Entering edit mode
2.7 years ago
helloword
•
0
Hello. Is there any possibility that Exonerate, the sequence alignment tool, returns only cigar string? I mean how could we print only the string without printing unnecessary stuff like below (or without parsing output)?
Command line:
[exonerate --model affine:global --exhaustive yes tube.fasta calm.fasta --showcigar yes --showalignment no]
Hostname: [beep]
(process:30145): WARNING **: 01:19:52.429: Exhaustively generating suboptimal alignments will be VERY SLOW
cigar: Query 0 100 + Target 0 100 + 266 M 13 D 3 M 13 I 2 M 5 I 1 M 66
vulgar: Query 0 100 + Target 0 100 + 266 M 13 13 G 0 3 M 13 13 G 2 0 M 5 5 G 1 0 M 66 66
-- completed exonerate analysis
Wanted output:
M 13 D 3 M 13 I 2 M 5 I 1 M 66
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