fix nonsynonymous keep

keep_synonymous.sh → keep_nonsynonymous.sh

-anvage synonymous --vcf diplodus_CDS.vcf \
---genome genomes/diplodus_genome_lgt6000.fasta \
---annotation annotation/sar_annotation.gff3 \
---output_prefix diplodus_CDS
-
-vcftools --positions <(awk '{print $1" "$2}' diplodus_CDS_uniprot_blast_filtered.tsv | sort | uniq) --vcf diplodus_CDS_nonsynonymous.vcf --recode --out diplodus_CDS_uniprot_nonsynonymous
-
-grep -v "^#" diplodus_CDS_uniprot_nonsynonymous.recode.vcf | awk '{ print $1"\t"$2}' | while read CHROMPOS; do grep "$CHROMPOS" diplodus_CDS_uniprot_blastx.tsv; done > diplodus_CDS_uniprot_nonsynonymous.tsv
-
 
 nonsynonymous_chrompos () {
 #1 vcf input
@@ -24,4 +15,5 @@ grep -v "^#" $4"_uniprot_nonsynonymous.recode.vcf" | awk '{ print $1"\t"$2}' | w
 
 }
 
-nonsynonymous_chrompos("mullus_CDS.vcf", "genomes/mullus_genome_lgt6000.fasta","annotation/mullus_annotation.gff3", "mullus_CDS","mullus_CDS_uniprot_blast_filtered.tsv")
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+nonsynonymous_chrompos diplodus_CDS.vcf genomes/diplodus_genome_lgt6000.fasta annotation/sar_annotation.gff3 diplodus_CDS diplodus_CDS_uniprot_blast_filtered.tsv
+nonsynonymous_chrompos mullus_CDS.vcf genomes/mullus_genome_lgt6000.fasta annotation/mullus_annotation.gff3 mullus_CDS mullus_CDS_uniprot_blast_filtered.tsv 
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