNP_annot.37_annot_ensembl_89_full_descr where chrom = \"$chrom\" and Start = \"$pos\" and Local_alleles = \"$ref/$alt\"'; execute stmt1;" | mariadb -A -N)
    readarray -t array <<< "$ensembldb"
    pos19=$(echo "PREPARE stmt2 FROM 'select hg19_pos from SNP_annot.mut_convert_pos where chrom = \"$chrom\" and hg38_pos = \"$pos\"'; execute stmt2;" | mariadb -A -N)
    hits=$(echo -e "$ensembldb" | wc -l)
    [ ! -z "$pos19" ] && awk -v line="$LINE" -v pos="$pos19" -v ensembl="$ensembldb" -v hit="$hits" 'BEGIN {print line"\t"ensembl"\t"hit"\t"pos}'
done

1.The variable LINE has rows like this:

CHROM   POS REF ALT QUAL    DP  Genotype
chr1    16495   G   C   1722.77 252 G/C
chr1    16719   T   A   145.77  189 T/A
chr1    16841   G   T   701.77  521 G/T
chr1    17626   G   A   154.77  124 G/A

2.The variable ensembldb is a MySQL query that returns multiple rows and converted to an array. It contains rows that I want to sort according to ordered_array and pick the first row that matches ordered_array.

@Law Some feedback on my answer would be nice. Doesn't it do what you want? :) — mickp
– mickp, Commented Jan 18, 2019 at 9:54

mickp · Accepted Answer · 2019-01-17 17:22:17Z

2

This awk might work for you:

awk 'FNR==NR{a[$5]=$0;next}{print a[$1]}' file_a file_b

If a and b are really arrays:

readarray -t a < <(awk 'FNR==NR{a[$5]=$0;next}{print a[$1]}' <(printf '%s\n' "${a[@]}") <(printf '%s\n' "${b[@]}"))

answered Jan 17, 2019 at 17:22

mickp

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7 Comments

user324810 Over a year ago

Could you please give some explanation on the command ? thank you in advance

user324810 Over a year ago

Also, shouldn't you be passing the arrays for awk as awk variables with -v argument ?

mickp Over a year ago

First of all, does the solution work for you? :) No point in explaining if it doesn't work.

user324810 Over a year ago

No, the solution is not working for me, sorry. I tried doing

readarray -t a < <(awk 'FNR==NR{ensembldb[$5]=$0;next}{print ensembldb[$1]}' <(printf '%s\n' "${ensembldb[@]}") <(printf '%s\n' "${ordered_array[@]}"))

and echo "$a" nothing's returned

mickp Over a year ago

Show the input properly in your question. For example what your a variable contains. It is not an array as I can see now after your edit BTW.

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