Yabish - problem with arg value if it is -1

google-code-export / yabi

Automatically exported from code.google.com/p/yabi

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Yabish - problem with arg value if it is -1 #34

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago

yabish ncbiblast --database "em_rel_mam" --stype dna --program blastn 
--seqrange "START-END" --format out --sequence yabi_tests/data/AA123456.fa 
--align 0 --gapalign true --filter F --gapext "-1" --gapopen "-1" 
--match_scores "2,-7" --dropoff 0 --exp 10 --scores 50 --alignments 50 --matrix 
"BLOSUM45" --uri "http://www.ebi.ac.uk/Tools/services/rest/ncbiblast/"
I think yabish interprets the --gapext value of -1 as another flag.

Original issue reported on code.google.com by ahunter.ccg@gmail.com on 7 Jul 2011 at 7:43

GoogleCodeExporter commented 9 years ago

Original comment by aahun...@gmail.com on 2 Feb 2012 at 3:12

Added labels: Component-Yabish
Removed labels: Component-Shell

GoogleCodeExporter commented 9 years ago

You have to escape the quotes around the arguments to make them pass through to 
yabi.

Ex.

"-1" will become \"-1\"

Please re-open if that doesn't work.

Original comment by szab...@gmail.com on 15 Aug 2012 at 3:01

Changed state: WontFix

GoogleCodeExporter commented 9 years ago

I have not tested yet but what if the user uses this in command line:

--gapopen -1

Original comment by amacgregor on 15 Aug 2012 at 3:47

GoogleCodeExporter commented 9 years ago

Original comment by szab...@gmail.com on 15 Aug 2012 at 7:02

Changed state: Accepted

GoogleCodeExporter commented 9 years ago

Fixed on tszabo in 7c1fa9a5f5f3.

Original comment by szab...@gmail.com on 15 Aug 2012 at 7:07

Changed state: Fixed

GoogleCodeExporter commented 9 years ago

This issue was closed by revision 7c1fa9a5f5f3.

Original comment by szab...@gmail.com on 16 Aug 2012 at 2:51