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Perl DBI API Reference

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HPerl DBI API Reference

This appendix describes the Perl DBI application programming interface.The API con-sists of a set of methods and attributes for communicating with database servers and ac-cessing databases from Perl scripts.The appendix also describes MySQL-specificextensions to DBI provided by DBD::mysql,the MySQL database driver.DBI is currently at version 1.601,although most of the material here applies to earlierversions as well.I assume here a minimum version of DBI 1.40,which requires at leastPerl 5.6.0 (and 5.6.1 is preferred to 5.6.0).I also assume a minimum version ofDBD::mysql 3.0000_0.Changes in DBI or DBD::mysql behavior introduced after thoseminimum versions are noted.For mysql_server_preparesupport,it is best to useDBD::mysql 3.0009 or higher because there were some changes to the default value ofthis feature in some of the preceding releases.To determine your versions of DBI and DBD::mysql,run this program:

#!/usr/bin/perl# dbi-version.pl - display DBI and DBD::mysql versionsuse strict;use warnings;use DBI;print "DBI::VERSION: $DBI::VERSION\n";use DBD::mysql;print "DBD::mysql::VERSION: $DBD::mysql::VERSION\n";

Some DBI methods and attributes are not discussed here,either because they do notapply to MySQL or because they are experimental methods that may change as they aredeveloped or may even be dropped.Some MySQL-specific DBD methods are not dis-cussed because they are obsolete.If you want more information about new or obsoletemethods,see the DBI documentation or the MySQL DBD documentation,which youcan get by running the following commands:

% perldoc DBI% perldoc DBI::FAQ% perldoc DBD::mysql

023_0672329387_xH.qxp 7/29/08 10:20 AM Page 11771178Appendix HPerl DBIAPIReferenceInformation is also available at http://dbi.perl.org/.The examples in this appendix are only brief code fragments.For complete clientscripts and instructions for writingthem,see Chapter 8,“Writing MySQL Programs Using Perl DBI.”

H.1Writing ScriptsEvery Perl script that uses the DBI module must include the following line:use DBI;It’s normally not necessary to include a useline for a particular DBD-level modulebecause DBI takes care of activating the proper module when you connect to the server.Typically,a DBI script opens a connection to a MySQL server using the connect()

method and closes the connection with disconnect().While the connection is open,SQL statements may be executed.The methods used to do this vary depending on thetype of statement.Non-SELECTstatements typically are performed with the do()

method.SELECTstatements typically are performed by passing the statement to

prepare(),and then calling execute(),and finally retrieving the result set a row at atime in a loop that repeatedly invokes a row-fetching method,such as fetchrow_array()

or fetchrow_hashref().When you execute statements from within a DBI script,each statement string mustconsist of a single SQL statement,and should not end with a semicolon character (‘;’) ora \gsequence.‘;’and \gare conventions of the mysqlclient program and are not usedfor DBI.

H.2DBI MethodsThe method descriptions here are written in a somewhat different format than is used forthe C functions in Appendix G,“C API Reference,”(online) and for the PHP functions inAppendix I,“PHP API Reference (online)”.Functions in those appendixes are written inprototype form,with return value types and parameter types listed explicitly.The descrip-tions here indicate parameter and return value types using variables,where the leadingcharacter of each variable indicates its type:‘$’for a scalar,‘@’for an array,and ‘%’for a hash(associative array).In addition,any parameter listed with a leading ‘\’signifies a referenceto a variable of the given type,not the variable itself.A variable name suffix of refindi-cates that the variable’s value is a reference.Certain variable names recur throughout this appendix and have the conventionalmeanings shownin Table H.1.

023_0672329387_xH.qxp 7/29/08 10:20 AM Page 11781179H.2DBI MethodsTable H.1Conventional Perl DBI Variable NamesNameMeaning$drhA handle to a driver object$dbhA handle to a database object$sthA handle to a statement (query) object$fhA handle to an open file$hA “generic” handle; the meaning depends on context$rcThe return code from operations that return true or false$rvThe return value from operations that return an integer$rowsThe return value from operations that return a row count$strThe return value from operations that return a string@aryAn array representing a list of values@row_aryAn array representing a row of values returned by a query

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perl 哈希引用

perl 哈希引用

perl 哈希引用Perl中，哈希引用可以通过以下方式进行定义和使用：1. 使用匿名哈希创建哈希引用：```perlmy $hash_ref = { key1 => 'value1', key2 => 'value2' };```在上述例子中，通过大括号`{}`定义一个匿名哈希，并将其赋值给变量`$hash_ref`。

2. 使用`->`操作符访问哈希引用中的元素：```perlprint $hash_ref->{key1}; # 输出"value1"```上述代码中，通过`$hash_ref`后跟`->{}`操作符来访问哈希引用中的元素。

3. 通过解引用将哈希引用转换为哈希使用：```perlmy %hash = %$hash_ref;print $hash{key2}; # 输出"value2"```在上述代码中，通过`%$hash_ref`的方式将哈希引用`$hash_ref`解引用为一个哈希，并将其赋值给变量`%hash`。

4. 使用箭头操作符创建嵌套哈希引用：```perlmy $nested_hash_ref = { key1 => { nested_key =>'nested_value' } };print $nested_hash_ref->{key1}->{nested_key}; # 输出"nested_value"```在上述例子中，通过大括号`{}`定义一个嵌套的匿名哈希，并将其赋值给变量`$nested_hash_ref`。

然后使用`->{}`操作符来访问嵌套哈希引用中的元素。

总的来说，Perl中的哈希引用提供了一种灵活的方式来处理复杂的数据结构，可以通过匿名哈希和`->{}`操作符来访问和操作哈希引用中的元素。

perl教程7——经典小骆驼配套讲解

perl教程7——经典小骆驼配套讲解

第七章Bioperl模块唐玉荣tangyurong@主要内容7.1 Bioperl模块简介7.2 Bioperl功能与用法1.Sequences类2.Alignments类3.Analysis类4.Databases类7.3 实例7.1 Bioperl模块简介1.什么是Bioperl–Bioperl是一组Perl模块，它的主要目的在于利用Perl解决生物学研究中的一些问题，主要是生物信息学中的各种实际问题，如获取分子数据，分析序列文件，序列比对，大批量BLAST等。

–Bioperl开发项目正式开始于1995年。

它是一个开放源代码项目，使用Perl语言开发，由OBF(Open BioinformaticsFoundation) 所支持。

Bioperl的官方主页是：2.Bioperl相关文档–Bioperl tutorial/Core/Latest/bptutorial.html –Mastering Perl for Bioinformatics: Introduction to bioperl /catalog/mperlbio/chapter/ch09.pdf –Bioperl documentation/Core/Latest/modules.html –Modules listing/bioperl-live/–Jason Stajich的Bioperl教程/Bioperl_Tutorials/–Beginner’s HOWTO by Brian Osborne & James Thompson /HOWTOs/Beginners/index.html–法国Pasteur Institute的Bioperl课程http://www.pasteur.fr/recherche/unites/sis/formation/bioperl/–WIBR Bioinformatics and Research Computing /bio/education/bioinfo-mini/unix-perl/ /~lehvasla/bioperl/7.2 Bioperl功能与用法1.Sequences类2.Alignments类3.Analysis类4.Databases类1.Sequences类–The Bio::SeqIO class–Sequence classes–Features and Location classes –Sequence analysis tools•The Bio::SeqIO class文档：/releases/bioperl-1.0.1/Bio/SeqIO.html 功能：格式转换例如:SwissProt格式转化为Fasta格式#! /usr/bin/perl–wuse strict;use Bio::SeqIO;my $in = Bio::SeqIO->newFh( -file => ’<seqs.sp’, -format => ’swiss’);my $out = Bio::SeqIO->newFh( -file => ’>seqs.fasta’, -format => ’fasta’);print $out $_ while <$in>;phred output phdQuality values (get a sequence of quality scores)qual GAME XML format gameACeDB sequence format aceRaw format (one sequence per line, no ID) rawGCG format GCGProtein Information Resource format PIRSCF tracefile format SCFSwissprot format swissGenBank format GenBankEMBL format EMBLFASTA format Fastadescription formatBio::SeqIO->newFh 中的format 说明：Swissprot格式ID 7LES_DROME STANDARD; PRT; 2554 AA.AC P13368; Q9TYI0; Q9U5V7; Q9VZ36;DT 01-JAN-1990 (Rel. 13, Created)DT 16-OCT-2001 (Rel. 40, Last sequence update)DT 15-JUN-2004 (Rel. 44, Last annotation update)DE Sevenless protein (EC 2.7.1.112).GN SEV OR HD-265 OR CG18085.OS Drosophila melanogaster(Fruit fly).OC Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota;OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha;OC Ephydroidea; Drosophilidae; Drosophila.OX NCBI_TaxID=7227;RN [1]RP SEQUENCE FROM N.A.RC STRAIN=Canton-S;RX MEDLINE=88282538; PubMed=2840202;RA Basler K., Hafen E.;RT "Control of photoreceptor cell fate by the sevenless protein requiresRT a functional tyrosine kinase domain.";RL Cell 54:299-311(1988).RN [2]RP SEQUENCE FROM N.A.RC STRAIN=Oregon-R;RX MEDLINE=88329706; PubMed=3138161;RA Bowtell D.L.L., Simon M.A., Rubin G.M.;RT "Nucleotide sequence and structure of the sevenless gene ofRT Drosophila melanogaster.";RL Genes Dev. 2:620-634(1988).CC -!-FUNCTION: Receptor for an extracellular signal required toCC instruct a cell to differentiate into an R7 photoreceptor. TheCC ligand for sev is the boss (bride of sevenless) protein on theCC surface of the neighboring R8 cell.CC -!-CATALYTIC ACTIVITY: ATP + a protein tyrosine = ADP + protein CC tyrosine phosphate.CC -!-SUBUNIT: May form a complex with drk and Sos.CC -!-DOMAIN: It is unclear whether the potential membrane spanning CC region near the N-terminus is present as a transmembrane domain inCC the native protein or serves as a cleaved signal sequence.CC -!-SIMILARITY: Belongs to the Tyr family of protein kinases. Insulin CC receptor subfamily.CC -!-SIMILARITY: Contains 7 fibronectin type III domains.CCDR EMBL; J03158; AAA28882.1; -.DR EMBL; X13666; CAA31960.1; ALT_INIT.DR EMBL; X13666; CAB55310.1; -.DR EMBL; AE003484; AAF47992.2; -.DR EMBL; AJ002917; CAA05752.1; -.DR PIR; A28912; TVFF7L.DR HSSP; P08069; 1JQH.DR FlyBase; FBgn0003366; sev.DR GO; GO:0005886; C:plasma membrane; IDA.DR GO; GO:0004713; F:protein-tyrosine kinase activity; IDA.DR GO; GO:0045467; P:R7 development; NAS.DR GO; GO:0008293; P:torso signaling pathway; NAS.DR InterPro; IPR003961; FN_III.DR InterPro; IPR008957; FN_III-like.DR InterPro; IPR000033; Ldl_receptor_rep.DR InterPro; IPR000719; Prot_kinase.DR InterPro; IPR002011; RecepttyrkinsII.DR InterPro; IPR001245; Tyr_pkinase.DR InterPro; IPR008266; Tyr_pkinase_AS.DR Pfam; PF00041; fn3; 6.DR Pfam; PF00069; Pkinase; 1.DR PRINTS; PR00109; TYRKINASE.DR ProDom; PD000001; Prot_kinase; 1.DR SMART; SM00060; FN3; 6.DR SMART; SM00135; LY; 2.DR SMART; SM00219; TyrKc; 1.DR PROSITE; PS50853; FN3; 7.DR PROSITE; PS00107; PROTEIN_KINASE_ATP; 1.DR PROSITE; PS50011; PROTEIN_KINASE_DOM; 1.DR PROSITE; PS00109; PROTEIN_KINASE_TYR; 1.DR PROSITE; PS00239; RECEPTOR_TYR_KIN_II; 1.KW Transferase; Tyrosine-protein kinase; Receptor; Vision; Transmembrane; KW Glycoprotein; ATP-binding; Phosphorylation; Repeat.FT DOMAIN 1 2123 Extracellular(Potential).FT TRANSMEM 2124 2147 Potential.FT DOMAIN 2148 2554 Cytoplasmic(Potential).FT DOMAIN 311 431 Fibronectin type-III 1.FT DOMAIN 436 528 Fibronectin type-III 2.FT DOMAIN 822 921 Fibronectin type-III 3.FT DOMAIN 1298 1392 Fibronectin type-III 4.FT DOMAIN 1680 1794 Fibronectin type-III 5.FT DOMAIN 1797 1897 Fibronectin type-III 6.FT DOMAIN 1898 1988 Fibronectin type-III 7.FT DOMAIN 2038 2046 Poly-Arg.FT DOMAIN 2209 2485 Protein kinase.FT CONFLICT 2271 2271C -> R (in Ref. 1).SQ SEQUENCE 2554 AA; 287022 MW; 09E238A0F27684F8 CRC64;MTMFWQQNVD HQSDEQDKQA KGAAPTKRLN ISFNVKIAVN VNTKMTTTHI NQQAPGTSSS SSNSQNASPS KIVVRQQSSS FDLRQQLARL GRQLASGQDG HGGISTILII NLLLLILLSI CCDVCRSHNY TVHQSPEPVS KDQMRLLRPK LDSDVVEKVA IWHKHAAAAP PSIVEGIAIS SRPQSTMAHH PDDRDRDRDP SEEQHGVDER MVLERVTRDC VQRCIVEEDL FLDEFGIQCE KADNGEKCYK TRCTKGCAQW YRALKELESC QEACLSLQFY PYDMPCIGAC EMAQRDYWHL QRLAISHLVE RTQPQLERAP RADGQSTPLT IRWAMHFPEH YLASRPFNIQ YQFVDHHGEE LDLEQEDQDA SGETGSSAWF NLADYDCDEY YVCEILEALI PYTQYRFRFE LPFGENRDEV LYSPATPAYQ TPPEGAPISA PVIEHLMGLD DSHLAVHWHP GRFTNGPIEG YRLRLSSSEG•Sequence类–创建一条序列use Bio::Seq;my $seq1 = Bio::Seq->new (-seq=> ’ATGAGTAGTAGTAAAGGTA’,-id => ’my seq’,-desc=> ’this is a new Seq’);–读取序列文件use Bio::SeqIO;my $seqin= Bio::SeqIO->new( -file => ’seq.fasta’,-format => ’fasta’);my $seq3 = $seqin->next_seq();use Bio::SeqIO;my $seqin2 = Bio::SeqIO->newFh( -file => ’seq.fasta’,-format => ’fasta’); my $seq4 = <$seqin2>;–从远程数据库中获取序列举例：•Create a sequence object for the MALK_ECOLI SwissProtentry•Print its Accession number and descriptionuse Bio::DB::SwissProt;my $database = new Bio::DB::SwissProt;my $seq= $database->get_Seq_by_id(’MALK_ECOLI’);print "Seq: ", $seq->accession_number(), " --", $seq->desc(), "\n\n"; Seq: P68187--Maltose/maltodextrin import ATP-binding protein malK(EC3.6.3.19).–根据SwissProt entry获取PDB结构entry$annotation = $seq->annotation();my @structures = ();foreach my $link ( $annotation->get_Annotations(’dblink’) ) { if ($link->database() eq’PDB’) {push (@structures, $link->primary_id());}}print "\nPDB Structures: ", join (" ", @structures), "\n";•Features and Location classes –Features class–Location class•Features Classes–Bio::SeqFeatureI–Bio::SeqFeature::Generic–Bio::SeqFeature::FeaturePair–Bio::SeqFeature::SimilarityPair–Bio::SeqFeature::Similarity–Bio::SeqFeature::Gene::–Bio::SeqFeature::Gene::ExonI–Bio::SeqFeature::Gene::Exon–Bio::SeqFeature::Gene::Transcript–Bio::SeqFeature::Gene::TranscriptI–Bio::SeqFeature::Gene::GeneStructureI –Bio::SeqFeature::Gene::GeneStructure–Adding a feature to a Genbank entryuse Bio::SeqFeature::Generic;use Bio::SeqIO;$in = Bio::SeqIO->newFh(-file => $ARGV[0]);$out = Bio::SeqIO->newFh();$seq= <$in>;$feat = new Bio::SeqFeature::Generic( -start => 10, -end => 100,-strand => -1,-primary => 'repeat',-source => 'repeatmasker',-score => 1000,-tag => {new => 1,author => 'someone',sillytag=> 'this is silly!' } ); $seq->add_SeqFeature($feat);print $out $seq;增加前的特征项:FEATURES Location/Qualifiers source 1..16705/organism="Pteropus dasymallus"/organelle="mitochondrion"/mol_type="genomic DNA"/db_xref="taxon:126282"gene 1..69/gene="tRNA-Phe“……………gene 15321..15390/gene="tRNA-Thr"tRNA15321..15390/gene="tRNA-Thr"gene complement(15390..15455)/gene="tRNA-Pro"tRNA complement(15390..15455)/gene="tRNA-Pro"D-loop 15456..16705/note="D-loop region"增加后的特征项:FEATURES Location/Qualifiers……….D-loop 15456..16705/note="D-loop region"repeat complement(10..100)/new="1"/author="someone"/sillytag="this is silly!"/note="score=1000"•Location Classes–Bio::LocationI–Bio::Location::Simple–Bio::Location::SplitLocationIet Bio::Location::Split–Bio::Location::FuzzyLocationIet Bio::Location::Fuzzy –Coordinate policies, for fuzzy location start and enddetermination:•interface: Bio::Location::CoordinatePolicyI,•default: Bio::Location::WidestCoordPolicy•Bio::Location::NarrowestCoordPolicy,Bio::Location::AvWithinCoordPolicy–specifies a location whose begin is before 30 and whose end is at 90my $fuzzylocation= new Bio::Location::Fuzzy(-start => ’<30’,-end => 90,-loc_type=> ’.’);符号说明:–’..’: EXACT–’^’: BETWEEN (a site between 2 bases), exemple: 123^124a site between bases 123 and 124. 145^177 a site between 2adjacent bases, somewhere between bases 145 and 177.–’.’: WITHIN (a base within a range), example : (102.110) is a site wihtin the 102 .. 110 range, inclusive.–’<’: BEFORE–’>’: AFTER•Sequence analysis tools–Bio::Tools::SeqStats/releases/bioperl-1.0.1/Bio/Tools/SeqStats.html –Bio::Tools::SeqWordshttp:/releases/bioperl-1.0.1/Bio/Tools/SeqWords.html/–Bio::Tools::SeqPattern/releases/bioperl-1.0.1/Bio/Tools/SeqPattern.html –Bio::SeqUtils/releases/bioperl-1.0.1/Bio/Tools/SeqUtils.html –Bio::Tools::RestrictionEnzyme/releases/bioperl-1.0.1/Bio/Tools/RestrictionEnzyme.html–Bio::Tools::Sigcleave/releases/bioperl-1.0.1/Bio/Tools/Sigcleave.html–Bio::Tools::SeqStats$seq_stats= Bio::Tools::SeqStats->new(-seq=>$seqobj); $seq_stats->count_monomers();$seq_stats->count_codons();$weight = $seq_stats->get_mol_wt($seqobj);–Bio::Tools::SeqWords$seq_word= Bio::Tools::SeqWords->new(-seq=> $seqobj); $seq_stats->count_words($word_length);–Bio::Tools::SeqPattern$pat = ’T[GA]AA...TAAT’;$pattern = new Bio::Tools::SeqPattern(-SEQ =>$pat, -TYPE=>’Dna’); $pattern->expand;$pattern->revcom;$pattern->alphabet_ok;–Bio::Tools::RestrictionEnzyme$re1 = new Bio::Tools::RestrictionEnzyme(-NAME =>’EcoRI’);@fragments = $re1->cut_seq($seqobj);$re2 = new Bio::Tools::RestrictionEnzyme( -NAME =>’EcoRV--GAT^ATC’, -MAKE =>’custom’);–Bio::Tools::Sigcleave$sigcleave_object= new Bio::Tools::Sigcleave(’-file’=>’sigtest.aa’,’-threshold’=>’3.5’,’-desc’=>’test sigcleave protein seq’,’-type’=>’AMINO ’); %raw_results= $sigcleave_object->signals;$formatted_output= $sigcleave_object->pretty_print;2.Alignments类–Bio::AlignIO/releases/bioperl-1.0/Bio/AlignIO.html –Bio::SimpleAlign/releases/bioperl-1.0/Bio/SimpleAlign.html –Bio::Tools::CodonTable/releases/bioperl-1.0/Bio/Tools/CodonTable.html–Bio::AlignIOFormat conversions with AlignIO:use Bio::AlignIO;$inputfilename= "testaln.fasta";$in = Bio::AlignIO->new(-file => $inputfilename, '-format' => 'fasta'); $out = Bio::AlignIO->new(-file => ">out.aln.pfam" , '-format' => 'pfam'); while ( my $aln= $in->next_aln() ) {$out->write_aln($aln);}Alignment result:use Bio::AlignIO;my $in = new Bio::AlignIO( -file =>, $ARGV[0], -format => 'clustalw' );my $aln= $in->next_aln();print "same length of all sequences: ", ($aln->is_flush()) ? "yes" : "no", "\n"; print "alignment length: ", $aln->length(), "\n";printf"identity: %.2f %%\n", $aln->percentage_identity();printf"identity of conserved columns: %.2f %%\n",$aln>overall_percentage_identity();infile.ALN文件内容:CLUSTAL W (1.82) multiple sequence alignmentBACR_HALAR ---------------MPEPGSEAIWLWLGTAGMFLGMLYFIARGWGETDSRRQKFYIATI BACR_HALHP -----------------------IWLWLGTAGMFLGMLYFIARGWGETDSRRQKFYIATI BACR_HALVA ---------------MPAPEGEAIWLWLGTAGMFLGMLYFIARGWGETDSRRQKFYIATI BACR_HALHS -------------------------LWLGTAGMFLGMLYFIARGWGETDGRRQKFYIATI BACR_HALSR --------MLQSGMSTYVPGGESIFLWVGTAGMFLGMLYFIARGWSVSDQRRQKFYIATI BACR_HALHA MLELLPTAVEGVSQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITT BACR_HALHM --------------------------GIGTLLMLIGTFYFIARGWGVTDKKAREYYAITI. :** * :* :**:.:* . :* :::* *BACR_HALAR LITAIAFVNYLAMALGFGLTIVEFAGEEHP--IYWARYSDWLFTTPLLLYDLGLLAGADR BACR_HALHP LITAIAFVNYLAMALGFGLTIVEFAGEEHP--IYWARYSDWLFTTPLLLYDLGLLAGADR BACR_HALVA LITAIAFVNYLAMALGFGLTIVEIAGEQRP--IYWARYSDWLFTTPLLLYDLGLLAGADR BACR_HALHS LITAIAFVNYLAMALGFGLTFIEFGGEQHP--IYWARYTDWLFTTPLLLYDLGLLAGADR BACR_HALSR MIAAIAFVNYLSMALGFGVTTIELGGEERA--IYWARYTDWLFTTPLLLYDLALLAGADR BACR_HALHA LVPAIAFTMYLSMLLGYGLTMVPFGGEQNP--IYWARYADWLFTTPLLLLDLALLVDADQ BACR_HALHM LVPGIASAAYLSMFFGIGLTTVEVAGMAEPLEIYYARYADWLFTTPLLLLDLALLANADR ::..** . **:* :* *:* : ..* .. **:***:********** **.**..**:BACR_HALAR NTITSLVSLDVLMIGTGLVATLSPGSGVLSAGAERLVWWGISTAFLLVLLYFLFSSLSGR BACR_HALHP NTITSLVSLDVLMIGTGLVATLSAGSGVLSAGAERLVWWGISTAFLLVLLYFLFSSLSGR BACR_HALVA NTISSLVSLDVLMIGTGLVATLSAGSGVLSAGAERLVWWGISTAFLLVLLYFLFSSLSGR BACR_HALHS NTIYSLVSLDVLMIGTGVVATLSAGSGVLSAGAERLVWWGISTAFLLVLLYFLFSSLSGR BACR_HALSR NTIYSLVGLDVLMIGTGALATLSAGSGVLPAGAERLVWWGISTGFLLVLLYFLFSNLTDR BACR_HALHA GTILALVGADGIMIGTGLVGALT------KVYSYRFVWWAISTAAMLYILYVLFFGFTSK BACR_HALHM TTIGTLIGVDALMIVTGLIGALS------HTPLARYTWWLFSTIAFLFVLYYLLTVLRSA ** :*:. * :** ** :.:*:..:. . * .** :** :* :** *: : .BACR_HALAR VADLPSDTRSTFKTLRNLVTVVWLVYPVWWLIGTEGIGLVGIGIETAGFMVIDLTAKVGF BACR_HALHP VADLPSDTRSTFKTLRNLVTVVWLVYPVWWLIGTEGIGLVGIGIETAGFMVIDLTA----BACR_HALVA VADLPSDTRSTFKTLRNLVTVVWLVYPVWWLVGTEGIGLVGIGIETAGFMVIDLVAKVGF BACR_HALHS VANLPSDTRSTFKTLRNLVTVVWLVYPVWWLVGSEGLGLVGIGIETAGFMVIDLVA----BACR_HALSR ASELSGDLQSKFSTLRNLVLVLWLVYPVLWLVGTEGLGLVGLPIETAAFMVLDLTAKIGF BACR_HALHA AESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGF BACR_HALHM AAELSEDVQTTFNTLTALVAVLWTAYPILWIIGTEGAGVVGLGVETLAFMVLDVTA----. .: : :.*..* :. *:* .**: *::*:** *:* : :** ***:*: *. . BACR_HALAR GIILLRS---HGVLDGAAETTGTGATPADDBACR_HALHP ------------------------------BACR_HALVA GIILLRS---HGVLDGAAETTGAGATATADBACR_HALHS ------------------------------BACR_HALSR GIILLQS---HAVLD-EGQTASEGAAVAD-BACR_HALHA GLILLRSRAIFGEAEAPEPSAGDGAAATSDBACR_HALHM ------------------------------. : . .. ::. .:: : .屏幕输出:same length of all sequences: yesalignment length: 270identity: 69.99 %identity of conserved columns: 28.52 %3.Analysis类–Blast/bioperl-live/–Genscan/releases/bioperl-1.0/Bio/Tools/Genscan.html•Blast–Bio::Tools::Run::StandAloneBlastRunning local Blastuse Bio::SeqIO;use Bio::Tools::Run::StandAloneBlast;my $Seq_in= Bio::SeqIO->new (-file => $ARGV[0], -format => 'fasta');my $query = $Seq_in->next_seq();my $factory = Bio::Tools::Run::StandAloneBlast->new('program' => 'blastp','database' => 'swissprot',);my $blast_report= $factory->blastall($query);my $result = $blast_report->next_result;while( my $hit = $result->next_hit()) {print "\thit name: ", $hit->name(), " significance: ", $hit->significance(), "\n";}Running Blast on a Swissprot entryuse Bio::SeqIO;use Bio::Tools::Run::StandAloneBlast;use Bio::DB::SwissProt;my $database = new Bio::DB::SwissProt;my $query = $database->get_Seq_by_id(’TAUD_ECOLI’);my $factory = Bio::Tools::Run::StandAloneBlast->new(’program’=> ’blastp’,’database’=> ’swissprot’,); my $blast_report= $factory->blastall($query);my $result = $blast_report->next_result;while( my $hit = $result->next_hit()) {print "\thit name: ", $hit->name()," significance: ", $hit->significance(), "\n";}Parsing from a Blast run resultuse Bio::SeqIO;use Bio::Tools::Run::StandAloneBlast;my $Seq_in= Bio::SeqIO->new (-file => $ARGV[0], -format => 'fasta');my $query = $Seq_in->next_seq();my $factory = Bio::Tools::Run::StandAloneBlast->new('program' => 'blastp','database' => 'swissprot',); my $blast_report= $factory->blastall($query);my $result = $blast_report->next_result;while( my $hit = $result->next_hit()) {print "\thit name: ", $hit->name(), " significance: ", $hit->significance(), "\n";while( my $hsp= $hit->next_hsp()) {print "E: ", $hsp->evalue(), "frac_identical: ", $hsp->frac_identical(), "\n";}}Parsing from a Blast fileuse Bio::SearchIO;my $blast_report= new Bio::SearchIO('-format' => 'blast', '-file' => $ARGV[0]); my $result = $blast_report->next_result;while( my $hit = $result->next_hit()) {print "\thit name: ", $hit->name(), "\n";while( my $hsp= $hit->next_hsp()) {print "E: ", $hsp->evalue(), "frac_identical: ", $hsp->frac_identical(), "\n";}}Running bl2sequse Bio::SeqIO;use Bio::Tools::Run::StandAloneBlast;my $query1_in = Bio::SeqIO->newFh( -file => $ARGV[0], -format => 'fasta' ); my $query1 = <$query1_in>;my $query2_in = Bio::SeqIO->newFh( -file => $ARGV[1], -format => 'fasta' ); my $query2 = <$query2_in>;$factory = Bio::Tools::Run::StandAloneBlast->new('program' => 'blastp'); $report = $factory->bl2seq($query1, $query2);while(my$hsp= $report->next_feature) {print "homology seq:\n", $hsp->homologySeq, "\n";print "sbjctSeq:\n", $hsp->sbjctSeq, "\n";}•Genscan–Bio::Tools::GenscanGenscan parsinguse Bio::Tools::Genscan;my $genscan_file= $ARGV[0];$genscan= Bio::Tools::Genscan->new(-file => $genscan_file);while(my$gene = $genscan->next_prediction()) {my $prot= $gene->predicted_protein;print "protein :\n", $prot->seq, "\n\n";}Genscan.out文件内容:GENSCAN 1.0Date run: 20-Jan-98Time: 11:02:22Sequence HUMRASH : 6453 bp: 68.19% C+G : Isochore 4 (57.00 -100.00 C+G%) Parameter matrix: HumanIso.smatPredicted genes/exons:Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..------------------------------------------------------1.01 Init + 1664 1774 111 1 0 94 83 212 0.997 21.331.02 Intr+ 2042 2220 179 1 2 104 66 408 0.997 40.121.03 Intr+ 2374 2533 160 1 1 89 94 302 0.999 32.081.04 Term + 3231 3350 120 2 0 115 48 202 0.961 18.31Predicted peptide sequence(s):>HUMRASH|GENSCAN_predicted_peptide_1|189_aa MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCKCVLS屏幕显示内容:protein: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLC VFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLV REIRQHKLRKLNPPDESGPGCMSCKCVLSGenscan parsing, with sub-sequencesuse Bio::Tools::Genscan;my $genscan_file= $ARGV[0];$genscan= Bio::Tools::Genscan->new(-file => $genscan_file); while(my$gene = $genscan->next_prediction()) {my $prot= $gene->predicted_protein;print "protein :\n", $prot->seq, "\n\n";# display genscan predicted cds(if -cds genscan option) my $predicted_cds= $gene->predicted_cds;print "predicted CDS: \n", $predicted_cds->seq, "\n\n";foreach my $exon($gene->exons()) {my $loc = $exon->location;print "exon-primary_tag: ",$exon->primary_tag, " coding? ",$exon->is_coding(), " start-end: ", $loc->start, "-", $loc->end, "\n";}foreach my $intron($gene->introns()) {my $loc = $intron->location;print "intron primary_tag: ",$intron->primary_tag, " start-end: ",$loc->start, "-", $loc->end, "\n";}print "---------------------------------\n";}输入文件:GENSCAN 1.0Date run: 30-Oct-101Time: 17:32:04Sequence HUMRASH : 6453 bp: 68.19% C+G : Isochore 4 (57 -100 C+G%)Parameter matrix: HumanIso.smatPredicted genes/exons:Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..------------------------------------------------------1.01 Init + 1664 1774 111 1 0 94 83 212 0.997 21.33 1.02 Intr+ 2042 2220 179 1 2 104 66 408 0.997 40.12 1.03 Intr+ 2374 2533 160 1 1 89 94 302 0.999 32.08 1.04 Term + 3231 3350 120 2 0 115 48 202 0.961 18.31Predicted peptide sequence(s):Predicted coding sequence(s):>HUMRASH|GENSCAN_predicted_peptide_1|189_aa MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPG CMSCKCVLS>HUMRASH|GENSCAN_predicted_CDS_1|570_bp atgacggaatataagctggtggtggtgggcgccggcggtgtgggcaagagtgcgctgacc atccagctgatccagaaccattttgtggacgaatacgaccccactatagaggattcctac cggaagcaggtggtcattgatggggagacgtgcctgttggacatcctggataccgccggc caggaggagtacagcgccatgcgggaccagtacatgcgcaccggggagggcttcctgtgt gtgtttgccatcaacaacaccaagtcttttgaggacatccaccagtacagggagcagatc aaacgggtgaaggactcggatgacgtgcccatggtgctggtggggaacaagtgtgacctg gctgcacgcactgtggaatctcggcaggctcaggacctcgcccgaagctacggcatcccc tacatcgagacctcggccaagacccggcagggagtggaggatgccttctacacgttggtg cgtgagatccggcagcacaagctgcggaagctgaaccctcctgatgagagtggccccggc tgcatgagctgcaagtgtgtgctctcctga输出文件:protein: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLC VFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLV REIRQHKLRKLNPPDESGPGCMSCKCVLSpredicted CDS: atgacggaatataagctggtggtggtgggcgccggcggtgtgggcaagagtgcgctgaccatccagctgatccagaacca ttttgtggacgaatacgaccccactatagaggattcctaccggaagcaggtggtcattgatggggagacgtgcctgttgg acatcctggataccgccggccaggaggagtacagcgccatgcgggaccagtacatgcgcaccggggagggcttcctgtgt gtgtttgccatcaacaacaccaagtcttttgaggacatccaccagtacagggagcagatcaaacgggtgaaggactcgga tgacgtgcccatggtgctggtggggaacaagtgtgacctggctgcacgcactgtggaatctcggcaggctcaggacctcg cccgaagctacggcatcccctacatcgagacctcggccaagacccggcagggagtggaggatgccttctacacgttggtg cgtgagatccggcagcacaagctgcggaagctgaaccctcctgatgagagtggccccggctgcatgagctgcaagtgtgt gctctcctgaexon-primary_tag: Initial coding? 1 start-end: 1664-1774exon-primary_tag: Internal coding? 1 start-end: 2042-2220exon-primary_tag: Internal coding? 1 start-end: 2374-2533exon-primary_tag: Terminal coding? 1 start-end: 3231-3350intron primary_tag: intron start-end: 1775-2041intron primary_tag: intron start-end: 2221-2373intron primary_tag: intron start-end: 2534-3230---------------------------------4.Databases类–Bio::Index::Swissprotuse Bio::Index::Swissprot;use Bio::SeqIO;my $out = Bio::SeqIO->newFh(-fh=>\*STDOUT, -format=>'fasta');my $Index_File_Name= shift;my $inx= Bio::Index::Swissprot->new(-filename=>$Index_File_Name); foreach my $id (@ARGV) {my $seq= $inx->fetch($id);print $out $seq;}7.3 实例1.获取序列统计信息–分子量、残基、密码子使用频度#!/usr/bin/perluse warnings;use Bio::Seq;use Bio::Tools::SeqStats ;$seqobj = Bio::Seq->new(-seq =>"aaaatgggggggggggccccgtt",-display_id => "#12345",-desc => "example 1" );$seq_stats = Bio::Tools::SeqStats->new($seqobj);$weight = $seq_stats->get_mol_wt();$monomer_ref = $seq_stats->count_monomers();$codon_ref = $seq_stats->count_codons();print "$weight\n$monomer_ref\n$codon_ref\n";ARRAY(0x1bf9024)HASH(0x1be0e98)HASH(0x1bf94d4)2.识别限制性酶切位点#!/usr/bin/perluse warnings;use Bio::Seq;use Bio::Tools::RestrictionEnzyme;$seqobj= Bio::Seq->new(-seq=>"aaaatgggggggggggccccgtt",-display_id=> "#12345",-desc=> "example 1" );$re = new Bio::Tools::RestrictionEnzyme(-NAME =>'EcoRI');@sixcutters= $re->available_list();$re1 = new Bio::Tools::RestrictionEnzyme(-NAME =>'EcoRI');@fragments = $re1->cut_seq($seqobj);print "@sixcutters\n@fragments";3.识别氨基酸剪切位点#!/usr/bin/perl use warnings;use Bio::Seq;use Bio::Tools::Sigcleave;$seqobj = Bio::Seq->new(-seq=>"AALLHHHHHHGGGGPPRTTTTTVVVVVVVVVVVVVVV");$sigcleave_object = new Bio::Tools::Sigcleave(-seq=>$seqobj, -threshod=>3.5,-desc=>'test sigcleave protein seq',-type=>'AMINO');$formatted_output = $sigcleave_object->pretty_print;print "$formatted_output\n";SIGCLEAVE of NONAME from: 1 to 37Report scores over 3.5Maximum score 3.6 at residue 3Sequence: AA--------------LLHHHHHHGGGGPPRTTTTTVVVVVVVVVVVVVVV | (signal) | (mature peptide)1 3。

perl usage用法

perl usage用法

perl usage用法Perl 是一种通用的脚本编程语言，易于学习和使用。

它在文本处理和系统管理方面非常强大，被广泛应用于日志分析、网页抓取、网络编程、数据库操作等各种领域。

本文将一步一步地回答关于Perl 用法的问题，为读者提供详细的指导和实例。

1. 什么是Perl？Perl（Practical Extraction and Reporting Language）是由Larry Wall 在1987 年开发的一种通用的脚本编程语言。

它具有强大的文本处理能力，灵活易用，被广泛认可为解决实际问题的工具。

2. 如何安装Perl？Perl 可以在多种操作系统上安装和运行，包括Windows、MacOS 和各种Linux 发行版。

可以从Perl 官方网站（Perl 解释器，并按照官方文档中的指引进行安装。

3. 如何编写Perl 程序？Perl 程序的文件扩展名通常为`.pl`。

使用文本编辑器创建一个新文件，然后在文件中输入Perl 代码。

Perl 代码以`#!/usr/bin/perl` 开始，表示这是一个Perl 程序。

可以在程序中使用注释（以`#` 开头）来增加代码的可读性。

4. 如何输出文本内容？在Perl 中，可以使用`print` 函数来输出文本内容。

例如，`print "Hello, World\n";` 将输出`"Hello, World"` 至标准输出。

其中`\n` 表示换行符。

5. 如何从用户获取输入？Perl 中获取用户输入可以使用`<>` 运算符。

例如，`input = <>;` 将获取用户输入，并将该输入保存到变量`input` 中。

6. 如何进行字符串处理？Perl 提供了丰富的字符串处理函数和操作符。

其中包括字符串连接符（`.`）、字符串重复操作符（`x`）、提取子字符串函数（`substr`）、字符串替换函数（`s/`）等。

perl hash数组

perl hash数组

perl hash数组Perl中的哈希数组是一种关联数组（也称为哈希表或字典），它是一种键-值对的集合。

可以使用特殊的语法来创建和访问哈希数组。

以下是创建和访问Perl哈希数组的一些基本示例：创建哈希数组：```perlmy %hash = ('key1', 'value1', 'key2', 'value2');```访问哈希数组中的值：```perlmy $value1 = $hash{'key1'}; # 获取键为'key1'的值# 或者使用可选的箭头操作符->my $value2 = $hash{'key2'};```将值存储到哈希数组中：```perl$hash{'key3'} = 'value3'; # 添加一个新的键值对# 或者使用可选的箭头操作符->$hash{'key4'} = 'value4';```遍历哈希数组中的键值对：```perlforeach my $key (keys %hash) {my $value = $hash{$key};# 对每个键值对执行操作}```可以通过键来删除哈希数组中的值：```perldelete $hash{'key1'};```这只是Perl哈希数组的一些基本操作示例。

Perl还提供了许多其他操作来操作和处理哈希数组，比如访问哈希数组的长度、检查键是否存在等等。