Pipe awk and grep to save a particular field of a file-CodePudding

What I want to achieve:

grep: extract lines with the contig number and length
awk: remove "length:" from column 2
sort: sort by length (in descending order)

Current code

grep "length:" test_reads.fa.contigs.vcake_output | awk -F:'{print $2}' |sort -g -r > contig.txt

Example content of test_reads.fa.contigs.vcake_output:

>Contig_11 length:42
ACTCTGAGTGATCTTGGCGTAATAGGCCTGCTTAATGATCGT
>Contig_0 length:99995
ATTTATGCCGTTGGCCACGAATTCAGAATCATATTA

Expected output

>Contig_0 99995
>Contig_11 42

CodePudding user response：

With your shown samples, please try following awk sort solution here.

awk -F'[: ]' '/^>/{print $1,$3}' Input_file | sort -nrk2

Explanation: Simple explanation would be, running awk program to read Input_file first, where setting field separator as : OR space and checking condition if line starts from > then printing its 1st and 2nd fields then sending its output(as a standard input) to sort command where sorting it from 2nd field to get required output.

CodePudding user response：

Assumptions:

if more than one row has the same length then additionally sort the 1st column using 'version' sort

Adding some additional lines to the sample input:

$ cat test_reads.fa.contigs.vcake_output
>Contig_0 length:99995
ATTTATGCCGTTGGCCACGAATTCAGAATCATATTA
>Contig_11 length:42
ACTCTGAGTGATCTTGGCGTAATAGGCCTGCTTAATGATCGT
>Contig_17 length:93
ACTCTGAGTGATCTTGGCGTAATAGGCCTGCTTAATGATCGT
>Contig_837 ignore-this-length:1000000
ACTCTGAGTGATCTTGGCGTAATAGGCCTGCTTAATGATCGT
>Contig_8 length:42
ACTCTGAGTGATCTTGGCGTAATAGGCCTGCTTAATGATCGT

One sed/sort idea:

$ sed -rn 's/(>[^ ] ) length:(.*)$/\1 \2/p' test_reads.fa.contigs.vcake_output | sort -k2,2nr -k1,1V

Where:

-En - enable extended regex support and suppress normal printing of input data
(>[^ ]) ) - (1st capture group) - > followed by 1 or more non-space characters
length: - space followed by length:
(.*) - (2nd capture group) - 0 or more characters (following the colon)
$ - end of line
\1 \2/p - print 1st capture group <space> 2nd capture group
-k2,2nr - sort by 2nd (spaced-delimited) field in reverse numeric order
-k1,1V - sort by 1st (space-delimited) field in Version order

This generates:

>Contig_0 99995
>Contig_17 93
>Contig_8 42
>Contig_11 42

CodePudding user response：

Perhaps this, combining grep and awk:

awk -F '[ :]' '$2 == "length" {print $1, $3}' file | sort ...