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comparison draw_features.xml @ 2:fcf01dad2ceb draft

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Uploaded
author greg
date Tue, 07 Feb 2023 18:16:34 +0000
parents 636eeb4fb9ac
children 3ba596014675
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1:7d47800ee5ac 2:fcf01dad2ceb
17 mkdir output_dir && 17 mkdir output_dir &&
18 18
19 #for $i in $feature_hits: 19 #for $i in $feature_hits:
20 #set file_name = $i.file_name 20 #set file_name = $i.file_name
21 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) 21 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
22 ln -s '$file_name' 'feature_hits_dir/$identifier' && 22 cat '$i' | awk '$7 != "."' | awk '{OFS="\t";locus=$7"\t"$8"\t"$9; if($5 > s[locus]){s[locus]=$5;id = sprintf("%.3f", $5); b[locus] = $1"\t"$2"\t"$3"\t"$4"\t"id"\t"$6}} END{for(i in b){print b[i]}}' | sort -k 1,1 -k2,2n > 'feature_hits_dir/$identifier' &&
23 #end for 23 #end for
24 24
25 python '$__tool_directory__/draw_features.py' 25 python '$__tool_directory__/draw_features.py'
26 --contigs 'contigs.fasta' 26 --contigs 'contigs.fasta'
27 --feature_hits_dir 'feature_hits_dir' 27 --feature_hits_dir 'feature_hits_dir'