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bioawk: Multiple fasta の sequence length を表示

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conda で簡単インストール

condaのサイト

 conda create -n bioawk_v1.0
 conda activate bioawk_v1.0
 conda install -c bioconda bioawk=1.0

ヘルプ

bioawk 
usage: bioawk [-F fs] [-v var=value] [-c fmt] [-tH] [-f progfile | 'prog'] [file ...]
bioawk -c help
bed:
  1:chrom 2:start 3:end 4:name 5:score 6:strand 7:thickstart 8:thickend 9:rgb 10:blockcount 11:blocksizes 12:blockstarts 
sam:
  1:qname 2:flag 3:rname 4:pos 5:mapq 6:cigar 7:rnext 8:pnext 9:tlen 10:seq 11:qual 
vcf:
  1:chrom 2:pos 3:id 4:ref 5:alt 6:qual 7:filter 8:info 
gff:
  1:seqname 2:source 3:feature 4:start 5:end 6:score 7:filter 8:strand 9:group 10:attribute 
fastx:
  1:name 2:seq 3:qual 4:comment 

実行

 bioawk -c fastx '{ print $name, length($seq) }' < sequences.fa

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