Mercurial > repos > petr-novak > repeat_annotation_pipeline3

comparison annotate_contigs.R @ 11:5366d5ea04bc draft

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planemo upload commit 9d1b19f98d8b7f0a0d1baf2da63a373d155626f8-dirty
author petr-novak
date Fri, 04 Aug 2023 12:35:32 +0000
parents 814cba36e435
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10:276efc4cb17f 11:5366d5ea04bc
16 sc_out = DNAStringSet(c(sc_trimmed_long, sc_trimmed_short_tarean)) 16 sc_out = DNAStringSet(c(sc_trimmed_long, sc_trimmed_short_tarean))
17 } 17 }
18 18
19 ## annotate_rm_fasta.R input.fasta annot.csv output.fasta 19 ## annotate_rm_fasta.R input.fasta annot.csv output.fasta
20 ## input 1 - input.fasta - contigs from clustering 20 ## input 1 - input.fasta - contigs from clustering
21 ## input 2 - annot.csv of clusters, firts column is CL number, seciond is annotation 21 ## input 2 - CLUSTER_TABLE.csv
22 ## 22 ##
23 ## output - clean conntigs with appended annotation 23 ## output - clean conntigs with appended annotation
24 24
25 ## find header row of annotation table 25 ## find header row of annotation table
26 x = readLines(commandArgs(T)[2]) 26 x = readLines(commandArgs(T)[2])