Parsing AME tsv file
I am trying to find a quick and easy way to parse an AME generated true positive sequences.tsv file to pull out just a 3 column BED, the format look as follows, any ideas would be awesome thanks!
motif_DB motif_ID seq_ID FASTA_score PWM_score class
Jaspar MA0004.1 chr5:144788829-144789179_shuf_2 2183 12.7135 fp
Jaspar MA0004.1 chr5:112339537-112339887_shuf_1 1713 12.7131 tp
Jaspar MA0004.1 chr16:94739915-94740265_shuf_1 1668 12.712 tp
1 answer
grep -v ^motif in.tsv | cut -f 3 | cut -d '_' -f 1 | tr ":-" "\t"
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Pierre Lindenbaum
That will be another grep or awk in the command :)
I think you can figure out how to do that?
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WouterDeCoster
I would add another grep to get lines with tp, prior to cut.
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WouterDeCoster
Ok figured it out seems to work like this for true positive intervals with specific motifs IDs:
grep -v ^motif sequences.tsv | grep -w tp | grep -w MA0258.2 | cut -f 2,3,6 | cut -d '_' -f 1 | tr ":-" "\t" | head
MA0258.2 chr12 15566967 15567317 tp
MA0258.2 chr11 88155633 88155983 tp
MA0258.2 chr15 51071410 51071760 tp
MA0258.2 chr14 22151488 22151838 tp
Thanks for your help.
Thanks very helpful!
Used this to get the following:
grep -v ^motif sequences.tsv | cut -f 2,3 | cut -d '_' -f 1 | tr ":-" "\t"
MA0258.2 chr12 15566967 15567317 tp
MA0258.2 chr11 88155633 88155983 tp
MA0258.2 chr15 51071410 51071760 tp
MA0258.2 chr14 22151488 22151838 tp
However can't quite figure out how to select only specific motif_IDs in the .tsv file as well as only tp (true positive) values for those specific motif IDs.
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