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- Loraine Scott
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8 ./pharo Pharo.image eval 3 + 4
9 ./pharo Pharo.image my_script.st
10 BioSequence newdna: atcggtcggctta.
11 BioSequence newambiguousdna: AAGTCAGTGTACTATTAGCATGCATGTGCAACACATTAGCTG. BioSequence newunambiguousdna: AAGTCAGTGTACTATTAGCATGCATGTGCAACACATTAGCTG. BioSequence newrna: auugccuacauaggc. BioSequence newprotein: AGFAVENDSA. abiosequence( sequence_size ) ([ letters_in_alphabet ] alphabet_class) [sequence_letters] ATGCTAGN assequence. a BioSequence(8) ([GATCN] IUPAC DNA) [ ATGCTAGN] RSWAFFGH assequence. IUPAC > Protein) [RSWAFFGH] a BioSequence(8) ([ACDEFGHIKLMNPQRSTVWY]
12 AGCUCGGCU assequence. a BioSequence(9) ([GAUCRYWSMKHBVDN] IUPAC > RNA > Ambiguous) [AGCUCGGCU] VPFSNATGVVRSPFEYPQYYLAE assequence a BioSequence(23) ([ACDEFGHIKLMNPQRSTVWY] IUPAC > Protein) [ VPFSNATGVVRSPFEYPQYYLAE]
13 (BioMutableSeq newrna: auugccuacauaggc ) at: 1 put: $g; yourself. a BioMutableSeq(15) ([GAUC] IUPAC > RNA > Unambiguous) [ guugccuacauaggc] (BioMutableSeq newunambiguousdna: ATGC ) seq: CGTA ; yourself.
14 ((BioSequence newdna: atcggtcggctta ) copyfrom: 3 to: 5) asstring. > cgg (BioSequence newunambiguousdna: AAGTCAGTGTACTATTAGCATGGCTG ) size. > 26 AGTACACTGGT assequence molecularweightnondegen > AGTACACTGGT assequence gc. (BioSequence newdna: AAGTCAGTGTACTATTAGCATGCATGTGCAACACATTAGCTG ) complement a BioSequence(42) ([GATCN] IUPAC DNA) [ TTCAGTCACATGATAATCGTACGTACACGTTGTGTAATCGAC]
15 (BioSequence newambiguousdna: AcTG C NH ) reversecomplement. a BioSequence(9) ([ACGTWSMKRYBDHVN] IUPAC DNA > Ambiguous) [DN G CAgT] (BioSequence newunambiguousdna: GGGGaaaaaaaatttatatat ) reversecomplement a BioSequence(21) ([GATCN] IUPAC DNA) [ATATATAAATTTTTTTTCCCC] (BioMutableSeq newdna: AAGTCAGTGTACTATTAGCATGCATGTGCAACACATTAGCTG ) reversecomplement a BioMutableSeq(42) ([GATCN] IUPAC DNA) [ CAGCTAATGTGTTGCACATGCATGCTAATAGTACACTGACTT] myseq myseq := BioSequence newdna: AAGTCAGTGTACTATTAGCATGCATGTGCAACACATTAGCTG. myseq alphabet = myseq reversecomplement alphabet
16 (BioSequence newrna: AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG ) translate. a BioSequence(13) ([ACDEFGHIKLMNPQRSTVWY] IUPAC > Protein) [MAIVMGR *KGAR*] (BioSequence newrna: AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG ) translatetostop a BioSequence(7) ([ACDEFGHIKLMNPQRSTVWY] IUPAC > Protein) [MAIVMGR] dna protein dna := BioSequence newdna: atcggtcggctta. protein := BioSequence newprotein: AGFAVENDSA. protein, dna translate. (BioSequence newrna: AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG ) translatewithtableid: 2. a BioSequence(13) ([ACDEFGHIKLMNPQRSTVWY] IUPAC > Protein) [ MAIVMGRWKGAR*]
17 BioCodonTables currentcodontable a BioCodonTable [2] a Dictionary( AAA > K AAC > N AAG > K AAU > N ACA > T ACC > T ACG > T ACU > T AGC > S AGU > S AUA > M AUC > I AUG > M AUU > I CAA > Q CAC > H CAG > Q CAU > H CCA > P CCC > P CCG > P CCU > P CGA > R CGC > R CGG > R CGU > R CUA > L CUC > L CUG > L CUU > L GAA > E GAC > D GAG > E GAU > D GCA > A GCC > A GCG > A GCU > A GGA > G GGC > G GGG > G GGU > G GUA > V GUC > V GUG > V GUU > V UAC > Y UAU > Y UCA > S UCC > S UCG > S UCU > S UGA > W UGC > C UGG > W UGU > C UUA > L UUC > F UUG > L UUU > F ) BioCodonTables currentcodontable: BioCodonTables defaultcodontable
18 GTCG BioIUPACAlphabet ambiguousalphabets. --> an OrderedCollection( BioIUPACAmbiguousRNA BioIUPACAmbiguousDNA) BioIUPACAmbiguousDNA codes --> ACGTWSMKRYBDHVN BioIUPACAmbiguousRNA codes --> GAUCRYWSMKHBVDN BioIUPACAmbiguousDNA ambiguitycodes --> WSMKRYBDHVN BioIUPACAmbiguousRNA ambiguitycodes --> RYWSMKHBVDN
19 BioIUPACUnambiguousDNA codes --> GATCN BioIUPACUnambiguousRNA codes --> GAUC BioIUPACDNAExtended codes --> GATCBDSW BioIUPACProtein codes --> ACDEFGHIKLMNPQRSTVWY BioIUPACProteinExtended codes --> ACDEFGHIKLMNPQRSTVWYBXZJUO BioNullAlphabet codes --> - - sequence sequence := atcggtcggctta assequence. sequence alphabet. sequence := gccuacau assequence. sequence alphabet.
20 sequence sequence := BioSequence newprotein: mdstnvrsgmksrkkkpkttvidddddcmtcsacqslkllndfas. (BioSeqRecord new: sequence) id: P ; name: P20994 ; description: Protein A19 ; dbxrefs: #( Pfam:PF05077 InterPro:IPR DIP:2186N ); annotationat: #note put: A simple note ; yourself.
21 seq_records.xml BioMicrosatelliteLocus name: BM1818 ; chrlocation: D23S21 ; besimplerepeat; yourself
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23 #dnasequence asparser matches: TCGTACGA. --> true #dnasequence asparser matches: TCGTZZZACGA. --> false
24 #dnasequence asparser parse: TCGTACGA. --> TCGTACGA #dnasequence asparser parse: TCGTA3344CGA. --> end of input expected at 5 BioParser parseaccession: CAF > a BioAccession CAF (BioParser parseaccession: CAF ) isversioned --> true
25 (BioParser parseaccession: CAF ) version --> 1 XP_ asaccession version --> 2 BioParser parsemultifasta: (BioFASTAFile on: my_sequenceshm.fasta ) contents. BioParser tokenizefastaheader: >gi ref NC_ Acidithiobacillus ferrooxidans ATCC chromosome, complete genome. #( >gi ref NC_ Acidithiobacillus ferrooxidans ATCC chromosome, complete genome ) fastastring fastastring := >gi emb Z CIZ78533 C.irapeanum 5.8S rrna gene and ITS1 and ITS2 DNA CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGGAATAAACGATCGAGTG AATCCGGAGGACCGGTGTACTCAGCTCACCGGGGGCATTGCTCCCGTGGTGACCCTGATTTGTTGTTGGG CCGCCTCGGGAGCGTCCATGGCGGGTTTGAACCTCTAGCCCGGCGCAGTTTGGGCGCCAAGCCATATGAA AGCATCACCGGCGAATGGCATTGTCTTCCCCAAAACCCGGAGCGGCGGCGTGCTGTCGCGTGCCCAATGA ATTTTGATGACTCTCGCAAACGGGAATCTTGGCTCTTTGCATCGGATGGAAGGACGCAGCGAAATGCGAT
26 AAGTGGTGTGAATTGCAAGATCCCGTGAACCATCGAGTCTTTTGAACGCAAGTTGCGCCCGAGGCCATCA GGCTAAGGGCACGCCTGCTTGGGCGTCGCGCTTCGTCTCTCTCCTGCCAATGCTTGCCCGGCATACAGCC AGGCCGGCGTGGTGCGGATGTGAAAGATTGGCCCCTTGTGCCTAGGTGCGGCGGGTCCAAGAGCTGGTGT TTTGATGGCCCGGAACCCGGCAAGAGGTGGACGGATGCTGGCAGCAGCTGCCGTGCGAATCCCCCATGTT GTCGTGCTTGTCGGACAGGCAGGAGAACCCTTCCGAACCCCAATGGAGGGCGGTTGACCGCCATTCGGAT GTGACCCCAGGTCAGGCGGGGGCACCCGCTGAGTTTACGC >gi emb Z CCZ78532 C.californicum 5.8S rrna gene and ITS1 and ITS2 DNA CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGACAACAGAATATATGATCGAGTG AATCTGGAGGACCTGTGGTAACTCAGCTCGTCGTGGCACTGCTTTTGTCGTGACCCTGCTTTGTTGTTGG GCCTCCTCAAGAGCTTTCATGGCAGGTTTGAACTTTAGTACGGTGCAGTTTGCGCCAAGTCATATAAAGC ATCACTGATGAATGACATTATTGTCAGAAAAAATCAGAGGGGCAGTATGCTACTGAGCATGCCAGTGAAT TTTTATGACTCTCGCAACGGATATCTTGGCTCTAACATCGATGAAGAACGCAGCTAAATGCGATAAGTGG TGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCTCGAGGCCATCAGGCTAAG GGCACGCCTGCCTGGGCGTCGTGTGTTGCGTCTCTCCTACCAATGCTTGCTTGGCATATCGCTAAGCTGG CATTATACGGATGTGAATGATTGGCCCCTTGTGCCTAGGTGCGGTGGGTCTAAGGATTGTTGCTTTGATG GGTAGGAATGTGGCACGAGGTGGAGAATGCTAACAGTCATAAGGCTGCTATTTGAATCCCCCATGTTGTT GTATTTTTTCGAACCTACACAAGAACCTAATTGAACCCCAATGGAGCTAAAATAACCATTGGGCAGTTGA TTTCCATTCAGATGCGACCCCAGGTCAGGCGGGGCCACCCGCTGAGTTGAGGC. (BioParser parsemultifasta: fastastring) do: [ : seqrecord Transcript show: seqrecord name; cr; show: seqrecord size; cr; cr ]
27 align := BioAlignment new. align addsequence: ACTGCTAGCTAG ; addsequence: ACT CTAGCTAG ; addsequence: ACTGCTAGATAG ; addsequence: ACTGCTTGCTAG ; addsequence: ACTGCTTGATAG.
28 search search := BioNCBIWebBlastWrapper new nucleotide query: TCGAAATAACGCGTGTTCTCAACGCGGTCGCGCAGATGCCTTTGCTCATC AGATGCGACCGCAACCACGTCCGCCGCCTTGTTCGCCGTCCCCGTGCCTC AACCACCACCACGGTGTCGTCTTCCCCGAACGCGTCCCGGTCAGCCAGCC TCCACGCGCCGCGCGCGCGGAGTGCCCATTCGGGCCGCAGCTGCGACGGT GCCGCTCAGATTCTGTGTGGCAGGCGCGTGTTGGAGTCTAAA ; hitlistsize: 200; filterlowcomplexity; expectvalue: 10; blastn; formattypexml;
29 fetch. search outputtofile: blast, BioObject currentseconds,.xml.
30 mfasta fpath fpath := BioObject testfilesfulldirectoryname, Fasta_example_1.fa. mfasta := BioParser parsemultifasta: (BioFASTAFile on: fpath) contents. mfasta collect: #occurrencesofletters an OrderedCollection(a Dictionary($A->24 $C->18 $G->25 $T->23 ) a Dictionary($A->33 $C->30 $G->23 $T->34 ) a Dictionary($A->25 $C->30 $G->15 $T->39 ) a Dictionary($A->17 $C->9 $G->19 $T->15 ) a Dictionary($A->26 $C->17 $G->36 $T->41 ) a Dictionary($A->8 $C->4 $ G->11 $T->31 ) a Dictionary($A->31 $C->16 $G->17 $T->22 ) a Dictionary($A->16 $C->14 $G->15 $T->25 ) a Dictionary($A->14 $C->20 $G->11 $T->21 ) a Dictionary($A->20 $C->29 $G->25 $T->41 ) a Dictionary($A->12 $C->14 $G->8 $T->26 ) a Dictionary($A->26 $C->8 $ G->11 $T->24 ) a Dictionary($A->36 $C->37 $G->16 $T->36 ) a Dictionary($A->30 $C->30 $G->33 $T->27 ) a Dictionary($A->14 $C->11 $G->13 $T->20 ) a Dictionary($A->34 $C->31 $G->20 $T->27 ) a Dictionary($A->23 $C->31 $G->29 $T->37 ) a Dictionary($A->30 $C->42 $G->25 $T->31 ) a Dictionary($A->7 $C->23 $G->5 $T->18 ) a Dictionary($A->15 $C->28 $G->6 $T->18 ) a Dictionary($A->23 $C->44 $G->12 $T->37 ))
31 mfasta filepath filepath := BioObject testfilesfulldirectoryname, Fasta_example_1.fa. mfasta := BioParser parsemultifasta: (BioFASTAFile on: filepath) contents. BioCSVFormatter new exportfrom: (mfasta collect: #occurrencesofletters). A;24 G;25 C;18 T;23 A;33 G;23 C;30 T;34 A;25 G;15 C;30 T;39...
32 (BioEntrezClient new protein term: NP_ ; usewebenv; setfasta; fetch) outputtofile: NP_ fasta (BioEntrezClient new protein term: NP_ ; usewebenv; setseqid; fetch) outputtofile: NP_ seqid
33 (BioEntrezClient new nuccore uids: #( ); setgb; fetch) outputtofile: fetchnuccore3.gb result result := BioEntrezClient new pubmed uids: #( ); setmodexml; fetch. result outputtofile: efetch1.xml (BioEntrezClient new protein term: insulin AND homo ; search) outputtofile: insulin AND homo_protein.xml
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35 BioPEDMAPFilesLoader open. C:\BioSmalltalk\BioSmalltalkTestFiles\pedmap\sample_ped.ped > C:\ BioSmalltalk\BioSmalltalkTestFiles\pedmap\sample_ped.map
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37 BioPEDMAPFilesLoader open actionblock: [ : pedfilename : mapfilename... ]
38 BioRTDotPlot x: BioSequence atrandom y: BioSequence atrandom; window: 3; threshold: 2;
39 open. BioRTDotPlot sequence: BioSequence atrandom; window: 3; threshold: 2; open. open. fastaseqs g ds seqrange Read and parse FASTA file with multiple sequences fastaseqs := (BioParser parsemultifastafile: BioObject testfilesdirectoryname asfilereference / ls_orchid.fasta ). Filter sequences seqrange := fastaseqs select: [ : fastarec fastarec size between: 750 and: 790 ]. Build diagram g := RTGrapher new extent: 200; yourself.
40 ds := RTStackedDataSet new. ds points: seqrange; x: #name; y: #size. ds barshape width: 10. ds histogramwithbartitle: [ : e (e sequencedescription first: 15),... ]. g add: ds. Configure axis settings g axisy title: Count ; nodecimal. g axisx nolabel; notick; title: Sequence length (bp). Open visualization in a new window g open.
41 BioChrSelector open. BioHMMERWrapper new help; execute.
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43 samplesdir hmmfile stofile fastafile outputfile samplesdir := BioObject testfilesfulldirectoryname. hmmbuild globins4.hmm tutorial/globins4.sto hmmfile := samplesdir, globins4.hmm. stofile := samplesdir, globins4.sto. BioHMMERWrapper new addparameter: hmmfile; addparameter: stofile; runhmmbuild; execute. hmmsearch globins4.hmm uniprot sprot.fasta > globins4.out fastafile := samplesdir, globins45.fa. outputfile := samplesdir, globins4.out. BioHMMERWrapper new runhmmsearch; addparameter: hmmfile; addparameter: fastafile; addoption: o value: outputfile; execute.
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51 mkdir /c/biosmalltalk cd /c/biosmalltalk wget -O- get.pharo.org/50+vm bash -./pharo Pharo.image config BioSmalltalk ConfigurationOfBioSmalltalk --printversion -- install=development mkdir /usr/local/src/biosmalltalk cd /usr/local/src/biosmalltalk wget -O- get.pharo.org/50+vm bash -./pharo Pharo.image config BioSmalltalk ConfigurationOfBioSmalltalk --printversion -- install=development
52 ./pharo Pharo.image & Gofer it smalltalkhubuser: hernan project: BioSmalltalk ; configurationof: BioSmalltalk ; loaddevelopment Metacello new smalltalkhubuser: hernan project: PhyloclassTalk ; configuration: PhyloclassTalk ; version: #development; load.
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55 BioYourTestCase>>testFilesDirectoryName ^ super testfilesdirectoryname, BioObject filedirectoryclass slash, GenBankTestFiles
56 BioSerializationEngine serialize: anobject. (BioWebEngine for: anurl) httpget
57 BioSerializationEngine adapter #clientclass Answer a Symbol, the main external class name for this adapter #ispreferredadapter Private Answer <true> if the receiver is the best option for the current image and platform
58 ^ true
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61 blastxmltree filter: [: hit hit name = Hit_def and: [ hit value = Homo sapiens ] ] blastxmltree hitdefinitionsequalto: Homo sapiens.
62 dbname See superimplementor s comment ^ sra
63 biosample Set and answer the receiver s working database ^ self database: (BioEntrezSample new client: self) self assert: (BioEntrezDatabase dbclassof: biosample ) = BioEntrezSample.
64 BioFileFormat isregistered: CSV. BioFileFormat fileextensionfor: FASTA. BioFileFormat registerformat: CSV extensions: #( csv ) description: General Comma Separated Values format rootclass: BioCSVFile
65
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