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1 use DBI;
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2
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3 #
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4 # Database stuff
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5 #
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6
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7 $dbh; # database handler
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8 $db_name = 'largaespada_NGS_insertion_test';
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9 #my $db_username = 'insertion_larga';
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10 #my $db_password = 'uwtc.Pzc92';
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11 $db_username = 'sarvera';
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12 $db_password = 'fn101bcc';
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13
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14 $db_host = '127.0.0.1;mysql_local_infile=1';
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15 $db_type = 'mysql';
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16 $data_source = "DBI:$db_type:database=$db_name;host=$db_host";
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17
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18 #
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19 # global values
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20 #
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21 # allows multiple active instances to be running in the db...
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22 $proj = 'merge_science';
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23 $library_percent ='0.0001';
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24
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25 $CIS_total_pvalue = '0.05';
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26 $CIS_library_pvalue = '0.05';
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27 $CIS_region_pvalue = '0.05';
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28
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29 $cocis_threshold ='0.001';
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30
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31 $dbh = DBI->connect($data_source, $db_username, $db_password,
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32 { RaiseError => 1, AutoCommit => 0 });
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33
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34 sub resolve_barcodes {
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35 #2.1 map the barcodes to the sequences..must change (sequence, #) to length of barcode +1 based on barcode sequence length!.
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36 #Currently set up for 6,10,12 base barcodes.
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37 ####for 6mer barcodes...
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38 #$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,'%')");
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39 ####for 10mer barcodes...
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40 $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,'%')");
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41 #for 12mer barcodes...
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42 #$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,'%')");
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43
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44 $sth->execute;
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45
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46 }
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47
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48 sub resolve_IRDR {
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49 #2.3
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50 #different options available this section needs to be optomized for each dataset
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51 #for lung 454 data
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52 $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%'");
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53
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54 $sth->execute;
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55 $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_$proj where decoded_sequence like '_____TGTATGTAACTTCCGACTTCAACTG%'");
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56
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57
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58
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59 #$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_$proj where decoded_sequence like 'TTAAGTGTATGTAACTTCCGACTTCAACTG%'");
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60
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61 #for illumina data
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62 #$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_$proj where decoded_sequence like 'TGTATGTAAACTTCCGACTTCAACTG%'");
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63
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64 #for illumina_2 data
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65 #$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_$proj where decoded_sequence like '___TGTATGTAAACTTCCGACTTCAACTG%'");
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66
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67 #for MULV virus
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68 #$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%'");
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69 $sth->execute;
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70 }
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