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| | See: http://www.bioperl.org/wiki/Main_Page | | See: http://www.bioperl.org/wiki/Main_Page |
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| − | ==Perl and [[MySQL]]==
| |
| − | This section will just list a bunch of random examples. They are useful to give you an idea of what you can do with Perl, MySQL, and the [[:Category:Linux Command Line Tools|CLI]].
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| | | | |
| − | ''Note: These examples were taken from my course in Comparative Microbial Genomics at CBS (in Denmark).''
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| − |
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| − | <pre>
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| − | mysql -B -e "update cmp_genomics.features set note = '' where user = USER() and note not like 'tcs%' or note is null"
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| − | foreach accession (AE017042 AE016879 AL111168 AL645882 AP008232 AP009048 BA000021 CP000034)
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| − | foreach type (ecf s54 s70)
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| − | cat source/$accession.proteins.$type.sigmas.hmmsearch | \
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| − | perl -ne 'next unless /^CDS_(\d+)\-(\d+)_DIR([\-\+]+)\s+([0-9\-\.e]+)\s+([0-9\-\.e]+)\s+/;\
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| − | my ($start,$stop,$dir,$score,$evalue) = ($1,$2,$3,$4,$5);\
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| − | next unless $score > 0;\
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| − | print "update cmp_genomics.features set note = \"Sigma Factor '$type'\" \
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| − | where start=$start and stop = $stop and user = user() and accession = \"'$accession'\";\n";'\
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| − | | mysql
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| − | end
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| − | end
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| − | </pre>
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| − | <pre>
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| − | mysql -B -e "update cmp_genomics.features set note = '' where user = USER() and note not like 'sigma%' or note is null"
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| − | foreach accession (AE017042 AE016879 AL111168 AL645882 AP008232 AP009048 BA000021 CP000034)
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| − | foreach type (RRreciever HisKA_1 HisKA_2 HisKA_3 HWE_HK)
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| − | cat source/$accession.$type.TCS.hmmsearch | \
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| − | perl -ne 'next unless /^CDS_(\d+)\-(\d+)_DIR([\-\+]+)\s+([0-9\-\.e]+)\s+([0-9\-\.e]+)\s+/;\
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| − | my ($start,$stop,$dir,$score,$evalue) = ($1,$2,$3,$4,$5);\
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| − | next unless $score > 0; \
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| − | print "update cmp_genomics.features set note = \"TCS '$type'\" \
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| − | where start=$start and stop = $stop and user = user() and accession = \"'$accession'\";\n";'\
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| − | | mysql -B
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| − | end
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| − | end
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| − | </pre>
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| | | | |
| | ==External links== | | ==External links== |
Revision as of 23:51, 13 April 2007
Perl is a dynamic programming language.
Regex
see: Regular expression
Search and replace all "foo" with "bar" in filename:
perl -i -pe 's/foo/bar/gi' filename
Modules
Search and download: http://search.cpan.org/
Installing
perl -MCPAN -e shell
#Or,
perl -MCPAN -e "install Example::Module"
My favourites
BioPerl
See: http://www.bioperl.org/wiki/Main_Page
External links
This article is curently a "stub". This means it is an incomplete article needing further elaboration.
I always welcome suggestions, comments, and criticism. If you have something to contribute to this site, please follow this link: Contributing Information. Thank you!
