Convert prodigal output

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

• 381 views • link

updated 6.9 years ago by Mensur Dlakic

• written 6.9 years ago by max_19

1 answer

Assuming your Prodigal output is saved in ORFs.fas:

echo "ID1\tCDS_start\tCDS_end\tStrand\tID2" > output.txt
grep ">" ORFs.fas | perl -p -e 's/\>//g' | perl -p -e 's/\=/ /g' | perl -p -e 's/\;/ /g' | awk '{print $1"\t"$3"\t"$5"\t"$7"\t"$10}' >> output.txt

cat output.txt gives:

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

• 0 views • link

written 6.9 years ago by Mensur Dlakic

This works perfectly - thank you!

• 0 views • link

written 6.9 years ago by max_19