Could the order be changed so it reads precommand, process,
postcommand?
Current is hard to read
[cfljam@pgenome 09.submission_SSR_reads_sequin]$ moa show input
o /
mode o simple
name_sed o s/a/a/
output_dir o .
postcommand L
/data/moa/onion/20.genomic.sequencing/09.submission_SSR_reads_sequin/linux.tbl2asn
-i ../08.submission_SSR_reads/SSR_marker_reads.fasta -t
template_file.sbt -a s -y "singletons from
assembly of genomic skim sequence" -j "[organism=Allium cepa][genotype=CUDH2122]" -V vb -Z discreps -o SSR_reads.sqn -f SSR_reads.tbl
precommand L cat ../08.submission_SSR_reads/SSR_marker_reads.lst
| while read read_name; do grep $read_name
../08.submission_SSR_reads/DH2122_skim_seq.fasta.gff;done >
SSR_reads_SSRs.gff
process L awk '!/#/' SSR_reads_SSRs.gff | while read name type what
start stop rest; do echo ">Feature" $name; echo $start $stop
"repeat_region rpt_type tandem";echo $start $stop
"repeat_region
satellite microsatellite" ; done |sed 's/ /\t/g' > SSR_reads.tbl
project o (undefined)
title L format SSR reads for submission to Genbank
touch o T
MF