Closed:Convert prodigal output
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4.7 years ago
max_19 ▴ 170

Hi all!

I'd like to convert prodigals standard protein translation output file into a tab delimited file with just some key variables as shown below:

Prodigal output:

>1234_1 # 3 # 506 # 1 # ID=4_1;partial=11;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.554
HVRPRKPRLLPHHRLDRLSFARNPLPTPEDTWQDVVFTDESKFNLFGSDGPKTVW
REPGPPTQDYHIIETVKYGGGSVMAWGAITSRGVGALVFIETTMDAKVFVEVLESGLNET
LEKKHLKVKDVILQQDNDPK
>5678_1 # 3 # 470 # 1 # ID=6_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.472
SWNDRLEQATKAVNMSFHRGLRTSPYIFKHGYLPDLKCDAKHGKVRMSRDRLQ
AKHIRDRNYDYYTEKSIVKGKREITEEFPIGTPVAIFKRQ

Prefered output:

ID1       CDS_start   CDS_end   Strand    ID2
1234_1     3            506        1      4_1
5678_1     3            470        1      6_1

Anyone know a quick and easy way to accomplish this? I have tried somethings using "awk" but was not successful.

Thank you for any input.

prodigal protein • 229 views
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