Insert a sequence into a database, and loads a array of objects
1
Starting code
This is the PHP code used by this example.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | public function parseaseqdb(DatabaseInterface $databaseManager) { $databaseManager->recording("humandb", "GENBANK", "human.seq", "demo.seq"); // fetch() returns the parser that read the record, not the Sequence itself $oSequence = $databaseManager->fetch("NM_031438", "data/")->getSequence(); // New in biophp 1.1: wrap the parsed record into a validated DNA/RNA value object $oMolecularSequence = MolecularSequenceFactory::fromEntity($oSequence); $fGcContent = $oMolecularSequence->getGcContent(); return $this->render('default/parseseqdb.html.twig', ["sequence" => $oSequence, "gcContent" => $fGcContent] ); } |
2
Result
Result returned by BioPHP for the demonstration data.
Parsed record
| Primary accession | NM_031438 |
|---|---|
| Entry name | |
| Length | 3488 |
| Start / End | / |
| Molecule type | mRNA |
| Date | 29-DEC-2018 |
| Source | Homo sapiens (human) |
| Description | Homo sapiens nudix hydrolase 12 (NUDT12), transcript variant 1, mRNA. |
| Organism |
|
| Fragment | |
| Sequence | aagactgcat ccggctccag gaaaagcgag tgggatatcc caatctttgg actgcatcct ggttgcctct actgtggtca cctttgggaa gaaatgtctt ctgtaaaaag aagtctgaag caagaaatag ttactcagtt tcactgttca gctgctgaag gagatattgc caagttaaca ggaatactca gtcattctcc atctcttctc aatgaaactt ctgaaaatgg ctggactgct ttaatgtatg cggcaaggaa tgggcaccca gagatagtcc aatttctgct tgagaaaggg tgtgacagat caattgtcaa taaatcaagg cagactgcac tggacattgc tgtattttgg ggttataagc atatagctaa tttactagct actgctaaag gtgggaagaa gccttggttc ctaacgaatg aagtggaaga atgtgaaaat tattttagca aaacactact ggaccggaaa agtgaaaaga gaaataattc tgactggctg ctagctaaag aaagccatcc agccacagtt tttattcttt tctcagattt aaatcccttg gttactctag gtggcaataa agaaagtttc caacagccag aagttaggct ttgtcagctg aactacacag atataaagga ttatttggcc cagcctgaga agatcacctt gatttttctt ggagtagaac ttgaaataaa agacaaacta cttaattatg ctggtgaagt cccgagagag gaggaagatg gattggttgc ctggtttgct ctaggtatag atcctattgc tgctgaagaa ttcaagcaaa gacatgaaaa ttgttacttt cttcatcctc ctatgccagc ccttctgcaa ttgaaagaaa aagaagctgg ggttgtagct caagcaagat ctgttcttgc ctggcacagt cgatacaagt tttgcccaac ctgtggaaat gcaactaaaa ttgaagaagg tggctataag agattatgtt taaaagaaga ctgtcctagt ctcaatggcg tccataatac ctcataccca agagttgatc cagtagtaat catgcaagtt attcatccag atgggaccaa atgcctttta ggcaggcaga aaagatttcc cccaggcatg tttacttgcc ttgctggatt tattgagcct ggagagacaa tagaagatgc tgttaggaga gaagtagaag aggaaagtgg agtcaaagtt ggccatgttc agtatgttgc ttgtcaacca tggccaatgc cttcctcctt aatgattggt tgcttagctc tagcagtgtc tacagaaatt aaagttgaca agaatgaaat agaggatgcc cgctggttca ctagagaaca ggtcctggat gttctgacca aagggaagca gcaggcattc tttgtgccac caagccgagc tattgcacat caattaatca aacactggat tagaataaat cctaatctct aaatctaaga actaagcttt gagtattatt taataatttc taataacact cattcctcaa gtgatattag agattattca gtactcttga gagtgtcaca acacaaaata cgatgttggg ttttcgaaat attttcaaag tgttctgtct taatcacaaa ttcatatttt tacacatttt tacaatattg cctcagatta tgttaaattt gggtcagtct tctctgaact ttttctctct tggtttcttt tcttccttca cagttttatc tcacaaaacc atttttctaa taagagacat catgttggaa agatgttcta gaaatgtgca taaatttcag tgcctcttgt aagcattaaa ctgatgatga agaaagttcc tgatttgaga aatgaatcaa agtaatttta atgaattttt agcttgtatt agcttgagtt agctggcatt gattttttag tccttttgtt acctttaagt tgtcaatata tggtttttgt tcatctcccc attgtagtcc cacttgctct ttcctggggg ttccattgtt ctagcagtgg aggtgttata gtgtcgccac tcgtctaatt tgaccagtgt taagaatttt ctaatttaat aatttaatag tgatctcaat accacaccct catggaagga gaaaagcata ctattatatc tgggacctct cttttagacc taaaattaat taacatatct acttatatgt tacttatacc taaagctgtt attaagacaa accaagattc tctgcttttg cactgaaatt aaacttgaaa ggaattctcc tcaaaggtcg gatattaaat aagtcccagg cagatttaca tatttaattt aaaacattgg ctttatttca ttttgtgatg agtgatgtat ctgtgttaac aaaaaattgt ataatcatta ccaatactat ttattatgct caaatatatc ttggctttga ccttatttca acacattcta agaagccttg acaaagtaag tatattttag agctgaatca gtaagattct agagaaagca aaacatagta gttcacaatt ttgcaacata gaaagtcaca ttttgaaagg ctattttgaa attgatttaa tagctattat agtttatgaa tatcaaaatt tgtataattt gcatctttac taatgtatgc tagagctaca agagacctta aggataatat atgaaattag ctttccttat tttatagata aggaaaaaga aattgtgaaa ggtgaattta cctaattagt gaaagttaca taactaatta caacagtctg tactatataa tgcagaggac gattctccct gtaaaaggaa ctagaagcta ttactaaaaa tatatataga caaaattaaa agaaggaatg ataagaataa atttaattta ccaaatattg ttaattaaaa ttttagatac ttaacattta tttaacttaa ataaaagata actgtcagat aaaactttat tttactaatg agcagtgatt ttcttaggaa ttgatgaagg cttattggta tcaagaattt aaaccaaatt aaaactgaca gaggacattt agatacataa taaaattcga gctacataag tatatggaaa ataatgtacc ttgattatta tgaaatagag catcttgaaa ttcagtttta ctctaaatgt acttttaata cttgcagatt ctaagattac attgtaaaat tccaggtttt cataatgtta aaataggaaa gtagaatata aagtatcaac aagtgtagtt atacattttg ttttggatat ttaatcctta cttgggaaaa aatcagcatc taggtaaatt attattttaa taacaactct taaattgcca acctctgaga ggtgaaaagc tatgtaaata gaaggaatgg ccagttcaaa agaatagtag atgtgatagt gccgtgaatg tattctactg gaaatgaatg taataataca ttaaattttt aaaatcta |
New in biophp 1.1: GC content, computed by wrapping the record into a DnaSequence value object
34.116972477064
The code above is the one actually executed by this page. Find the other examples in the left-hand column, or the tools in BioTools.