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Laura Denies
PathoFact
Commits
db9dfcc4
Commit
db9dfcc4
authored
Apr 27, 2020
by
Valentina Galata
Browse files
changed file paths back (rm test/) in test/set-up.sh (issue
#30
)
parent
6af75675
Changes
1
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test/set-up.sh
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db9dfcc4
#!/bin/bash -l
# modify *.faa: rm record descriptions
sed
-i
'/^>/ s/ .*//'
test
/
test_sample.faa
sed
-i
'/^>/ s/ .*//'
test_sample.faa
# *.gff to *.contig: contig ID, feature ID
sed
-n
'/^##gff/,/^##FASTA/p'
test
/
test_sample.gff |
grep
-v
'^#'
|
cut
-f1
,9 |
cut
-d
';'
-f1
|
sed
's/ID=//'
>
test
/
test_sample.contig
sed
-n
'/^##gff/,/^##FASTA/p'
test_sample.gff |
grep
-v
'^#'
|
cut
-f1
,9 |
cut
-d
';'
-f1
|
sed
's/ID=//'
>
test_sample.contig
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