Renaming header of contig file by awk

Question

[waqasnayab]

Hi,

I have a contig file:

>NODE_1_length_248_cov_3.157258
AAGGACTTGAGGGGCCTAACCTACCCTCAAGCATGCTCCCCGAAAGATTCCATCCATCCT
AGTCTTTTGAGGACAAATCCTACTGTGTAGACGAGTCATAGGGCAGACATTCGCGACGAA
TGGATCCGCCGGCCTCATCAGATAATTGAGACCGTCAACTGCCAGGTGCTCAAGAGGTTC
CTGGTTAAGTCTCCCTAGGCGTGGGAACTCTTTATGCATCGTTAACGTCCATCGGCTGAG
TGCCCACAGCGTTACTCAAGGCAGATTATACTGGGgag
>NODE_2_length_89_cov_4.494382
GTCGATAGATCTATGTGTTTAGACATGTAGATCAGTGGTCGTTGTGATGAGCGTAGCGCT
TGCGGAACGTGCACGAGTATACTATCACCGCCGGATTTTAATGCAGAGAGGTTCCCGAg
>NODE_3_length_79_cov_3.227848

and so on ........

I need to change the header in the following way:

>Contig1.1
AAGGACTTGAGGGGCCTAACCTACCCTCAAGCATGCTCCCCGAAAGATTCCATCCATCCT
AGTCTTTTGAGGACAAATCCTACTGTGTAGACGAGTCATAGGGCAGACATTCGCGACGAA
TGGATCCGCCGGCCTCATCAGATAATTGAGACCGTCAACTGCCAGGTGCTCAAGAGGTTC
CTGGTTAAGTCTCCCTAGGCGTGGGAACTCTTTATGCATCGTTAACGTCCATCGGCTGAG
TGCCCACAGCGTTACTCAAGGCAGATTATACTGGGgag
>Contig1.2
GTCGATAGATCTATGTGTTTAGACATGTAGATCAGTGGTCGTTGTGATGAGCGTAGCGCT
TGCGGAACGTGCACGAGTATACTATCACCGCCGGATTTTAATGCAGAGAGGTTCCCGAg
>Contig1.3

and so on........

I tried this awk command:

cat contig_1.fa | awk '{print (NR%4 == 1) ? ">Contig1." ++i : $0}' > contig_1_rename.fa

the output is:

contig_1_rename.fa

>Contig1.1
AAGGACTTGAGGGGCCTAACCTACCCTCAAGCATGCTCCCCGAAAGATTCCATCCATCCT
AGTCTTTTGAGGACAAATCCTACTGTGTAGACGAGTCATAGGGCAGACATTCGCGACGAA
TGGATCCGCCGGCCTCATCAGATAATTGAGACCGTCAACTGCCAGGTGCTCAAGAGGTTC
>Contig1.2
TGCCCACAGCGTTACTCAAGGCAGATTATACTGGGgag
>NODE_2_length_89_cov_4.494382
GTCGATAGATCTATGTGTTTAGACATGTAGATCAGTGGTCGTTGTGATGAGCGTAGCGCT
>Contig1.3

seems to me inserting header after every four lines instead of replacing the header. how to give a pattern search and replace in awk command rather than mentioning line (NR)?

Thanks,
Waqas.

Answer 1

[Alex Reynolds]

Another approach is to modify the header line and leave the sequence lines untouched:

$ awk ' \
    BEGIN { \
        contigIdx = 1; \
    } \
    { \
        if ($0 ~ /^>/) { \
            print ">Contig1."contigIdx; \
            contigIdx++; \
        } \
        else { \
            print $0; \
        } \
    }' sequences.fa > sequences_renamed.fa

The pattern /^>/ matches lines which start with the character >.

[waqasnayab]

Thanks, its great, worked fine,

Answer 2

[seta]

Also, you can use the following awk command:

awk '/^>/{print "> contig" ++i; next}{print}' < file.fasta > output.fasta