Add ID, motifs, and motif counts to VCF #2
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fellen31
commented
May 16, 2024
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| pub fn create_mc(motifs_string: &str, repeats: &str) -> String { | ||
| let motifs: Vec<String> = motifs_string.split(',').map(|s| s.to_string()).collect(); | ||
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| let mut motif_counts = vec![0; motifs.len()]; | ||
| for motif in motifs.iter() { | ||
| let mut start = 0; | ||
| while let Some(index) = repeats[start..].find(motif) { | ||
| motif_counts[motifs.iter().position(|x| x == motif).unwrap()] += 1; | ||
| start += index + motif.len(); | ||
| } | ||
| } | ||
| motif_counts.iter().map(|count| count.to_string()).collect::<Vec<String>>().join("_") | ||
| } | ||
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Will not work when the motif contains N though...
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Hi @fellen31 Wouter |
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Adds ID, motifs, and motif counts to the output VCF:
chr4 39348424 . AAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA AAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAG,AAAAAGAAAAGAAAAGAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAG . . REPID=RFC1;MOTIFS=AAAAG,AAAGG,AAGGG,AAGAG,AGAGG,AACGG,GGGAC,AAAGGG;END=39348479;STDEV=2,7 GT:RB:FRB:SUP:MC:SC 1|2:6,520:61,575:17,14:12_0_0_0_0_0_0_0,114_0_0_0_0_0_0_0:183,1725