Mercurial > repos > jesse-erdmann > tapdance
view lib/config.pl @ 3:17ce4f3bffa2 default tip
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author | jesse-erdmann |
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date | Tue, 24 Jan 2012 18:33:41 -0500 |
parents | 1437a2df99c0 |
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use DBI; # # Database stuff # $dbh; # database handler $db_name = 'largaespada_NGS_insertion_test'; #my $db_username = 'insertion_larga'; #my $db_password = 'uwtc.Pzc92'; $db_username = 'sarvera'; $db_password = 'fn101bcc'; $db_host = '127.0.0.1;mysql_local_infile=1'; $db_type = 'mysql'; $data_source = "DBI:$db_type:database=$db_name;host=$db_host"; # # global values # # allows multiple active instances to be running in the db... $proj = 'merge_science'; $library_percent ='0.0001'; $CIS_total_pvalue = '0.05'; $CIS_library_pvalue = '0.05'; $CIS_region_pvalue = '0.05'; $cocis_threshold ='0.001'; $dbh = DBI->connect($data_source, $db_username, $db_password, { RaiseError => 1, AutoCommit => 0 }); sub resolve_barcodes { #2.1 map the barcodes to the sequences..must change (sequence, #) to length of barcode +1 based on barcode sequence length!. #Currently set up for 6,10,12 base barcodes. ####for 6mer barcodes... #$sth = $dbh->prepare("create table illumina_decoded_$proj select library, id, substring(sequence,7) as decoded_sequence from barcode_$proj,illumina_raw_$proj where sequence like concat(seq,'%')"); ####for 10mer barcodes... $sth = $dbh->prepare("create table illumina_decoded_$proj select library, id, substring(sequence,11) as decoded_sequence from barcode_$proj,illumina_raw_$proj where sequence like concat(seq,'%')"); #for 12mer barcodes... #$sth = $dbh->prepare("create table illumina_decoded_$proj select library, id, substring(sequence,13) as decoded_sequence from barcode_$proj,illumina_raw_$proj where sequence like concat(seq,'%')"); $sth->execute; } sub resolve_IRDR { #2.3 #different options available this section needs to be optomized for each dataset #for lung 454 data $sth = $dbh->prepare("create table illumina_without_IRDR_$proj select library,id,substring(decoded_sequence,32) as insertion_sequence, 'good' as type from illumina_decoded_$proj where decoded_sequence like '_____TGTATGTAAACTTCCGACTTCAACTG%'"); $sth->execute; $sth = $dbh->prepare("insert into illumina_without_IRDR_$proj select library,id,substring(decoded_sequence,31) as insertion_sequence, 'good' as type from illumina_decoded_$proj where decoded_sequence like '_____TGTATGTAACTTCCGACTTCAACTG%'"); #$sth = $dbh->prepare("create table illumina_without_IRDR_$proj select library,id,substring(decoded_sequence,31) as insertion_sequence, 'good' as type from illumina_decoded_$proj where decoded_sequence like 'TTAAGTGTATGTAACTTCCGACTTCAACTG%'"); #for illumina data #$sth = $dbh->prepare("create table illumina_without_IRDR_$proj select library,id,substring(decoded_sequence,27) as insertion_sequence, 'good' as type from illumina_decoded_$proj where decoded_sequence like 'TGTATGTAAACTTCCGACTTCAACTG%'"); #for illumina_2 data #$sth = $dbh->prepare("create table illumina_without_IRDR_$proj select library,id,substring(decoded_sequence,30) as insertion_sequence, 'good' as type from illumina_decoded_$proj where decoded_sequence like '___TGTATGTAAACTTCCGACTTCAACTG%'"); #for MULV virus #$sth = $dbh->prepare("create table illumina_without_IRDR_$proj select library,id,substring(decoded_sequence,26) as insertion_sequence, 'good' as type from illumina_decoded_$proj where decoded_sequence like 'CCAAACCTACAGGTGGGGTCTTTCA%'"); $sth->execute; }