#33 ✓invalid
john.mccallum (at plantandfood)

order of attributes in moa show

Reported by john.mccallum (at plantandfood) | June 20th, 2011 @ 09:57 PM | in v1.1

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

Comments and changes to this ticket

Please Sign in or create a free account to add a new ticket.

With your very own profile, you can contribute to projects, track your activity, watch tickets, receive and update tickets through your email and much more.

New-ticket Create new ticket

Create your profile

Help contribute to this project by taking a few moments to create your personal profile. Create your profile »

lightweight workflows for bioinformatics

Shared Ticket Bins

People watching this ticket

Pages