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How can I convert this pairwise format to fasta?

Hi, Not sure if this is a known file type in bioinformatics or not. But how could I go about changing this to fasta format?

M03972:384:000000000-KDHHW:1:1101:8022:20849    83  Consensus_7-INT.v2_threshold_0_quality_20   4766    42  153M    =   4766    -153
GCAGTATTCATTCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAAACTAAAGAACTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGGC
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GCAGTATTCATTCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAAACTAAAGAACTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGAC

M03972:384:000000000-KDHHW:1:1101:8022:20849    163 Consensus_7-INT.v2_threshold_0_quality_20   4766    42  128M    =   4766    153
GCAGTATTCATTCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAAACTAAAGAACTACAAAAACAAATTACAAAAATTCA
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GCAGTATTCATTCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAAACTAAAGAACTACAAAAACAAATTACAAAAATTCA

Each entry in the file is 4 lines. lines 1 and 3 are IDs, lines 2 and 4 would be sequence. Has anyone seen this before?

fasta python bash
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updated by GenoMax GenoMax • written by SaltedPork SaltedPork

1 answer

This seems to be the output from sam2pairwise program: https://github.com/mlafave/sam2pairwise

A quick/dirty way may be

$ grep -A 1 ^M039 file.fa --no-group-separator | sed 's/^M03972/>M03972/g' | cut -f1 -d ' '
>M03972:384:000000000-KDHHW:1:1101:8022:20849
GCAGTATTCATTCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAAACTAAAGAACTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGGC
>M03972:384:000000000-KDHHW:1:1101:8022:20849
GCAGTATTCATTCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAAACTAAAGAACTACAAAAACAAATTACAAAAATTCA
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written by GenoMax GenoMax

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