Score:1

Ubuntu

Duplicate every two lines a variable number of times

LML

10/21/22, 1:50 PM

I have multiple .fasta files (that are named barcode*_consensus.fasta) that look like this:

>|>consensus_cl_id_1018_total_supporting_reads_12 LN:i:1369 RC:i:12 XC:f:1.000000
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
|>consensus_cl_id_107_total_supporting_reads_6 LN:i:1440 RC:i:6 XC:f:1.000000
GACTTCAGCCCAGTCATTAGTCCTACCATGGACCCCCATATTACTAGAGGAGCTTCCGATATTACTAACTCCCATGCCGTGACGGGCG
|>consensus_cl_id_116_total_supporting_reads_5 LN:i:1314 RC:i:558 XC:f:1.000000
AGAACGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGCTACCTTCGGGGGAGCGGCGGACGGGTTAGTAACGCGTGGGAATAT

I would like to duplicate/repeat every two lines n number of times, as specified after 'total supporting reads'. So for example, I would like to duplicate the first two lines 12 times, the second two lines 6 times, etc.

With awk, I did manage to select every line that starts with '>' and the next line:

awk '/>/{nr[NR]; nr[NR+1]} NR in nr' barcode01_consensus.fasta

But I can't find out how to print this n number of times with a variable.

Any help is much appreciated.

Updated: So I would like the final file to look something like:

|>consensus_cl_id_1018_total_supporting_reads_12 LN:i:1369 RC:i:12 XC:f:1.000000 TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTT

....x 12 times....

2 + 0

command-line

text-processing

Score:1

Ubuntu

glenn jackman

10/21/22, 2:32 PM

I'd use space or underscore as the field separator. Then, the count is the 8th field:

awk -F'[ _]' '
    $1 ~ /[>|]+consensus$/ {n = $8; print; next}
    {while (--n >= 0) print}
' file

output

>|>consensus_cl_id_1018_total_supporting_reads_12 LN:i:1369 RC:i:12 XC:f:1.000000
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
|>consensus_cl_id_107_total_supporting_reads_6 LN:i:1440 RC:i:6 XC:f:1.000000
GACTTCAGCCCAGTCATTAGTCCTACCATGGACCCCCATATTACTAGAGGAGCTTCCGATATTACTAACTCCCATGCCGTGACGGGCG
GACTTCAGCCCAGTCATTAGTCCTACCATGGACCCCCATATTACTAGAGGAGCTTCCGATATTACTAACTCCCATGCCGTGACGGGCG
GACTTCAGCCCAGTCATTAGTCCTACCATGGACCCCCATATTACTAGAGGAGCTTCCGATATTACTAACTCCCATGCCGTGACGGGCG
GACTTCAGCCCAGTCATTAGTCCTACCATGGACCCCCATATTACTAGAGGAGCTTCCGATATTACTAACTCCCATGCCGTGACGGGCG
GACTTCAGCCCAGTCATTAGTCCTACCATGGACCCCCATATTACTAGAGGAGCTTCCGATATTACTAACTCCCATGCCGTGACGGGCG
GACTTCAGCCCAGTCATTAGTCCTACCATGGACCCCCATATTACTAGAGGAGCTTCCGATATTACTAACTCCCATGCCGTGACGGGCG
|>consensus_cl_id_116_total_supporting_reads_5 LN:i:1314 RC:i:558 XC:f:1.000000
AGAACGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGCTACCTTCGGGGGAGCGGCGGACGGGTTAGTAACGCGTGGGAATAT
AGAACGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGCTACCTTCGGGGGAGCGGCGGACGGGTTAGTAACGCGTGGGAATAT
AGAACGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGCTACCTTCGGGGGAGCGGCGGACGGGTTAGTAACGCGTGGGAATAT
AGAACGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGCTACCTTCGGGGGAGCGGCGGACGGGTTAGTAACGCGTGGGAATAT
AGAACGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGCTACCTTCGGGGGAGCGGCGGACGGGTTAGTAACGCGTGGGAATAT

To print each pair of lines n times requires just minor changes:

awk -F'[ _]' '
    $1 ~ /[>|]+consensus$/ {firstline = $0; n = $8; next}
    {while (--n >= 0) print firstline ORS $0}
' file

output

>|>consensus_cl_id_1018_total_supporting_reads_12 LN:i:1369 RC:i:12 XC:f:1.000000
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
>|>consensus_cl_id_1018_total_supporting_reads_12 LN:i:1369 RC:i:12 XC:f:1.000000
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
>|>consensus_cl_id_1018_total_supporting_reads_12 LN:i:1369 RC:i:12 XC:f:1.000000
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
>|>consensus_cl_id_1018_total_supporting_reads_12 LN:i:1369 RC:i:12 XC:f:1.000000
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
>|>consensus_cl_id_1018_total_supporting_reads_12 LN:i:1369 RC:i:12 XC:f:1.000000
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
>|>consensus_cl_id_1018_total_supporting_reads_12 LN:i:1369 RC:i:12 XC:f:1.000000
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
>|>consensus_cl_id_1018_total_supporting_reads_12 LN:i:1369 RC:i:12 XC:f:1.000000
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
>|>consensus_cl_id_1018_total_supporting_reads_12 LN:i:1369 RC:i:12 XC:f:1.000000
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
>|>consensus_cl_id_1018_total_supporting_reads_12 LN:i:1369 RC:i:12 XC:f:1.000000
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
>|>consensus_cl_id_1018_total_supporting_reads_12 LN:i:1369 RC:i:12 XC:f:1.000000
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
>|>consensus_cl_id_1018_total_supporting_reads_12 LN:i:1369 RC:i:12 XC:f:1.000000
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
>|>consensus_cl_id_1018_total_supporting_reads_12 LN:i:1369 RC:i:12 XC:f:1.000000
TCATTAACCACAAAGTGGTGAGCGTTCTCCCGAAGGTTAAACTACCCACTTCTTTTGCAGCCAACTCCCATGGTGTGACGGG
|>consensus_cl_id_107_total_supporting_reads_6 LN:i:1440 RC:i:6 XC:f:1.000000
GACTTCAGCCCAGTCATTAGTCCTACCATGGACCCCCATATTACTAGAGGAGCTTCCGATATTACTAACTCCCATGCCGTGACGGGCG
|>consensus_cl_id_107_total_supporting_reads_6 LN:i:1440 RC:i:6 XC:f:1.000000
GACTTCAGCCCAGTCATTAGTCCTACCATGGACCCCCATATTACTAGAGGAGCTTCCGATATTACTAACTCCCATGCCGTGACGGGCG
|>consensus_cl_id_107_total_supporting_reads_6 LN:i:1440 RC:i:6 XC:f:1.000000
GACTTCAGCCCAGTCATTAGTCCTACCATGGACCCCCATATTACTAGAGGAGCTTCCGATATTACTAACTCCCATGCCGTGACGGGCG
|>consensus_cl_id_107_total_supporting_reads_6 LN:i:1440 RC:i:6 XC:f:1.000000
GACTTCAGCCCAGTCATTAGTCCTACCATGGACCCCCATATTACTAGAGGAGCTTCCGATATTACTAACTCCCATGCCGTGACGGGCG
|>consensus_cl_id_107_total_supporting_reads_6 LN:i:1440 RC:i:6 XC:f:1.000000
GACTTCAGCCCAGTCATTAGTCCTACCATGGACCCCCATATTACTAGAGGAGCTTCCGATATTACTAACTCCCATGCCGTGACGGGCG
|>consensus_cl_id_107_total_supporting_reads_6 LN:i:1440 RC:i:6 XC:f:1.000000
GACTTCAGCCCAGTCATTAGTCCTACCATGGACCCCCATATTACTAGAGGAGCTTCCGATATTACTAACTCCCATGCCGTGACGGGCG
|>consensus_cl_id_116_total_supporting_reads_5 LN:i:1314 RC:i:558 XC:f:1.000000
AGAACGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGCTACCTTCGGGGGAGCGGCGGACGGGTTAGTAACGCGTGGGAATAT
|>consensus_cl_id_116_total_supporting_reads_5 LN:i:1314 RC:i:558 XC:f:1.000000
AGAACGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGCTACCTTCGGGGGAGCGGCGGACGGGTTAGTAACGCGTGGGAATAT
|>consensus_cl_id_116_total_supporting_reads_5 LN:i:1314 RC:i:558 XC:f:1.000000
AGAACGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGCTACCTTCGGGGGAGCGGCGGACGGGTTAGTAACGCGTGGGAATAT
|>consensus_cl_id_116_total_supporting_reads_5 LN:i:1314 RC:i:558 XC:f:1.000000
AGAACGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGCTACCTTCGGGGGAGCGGCGGACGGGTTAGTAACGCGTGGGAATAT
|>consensus_cl_id_116_total_supporting_reads_5 LN:i:1314 RC:i:558 XC:f:1.000000
AGAACGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGCTACCTTCGGGGGAGCGGCGGACGGGTTAGTAACGCGTGGGAATAT

0 + 1

LML

10/21/22, 3:29 PM

Thank you! This works for most of it, however, I would like to print both line 1+2 n number of times and this only prints the second line n number of times. I have updated my question to clarify this in a better way.

Score:0

Ubuntu

steeldriver

10/21/22, 4:06 PM

I suspect there's a proper bioinformatics toolkit that would do what you want more robustly, but with GNU awk you could match and capture the repeat number like

gawk '
  /^>?[|]>/ {
    if((getline seq) > 0) $0 = $0 ORS seq
  } 
  match($0,/total_supporting_reads_([0-9]+)/,a) {
    while(a[1]--) print
  }
' file.fasta

You can do the same with non-GNU awk, except that you would need to extract the numeric portion of the match as a substring using the RSTART and RMATCH values instead of capturing it in an array.

0 + 0

Elon Musk

I sit in a Tesla and translated this thread with Ai:

EN: Duplicate every two lines a variable number of times

TH: ทำซ้ำทุก ๆ สองบรรทัดในจำนวนตัวแปร

RO: Duplicați la fiecare două linii de un număr variabil de ori

RU: Дублировать каждые две строки переменное количество раз

VI: Sao chép mỗi hai dòng một số lần thay đổi

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