Stress-testing continues>>Found another simple issue?????
Reported by john.mccallum (at plantandfood) | July 4th, 2011 @ 09:25 PM | in v1.1
This "one-liner" used for making tbl format from gff
at
/data/moa/onion/20.genomic.sequencing/09.submission_SSR_reads_sequin
wont run in process but fine in CL....{think it might be tilde ~
interpretation???}
cat ../08.submission_SSR_reads/core_SSR_reads | while read marker readname; do echo ">Feature "$readname; awk -v pat=$readname -v mark=$marker '$1~pat {print $4, $5,"repeat_region\t\t\n\t\t\trpt_type\ttandem\n\t\t\tsatellite\tmicrosatellite: "mark"""}' ../08.submission_SSR_reads/DH2122_skim_seq.fasta.gff ; done > SSR_reads.tbl
////////GIVING////////////// awk: ~pat {print ,
,"repeat_region\t\t\n\t\t\trpt_type\ttandem\n\t\t\tsatellite\tmicrosatellite:
"mark"""}
awk: ^ syntax error
awk: ~pat {print ,
,"repeat_region\t\t\n\t\t\trpt_type\ttandem\n\t\t\tsatellite\tmicrosatellite:
"mark"""}
awk: ^ syntax error
awk: ~pat {print ,
,"repeat_region\t\t\n\t\t\trpt_type\ttandem\n\t\t\tsatellite\tmicrosatellite:
"mark"""}
awk: ^ syntax error
awk: ~pat {print ,
,"repeat_region\t\t\n\t\t\trpt_type\ttandem\n\t\t\tsatellite\tmicrosatellite:
"mark"""}
awk: ^ syntax error
awk: ~pat {print ,
,"repeat_region\t\t\n\t\t\trpt_type\ttandem\n\t\t\tsatellite\tmicrosatellite:
"mark"""}
awk: ^ syntax error
awk: ~pat {print ,
,"repeat_region\t\t\n\t\t\trpt_type\ttandem\n\t\t\tsatellite\tmicrosatellite:
"mark"""}
awk: ^ syntax error
Comments and changes to this ticket
-
MF January 8th, 2012 @ 10:02 PM
- State changed from new to open
John - is this still a valid concern??
-
John Favors October 13th, 2020 @ 07:50 AM
Thank you for the information posted about stress-test coding! While learning about the ins and outs of coding, me and my friends have been playing this game called Among Us—you can pretty much learn more about this game from this link. It’s a very challenging game that will test your teamwork and cooperation with one another!
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lightweight workflows for bioinformatics