in reply to need help with a regex

Rather than just the textual description you included above, it is generally much better to include a small sample of your actual input wrapped in code tags. Note that your post has been misformatted as a result. See Writeup Formatting Tips. Also, please provide sample output, as I have a great deal of trouble following your spec. See How do I post a question effectively?.

I note that your posted code has several basic syntactic issues. Are you learning Perl from a book, or are you attempting to modify someone else's script? Do you have any background in programming in general? These issues include using a capitalized AND (vs. and, Perl is case sensitive), Modifiers on your regular expressions that are inappropriate for what you are trying to do, and a wholly incorrect block structure. Telling us where you are will let us better guide your development as a programmer and point you to more useful resources.

I am loathe to leave this node without a concrete bit of suggested code, but I am at a loss for how to even modify the posted code to "work".

Replies are listed 'Best First'.
Re^2: need help with a regex
by aquinom (Sexton) on Oct 22, 2010 at 20:10 UTC
    Sorry about the messy code I wrote I know it wasn't actually legit I was just in a hurry and trying to get the basic idea across. Here's a snip from what I'm parsing:

    >P30450 | Homo sapiens (Human). | NCBI_TaxID=9606; | 365 | Name=HLA-A; Synonyms=HLAA;M

    MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFYTSVSRPGRGEPRFIAVGYVDDT
    QFVRFDSDAASQRMEPRAPWIEQEGPEYWDRNTRNVKAHSQTDRANLGTLRGYYNQSEDGS
    TIQRMYGCDVGPDGRFLRGYQQDAYDGKDYIALNEDLRSWTAADMAAQITQRKW
    ETAHEAEQWRAYLEGRCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATL
    RCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWASVVVPSGQEQ
    RYTCHVQHEGLPKPLTLRWEPSSQPTIPIVGIIAGLVLFGAVIAGAVVAAVMWRRKS
    SDRKGGSYSQAASSDSAQGSDMSLTACKV

    and the output should look like:
    Hydrophobic stretch found in: P30450 | Homo sapiens (Human). | NCBI_TaxID=9606; | 365 | Name=HLA-A; Synonyms=HLAA;
    AVVAAVMW
    The match was at position: 325
    Hydrophobic stretch found in:
    A7MBM2 | Homo sapiens (Human). | NCBI_TaxID=9606; | 1401 | Name=DISP2; Synonyms=DISPB, KIAA1742;
    VAVLMLCLAVIFLC
    The match was at potistion: 170
    LLALVAIFF
    The match was at potistion: 493
    IWICWFAALAA
    The match was at potistion: 705
    LALALAFA
    The match was at potistion: 970
    Hydrophobic region(s) found in 2 sequences out of 15 sequences

[reply]
      Like I said, where are the <code> tags around your input and output? Embedding text in HTML is notorious for changing formatting. A regular expression I write will very likely fail because the character sequence displayed on the screen will differ from what you have in your file. I also note your "desired output" is significantly different from what you specified in the original post. For example, the word "Hydrophobic" appears nowhere the OP and the word "contains" appears nowhere in the new spec.

      Sorry about the messy code I wrote I know it wasn't actually legit
      Writing pseudocode is considered good practice when you don't know a language. That means explain clearly what you want an algorithm to do, not just posting gibberish from the target language.

      I was just in a hurry and trying to get the basic idea across
      Which you did not do, nor have you done effectively yet. Perhaps the more verbose How To Ask Questions The Smart Way may provide clear guidance on how to effective construct questions on internet forums.

      You still did not answer my questions on your own experience level. I will assume you are an extreme novice with access to a working script crafted by another. I can give you aid on this particular problem, but if you expect to get anywhere in the long run, you will need to learn some very basic coding concepts you apparently lack.

      In examining your desired output, I note that several of your character sequences do not appear in your text block, e.g. "VAVLMLCLAVIFLC", "LLALVAIFF", ... I note that "AVVAAVMW" is cited at "position: 325". This makes me suspect that the orginal file you are parsing does not contain the white space you are posting or modifies the input before filtering.

      I have modified your originally posted code to do something like what you request, though the numbers are wrong. 

      #!/usr/bin/perl
use strict;
use warnings;

local $/; # Slurp
my $content = <DATA>;

my ($header) = $content =~ /^(>.*?)$/m;
while ($content =~ /^[\w]+?([VMFWLCA]{8,})[\w]+?$/mg) {
    my $sequence = $1;
    print $header, "contains $sequence at position ", pos($content) - 
+length($sequence), "\n";
}
__DATA__
>P30450 | Homo sapiens (Human). | NCBI_TaxID=9606; | 365 | Name=HLA-A;
+ Synonyms=HLAA;M

MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFYTSVSRPGRGEPRFIAVGYVDDT
QFVRFDSDAASQRMEPRAPWIEQEGPEYWDRNTRNVKAHSQTDRANLGTLRGYYNQSEDGS
TIQRMYGCDVGPDGRFLRGYQQDAYDGKDYIALNEDLRSWTAADMAAQITQRKW
ETAHEAEQWRAYLEGRCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATL
RCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWASVVVPSGQEQ
RYTCHVQHEGLPKPLTLRWEPSSQPTIPIVGIIAGLVLFGAVIAGAVVAAVMWRRKS
SDRKGGSYSQAASSDSAQGSDMSLTACKV

      [download]

      outputs

      >P30450 | Homo sapiens (Human). | NCBI_TaxID=9606; | 365 | Name=HLA-A; Synonyms=HLAA;Mcontains AVVAAVMW at position 420

      I leave modifying it to get what you expect as an exercise for you. You will likely want to read the documentation at perlsyn, perlre, perlretut, pos and length.

[reply]
[d/l]
[select]
        while ($content =~ /^[\w]+?([VMFWLCA]{8,})[\w]+?$/mg) {
    my $sequence = $1;
    print $header, "contains $sequence at position ", pos($content) - 
+length($sequence), "\n";
}

        [download]

        What did you want "pos($content) - length($sequence)" to give you?    The whole pattern starts at 371 and ends at 428 while the contents of $1 start at 416 and end at 424 so 420 is somewhere in the middle of $1.    Have a look at the @- and @+ arrays for the start and end positions of matches.

[reply]
[d/l]
        Heh that's actually pretty similar to what I had originally coded and contains the same problem, the problem is 2 fold: for some reason /g isn't resetting the counter for each new line it goes through looking for the regex so I'm getting position numbers in the 10,000s, and 2: if I simply delete the header after the first print statement, the code isn't iterating over each header line and priting the next one that contains the sequence match/s in the next line. I tried doing a while loop over the text file looking at each header and storing it then doing a while loop over the text looking for the sequence pattern and storing it. I was thinking about then saying if the sequence was found (defined $1) print the header and the sequence but I can't figure out how to associate the two (a more complete text file to use from:) 
        >P31946 | Homo sapiens (Human). | NCBI_TaxID=9606; | 246 |    Name=YWH
+AB;
MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQK
+TERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDN
+KQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTL
+NEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN
>P62258 | Homo sapiens (Human). | NCBI_TaxID=9606; | 255 |    Name=YWH
+AE;
MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKE
+ENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATGN
+DRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDT
+LSEESYKDSTLIMQLLRDNLTLWTSDMQGDGEEQNKEALQDVEDENQ
>Q04917 | Homo sapiens (Human). | NCBI_TaxID=9606; | 246 |    Name=YWH
+AH; Synonyms=YWHA1;
MGDREQLLQRARLAEQAERYDDMASAMKAVTELNEPLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKT
+MADGNEKKLEKVKAYREKIEKELETVCNDVLSLLDKFLIKNCNDFQYESKVFYLKMKGDYYRYLAEVAS
+GEKKNSVVEASEAAYKEAFEISKEQMQPTHPIRLGLALNFSVFYYEIQNAPEQACLLAKQAFDDAIAEL
+DTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDEEAGEGN
>P30450 | Homo sapiens (Human). | NCBI_TaxID=9606; | 365 |    Name=HLA
+-A; Synonyms=HLAA;
MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRME
+PRAPWIEQEGPEYWDRNTRNVKAHSQTDRANLGTLRGYYNQSEDGSHTIQRMYGCDVGPDGRFLRGYQQ
+DAYDGKDYIALNEDLRSWTAADMAAQITQRKWETAHEAEQWRAYLEGRCVEWLRRYLENGKETLQRTDA
+PKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWASVVVPSGQ
+EQRYTCHVQHEGLPKPLTLRWEPSSQPTIPIVGIIAGLVLFGAVIAGAVVAAVMWRRKSSDRKGGSYSQ
+AASSDSAQGSDMSLTACKV
>Q156A1 | Homo sapiens (Human). | NCBI_TaxID=9606; | 80 |    Name=ATXN
+8;
MQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ
+QQQQQQQQQQ
>Q9UQB9 | Homo sapiens (Human). | NCBI_TaxID=9606; | 309 |    Name=AUR
+KC; Synonyms=AIE2, AIK3, ARK3, STK13;
MSSPRAVVQLGKAQPAGEELATANQTAQQPSSPAMRRLTVDDFEIGRPLGKGKFGNVYLARLKESHFIVA
+LKVLFKSQIEKEGLEHQLRREIEIQAHLQHPNILRLYNYFHDARRVYLILEYAPRGELYKELQKSEKLD
+EQRTATIIEELADALTYCHDKKVIHRDIKPENLLLGFRGEVKIADFGWSVHTPSLRRKTMCGTLDYLPP
+EMIEGRTYDEKVDLWCIGVLCYELLVGYPPFESASHSETYRRILKVDVRFPLSMPLGARDLISRLLRYQ
+PLERLPLAQILKHPWVQAHSRRVLPPCAQMAS
>O75366 | Homo sapiens (Human). | NCBI_TaxID=9606; | 819 |    Name=AVI
+L;
MPLTSAFRAVDNDPGIIVWRIEKMELALVPVSAHGNFYEGDCYVILSTRRVASLLSQDIHFWIGKDSSQD
+EQSCAAIYTTQLDDYLGGSPVQHREVQYHESDTFRGYFKQGIIYKQGGVASGMKHVETNTYDVKRLLHV
+KGKRNIRATEVEMSWDSFNRGDVFLLDLGKVIIQWNGPESNSGERLKAMLLAKDIRDRERGGRAEIGVI
+EGDKEAASPELMKVLQDTLGRRSIIKPTVPDEIIDQKQKSTIMLYHISDSAGQLAVTEVATRPLVQDLL
+NHDDCYILDQSGTKIYVWKGKGATKAEKQAAMSKALGFIKMKSYPSSTNVETVNDGAESAMFKQLFQKW
+SVKDQTMGLGKTFSIGKIAKVFQDKFDVTLLHTKPEVAAQERMVDDGNGKVEVWRIENLELVPVEYQWY
+GFFYGGDCYLVLYTYEVNGKPHHILYIWQGRHASQDELAASAYQAVEVDRQFDGAAVQVRVRMGTEPRH
+FMAIFKGKLVIFEGGTSRKGNAEPDPPVRLFQIHGNDKSNTKAVEVPAFASSLNSNDVFLLRTQAEHYL
+WYGKGSSGDERAMAKELASLLCDGSENTVAEGQEPAEFWDLLGGKTPYANDKRLQQEILDVQSRLFECS
+NKTGQFVVTEITDFTQDDLNPTDVMLLDTWDQVFLWIGAEANATEKESALATAQQYLHTHPSGRDPDTP
+ILIIKQGFEPPIFTGWFLAWDPNIWSAGKTYEQLKEELGDAAAIMRITADMKNATLSLNSNDSEPKYYP
+IAVLLKNQNQELPEDVNPAKKENYLSEQDFVSVFGITRGQFAALPGWKQLQMKKEKGLF
>Q9UPA5 | Homo sapiens (Human). | NCBI_TaxID=9606; | 3926 |    Name=BS
+N; Synonyms=KIAA0434, ZNF231;
MGNEVSLEGGAGDGPLPPGGAGPGPGPGPGPGAGKPPSAPAGGGQLPAAGAARSTAVPPVPGPGPGPGPG
+PGPGSTSRRLDPKEPLGNQRAASPTPKQASATTPGHESPRETRAQGPAGQEADGPRRTLQVDSRTQRSG
+RSPSVSPDRGSTPTSPYSVPQIAPLPSSTLCPICKTSDLTSTPSQPNFNTCTQCHNKVCNQCGFNPNPH
+LTQVKEWLCLNCQMQRALGMDMTTAPRSKSQQQLHSPALSPAHSPAKQPLGKPDQERSRGPGGPQPGSR
+QAETARATSVPGPAQAAAPPEVGRVSPQPPQPTKPSTAEPRPPAGEAPAKSATAVPAGLGATEQTQEGL
+TGKLFGLGASLLTQASTLMSVQPEADTQGQPAPSKGTPKIVFNDASKEAGPKPLGSGPGPGPAPGAKTE
+PGARMGPGSGPGALPKTGGTTSPKHGRAEHQAASKAAAKPKTMPKERAICPLCQAELNVGSKSPANYNT
+CTTCRLQVCNLCGFNPTPHLVEKTEWLCLNCQTKRLLEGSLGEPTPLPPPTSQQPPVGAPHRASGTSPL
+KQKGPQGLGQPSGPLPAKASPLSTKASPLPSKASPQAKPLRASEPSKTPSSVQEKKTRVPTKAEPMPKP
+PPETTPTPATPKVKSGVRRAEPATPVVKAVPEAPKGGEAEDLVGKPYSQDASRSPQSLSDTGYSSDGIS
+SSQSEITGVVQQEVEQLDSAGVTGPHPPSPSEIHKVGSSMRPLLQAQGLAPSERSKPLSSGTGEEQKQR
+PHSLSITPEAFDSDEELEDILEEDEDSAEWRRRREQQDTAESSDDFGSQLRHDYVEDSSEGGLSPLPPQ
+PPARAAELTDEDFMRRQILEMSAEEDNLEEDDTATSGRGLAKHGTQKGGPRPRPEPSQEPAALPKRRLP
+HNATTGYEELLPEGGSAEATDGSGTLQGGLRRFKTIELNSTGSYGHELDLGQGPDPSLDREPELEMESL
+TGSPEDRSRGEHSSTLPASTPSYTSGTSPTSLSSLEEDSDSSPSRRQRLEEAKQQRKARHRSHGPLLPT
+IEDSSEEEELREEEELLREQEKMREVEQQRIRSTARKTRRDKEELRAQRRRERSKTPPSNLSPIEDASP
+TEELRQAAEMEELHRSSCSEYSPSPSLDSEAEALDGGPSRLYKSGSEYNLPTFMSLYSPTETPSGSSTT
+PSSGRPLKSAEEAYEEMMRKAELLQRQQGQAAGARGPHGGPSQPTGPRGLGSFEYQDTTDREYGQAAQP
+AAEGTPASLGAAVYEEILQTSQSIVRMRQASSRDLAFAEDKKKEKQFLNAESAYMDPMKQNGGPLTPGT
+SPTQLAAPVSFSTPTSSDSSGGRVIPDVRVTQHFAKETQDPLKLHSSPASPSSASKEIGMPFSQGPGTP
+ATTAVAPCPAGLPRGYMTPASPAGSERSPSPSSTAHSYGHSPTTANYGSQTEDLPQAPSGLAAAGRAAR
+EKPLSASDGEGGTPQPSRAYSYFASSSPPLSPSSPSESPTFSPGKMGPRATAEFSTQTPSPAPASDMPR
+SPGAPTPSPMVAQGTQTPHRPSTPRLVWQESSQEAPFMVITLASDASSQTRMVHASASTSPLCSPTETQ
+PTTHGYSQTTPPSVSQLPPEPPGPPGFPRVPSAGADGPLALYGWGALPAENISLCRISSVPGTSRVEPG
+PRTPGTAVVDLRTAVKPTPIILTDQGMDLTSLAVEARKYGLALDPIPGRQSTAVQPLVINLNAQEHTFL
+ATATTVSITMASSVFMAQQKQPVVYGDPYQSRLDFGQGGGSPVCLAQVKQVEQAVQTAPYRSGPRGRPR
+EAKFARYNLPNQVAPLARRDVLITQMGTAQSIGLKPGPVPEPGAEPHRATPAELRSHALPGARKPHTVV
+VQMGEGTAGTVTTLLPEEPAGALDLTGMRPESQLACCDMVYKLPFGSSCTGTFHPAPSVPEKSMADAAP
+PGQSSSPFYGPRDPEPPEPPTYRAQGVVGPGPHEEQRPYPQGLPGRLYSSMSDTNLAEAGLNYHAQRIG
+QLFQGPGRDSAMDLSSLKHSYSLGFADGRYLGQGLQYGSVTDLRHPTDLLAHPLPMRRYSSVSNIYSDH
+RYGPRGDAVGFQEASLAQYSATTAREISRMCAALNSMDQYGGRHGSGGGGPDLVQYQPQHGPGLSAPQS
+LVPLRPGLLGNPTFPEGHPSPGNLAQYGPAAGQGTAVRQLLPSTATVRAADGMIYSTINTPIAATLPIT
+TQPASVLRPMVRGGMYRPYASGGITAVPLTSLTRVPMIAPRVPLGPTGLYRYPAPSRFPIASSVPPAEG
+PVYLGKPAAAKAPGAGGPSRPEMPVGAAREEPLPTTTPAAIKEAAGAPAPAPLAGQKPPADAAPGGGSG
+ALSRPGFEKEEASQEERQRKQQEQLLQLERERVELEKLRQLRLQEELERERVELQRHREEEQLLVQREL
+QELQTIKHHVLQQQQEERQAQFALQREQLAQQRLQLEQIQQLQQQLQQQLEEQKQRQKAPFPAACEAPG
+RGPPLAAAELAQNGQYWPPLTHAAFIAMAGPEGLGQPREPVLHRGLPSSASDMSLQTEEQWEASRSGIK
+KRHSMPRLRDACELESGTEPCVVRRIADSSVQTDDEDGESRYLLSRRRRARRSADCSVQTDDEDSAEWE
+QPVRRRRSRLPRHSDSGSDSKHDATASSSSAAATVRAMSSVGIQTISDCSVQTEPDQLPRVSPAIHITA
+ATDPKVEIVRYISAPEKTGRGESLACQTEPDGQAQGVAGPQLVGPTAISPYLPGIQIVTPGPLGRFEKK
+KPDPLEIGYQAHLPPESLSQLVSRQPPKSPQVLYSPVSPLSPHRLLDTSFASSERLNKAHVSPQKHFTA
+DSALRQQTLPRPMKTLQRSLSDPKPLSPTAEESAKERFSLYQHQGGLGSQVSALPPNSLVRKVKRTLPS
+PPPEEAHLPLAGQASPQLYAASLLQRGLTGPTTVPATKASLLRELDRDLRLVEHESTKLRKKQAELDEE
+EKEIDAKLKYLELGITQRKESLAKDRGGRDYPPLRGLGEHRDYLSDSELNQLRLQGCTTPAGQFVDFPA
+TAAAPATPSGPTAFQQPRFQPPAPQYSAGSGGPTQNGFPAHQAPTYPGPSTYPAPAFPPGASYPAEPGL
+PNQQAFRPTGHYAGQTPMPTTQSTLFPVPADSRAPLQKPRQTSLADLEQKVPTNYEVIASPVVPMSSAP
+SETSYSGPAVSSGYEQGKVPEVPRAGDRGSVSQSPAPTYPSDSHYTSLEQNVPRNYVMIDDISELTKDS
+TSTAPDSQRLEPLGPGSSGRPGKEPGEPGVLDGPTLPCCYARGEEESEEDSYDPRGKGGHLRSMESNGR
+PASTHYYGDSDYRHGARVEKYGPGPMGPKHPSKSLAPAAISSKRSKHRKQGMEQKISKFSPIEEAKDVE
+SDLASYPPPAVSSSLVSRGRKFQDEITYGLKKNVYEQQKYYGMSSRDAVEDDRIYGGSSRSRAPSAYSG
+EKLSSHDFSGWGKGYEREREAVERLQKAGPKPSSLSMAHSRVRPPMRSQASEEESPVSPLGRPRPAGGP
+LPPGGDTCPQFCSSHSMPDVQEHVKDGPRAHAYKREEGYILDDSHCVVSDSEAYHLGQEETDWFDKPRD
+ARSDRFRHHGGHAVSSSSQKRGPARHSYHDYDEPPEEGLWPHDEGGPGRHASAKEHRHGDHGRHSGRHT
+GEEPGRRAAKPHARDLGRHEARPHSQPSSAPAMPKKGQPGYPSSAEYSQPSRASSAYHHASDSKKGSRQ
+AHSGPAALQSKAEPQAQPQLQGRQAAPGPQQSQSPSSRQIPSGAASRQPQTQQQQQGLGLQPPQQALTQ
+ARLQQQSQPTTRGSAPAASQPAGKPQPGPSTATGPQPAGPPRAEQTNGSKGTAKAPQQGRAPQAQPAPG
+PGPAGVKAGARPGGTPGAPAGQPGADGESVFSKILPGGAAEQAGKLTEAVSAFGKKFSSFW
>Q9NSI6 | Homo sapiens (Human). | NCBI_TaxID=9606; | 2320 |    Name=BR
+WD1; Synonyms=C21orf107, WDR9;
MAEPSSARRPVPLIESELYFLIARYLSAGPCRRAAQVLVQELEQYQLLPKRLDWEGNEHNRSYEELVLSN
+KHVAPDHLLQICQRIGPMLDKEIPPSISRVTSLLGAGRQSLLRTAKDCRHTVWKGSAFAALHRGRPPEM
+PVNYGSPPNLVEIHRGKQLTGCSTFSTAFPGTMYQHIKMHRRILGHLSAVYCVAFDRTGHRIFTGSDDC
+LVKIWSTHNGRLLSTLRGHSAEISDMAVNYENTMIAAGSCDKIIRVWCLRTCAPVAVLQGHTGSITSLQ
+FSPMAKGSQRYMVSTGADGTVCFWQWDLESLKFSPRPLKFTEKPRPGVQMLCSSFSVGGMFLATGSTDH
+VIRMYFLGFEAPEKIAELESHTDKVDSIQFCNNGDRFLSGSRDGTARIWRFEQLEWRSILLDMATRISG
+DLSSEEERFMKPKVTMIAWNQNDSIVVTAVNDHVLKVWNSYTGQLLHNLMGHADEVFVLETHPFDSRIM
+LSAGHDGSIFIWDITKGTKMKHYFNMIEGQGHGAVFDCKFSQDGQHFACTDSHGHLLIFGFGCSKPYEK
+IPDQMFFHTDYRPLIRDSNNYVLDEQTQQAPHLMPPPFLVDVDGNPHPTKYQRLVPGRENSADEHLIPQ
+LGYVATSDGEVIEQIISLQTNDNDERSPESSILDGMIRQLQQQQDQRMGADQDTIPRGLSNGEETPRRG
+FRRLSLDIQSPPNIGLRRSGQVEGVRQMHQNAPRSQIATERDLQAWKRRVVVPEVPLGIFRKLEDFRLE
+KGEEERNLYIIGRKRKTLQLSHKSDSVVLVSQSRQRTCRRKYPNYGRRNRSWRELSSGNESSSSVRHET
+SCDQSEGSGSSEEDEWRSDRKSESYSESSSDSSSRYSDWTADAGINLQPPLRTSCRRRITRFCSSSEDE
+ISTENLSPPKRRRKRKKENKPKKENLRRMTPAELANMEHLYEFHPPVWITDTTLRKSPFVPQMGDEVIY
+FRQGHEAYIEAVRRNNIYELNPNKEPWRKMDLRDQELVKIVGIRYEVGPPTLCCLKLAFIDPATGKLMD
+KSFSIRYHDMPDVIDFLVLRQFYDEARQRNWQSCDRFRSIIDDAWWFGTVLSQEPYQPQYPDSHFQCYI
+VRWDNTEIEKLSPWDMEPIPDNVDPPEELGASISVTTDELEKLLYKPQAGEWGQKSRDEECDRIISGID
+QLLNLDIAAAFAGPVDLCTYPKYCTVVAYPTDLYTIRMRLVNRFYRRLSALVWEVRYIEHNARTFNEPE
+SVIARSAKKITDQLLKFIKNQHCTNISELSNTSENDEQNAEDLDDSDLPKTSSGRRRVHDGKKSIRATN
+YVESNWKKQCKELVNLIFQCEDSEPFRQPVDLVEYPDYRDIIDTPMDFGTVRETLDAGNYDSPLEFCKD
+IRLIFSNAKAYTPNKRSKIYSMTLRLSALFEEKMKKISSDFKIGQKFNEKLRRSQRFKQRQNCKGDSQP
+NKSIRNLKPKRLKSQTKIIPELVGSPTQSTSSRTAYLGTHKTSAGISSGVTSGDSSDSAESSERRKRNR
+PITNGSTLSESEVEDSLATSLSSSASSSSEESKESSRARESSSRSGLSRSSNLRVTRTRAAQRKTGPVS
+LANGCGRKATRKRVYLSDSDNNSLETGEILKARAGNNRKVLRKCAAVAANKIKLMSDVEENSSSESVCS
+GRKLPHRNASAVARKKLLHNSEDEQSLKSEIEEEELKDENQPLPVSSSHTAQSNVDESENRDSESESDL
+RVARKNWHANGYKSHTPAPSKTKFLKIESSEEDSKSHDSDHACNRTAGPSTSVQKLKAESISEEADSEP
+GRSGGRKYNTFHKNASFFKKTKILSDSEDSESEEQDREDGKCHKMEMNPISGNLNCDPIAMSQCSSDHG
+CETDLDSDDDKIEKPNNFMKDSASQDNGLSRKISRKRVCSSDSDSSLQVVKKSSKARTGLLRITRRCAA
+TAANKIKLMSDVEDVSLENVHTRSKNGRKKPLHLACTTAKKKLSDCEGSVHCEVPSEQYACEGKPPDPD
+SEGSTKVLSQALNGDSDSEDMLNSEHKHRHTNIHKIDAPSKRKSSSVTSSGEDSKSHIPGSETDRTFSS
+ESTLAQKATAENNFEVELNYGLRRWNGRRLRTYGKAPFSKTKVIHDSQETAEKEVKRKRSHPELENVKI
+SETTGNSKFRPDTSSKSSDLGSVTESDIDCTDNTKTKRRKTKGKAKVVRKEFVPRDREPNTKVRTCMHN
+QKDAVQMPSETLKAKMVPEKVPRRCATVAANKIKIMSNLKETISGPENVWIRKSSRKLPHRNASAAAKK
+KLLNVYKEDDTTINSESEKELEDINRKMLFLRGFRSWKENAQ
>Q96KE9 | Homo sapiens (Human). | NCBI_TaxID=9606; | 485 |    Name=BTB
+D6; Synonyms=BDPL;
MAAELYAPASAAAADLANSNAGAAVGRKAGPRSPPSAPAPAPPPPAPAPPTLGNNHQESPGWRCCRPTLR
+ERNALMFNNELMADVHFVVGPPGATRTVPAHKYVLAVGSSVFYAMFYGDLAEVKSEIHIPDVEPAAFLI
+LLKYMYSDEIDLEADTVLATLYAAKKYIVPALAKACVNFLETSLEAKNACVLLSQSRLFEEPELTQRCW
+EVIDAQAEMALRSEGFCEIDRQTLEIIVTREALNTKEAVVFEAVLNWAEAECKRQGLPITPRNKRHVLG
+RALYLVRIPTMTLEEFANGAAQSDILTLEETHSIFLWYTATNKPRLDFPLTKRKGLAPQRCHRFQSSAY
+RSNQWRYRGRCDSIQFAVDRRVFIAGLGLYGSSSGKAEYSVKIELKRLGVVLAQNLTKFMSDGSSNTFP
+VWFEHPVQVEQDTFYTASAVLDGSELSYFGQEGMTEVQCGKVAFQFQCSSDSTNGTGVQGGQIPELIFY
+A
>P0C7T9 | Homo sapiens (Human). | NCBI_TaxID=9606; | 278 |    Name=BZW
+1L1;
MENSERNKLAMLTGVLLANGTLNASILNSLYNENLVKEGVSAAFAVKLFKSWINEKDINAVAASLRKVSM
+DNRLMELFPANKQSVEHFTKYFTEAGLKELSEYVRNQQTIGARKELQKELQEQMSRGDPFKDIILYVKE
+EMKKNNIPEPVVIGIVWSSVMSTVEWNKKEELVAEQAIKHLKQYSPLLAAFTTQGQSELTLLLKIQEYC
+YDNIHFMKAFQKIVVLFYKAEVLSEEPILKWYKDAHVAKGKSVFLEQMKKFVEWLKNAEEESESEAEEG
+D
>Q8IYA2 | Homo sapiens (Human). | NCBI_TaxID=9606; | 1237 |    Name=CC
+DC144C;
MVSWGGEKRGGAEGSPKPAVYATRKTGSVRSQEDQWYLGYPGDQWSSGFSYSWWKNSVGSESKHGEGALD
+QPQHDVRLEDLGELHRAARSGDVPGVEHVLVPGDTGVDKRDRKKSIQQLVPEYKEKQTPESLPQNNNPD
+WHPTNLTLSDETCQRSKNLKVDDKCPSVSPSMPENQSATKELGQMNLTEREKMDTGVKTSQEPEMAKDC
+DREDIPIYPVLPHVQKSEEMRIEQGKLEWKNQLKLVINELKQRFGEIYEKYKIPACPEEEPLLDNSTRG
+TDVKDIPFNLTNNIPGCEEEDASEISVSVVFETFPEQKEPSLKNIIHSYYHPYSGSQEHVCQSSSKLHL
+HENKLDCDNDNKPGIGHIFSTDKNFHNDASTKKARNPEVVTVEMKEDQEFDLQMTKNMNQNSDSGSTNN
+YKSLKPKLENLSSLPPDSDRTSEVYLHEELQQDMQKFKNEVNTLEEEFLALKKENVQLHKEVEEEMEKH
+RSNSTELSGTLTDGTTVGNDDDGLNQQIPRKENGEHDRLALKQENEEKRNADMLYNKDSEQLRIKEEEC
+GKVVETKQQLKWNLRRLVKELRTVVQERNDAQKQLSEEQDARILQDQILTSKQKELEMAQKKRNPEISH
+RHQKEKDLFHENCMLQEEIALLRLEIDTIKNQNKQKEKKYFEDIEVVKEKNDNLQKIIKRNEETLTETI
+LQYSGQLNNLTAENKMLNSELENGKENQERLEIEMESYRCRLAAAVHDCDQSQTARDLKLDFQRTRQEW
+VRLHDKMKVDMSGLQAKNEILSEKLSNAESKINSLQIQLHNTRDALGRESLILERVQRDLSQTQCQKKE
+TEQMYQSKLKKYIAKQESVEERLSQLQSENMLLRQQLDDVHKKANSQEKTISTIQDQFHSAAKNLQAES
+EKQILSLQEKNKELMDEYNHLKERMDQCEKEKAGRKIDLTEAQETVPSRCLHLDAENEVLQLQQTLFSM
+KAIQKQCETLQKNKKQLKQEVVNLKSYMERNMLERGEAEWHKLLIEERARKEIEEKLNEAILTLQKQAA
+VSHEQLAQLREDNTTSIKTQMELTVIDLESEISRIKTSQADFNKTKLERYKELYLEEVKVRESLSNELS
+RTNEMIAEVSTQLTVEKEQTRSRSLFTAYATRPVLESPCVGNLNDSEGLNRKHIPRKKRSALKDMESYL
+LKMQQKLQNDLTAEVAGSSQTGLHRIPQCSSFSSSSLHLLLCSICQPFFLILQLLLNMNLDPI
>A7MBM2 | Homo sapiens (Human). | NCBI_TaxID=9606; | 1401 |    Name=DI
+SP2; Synonyms=DISPB, KIAA1742;
MDGDSSSSSGGSGPAPGPGPEGEQRPEGEPLAPDGGSPDSTQTKAVPPEASPERSCSLHSCPLEDPSSSS
+GPPPTTSTLQPVGPSSPLAPAHFTYPRALQEYQGGSSLPGLGDRAALCSHGSSLSPSPAPSQRDGTWKP
+PAVQHHVVSVRQERAFQMPKSYSQLIAEWPVAVLMLCLAVIFLCTLAGLLGARLPDFSKPLLGFEPRDT
+DIGSKLVVWRALQALTGPRKLLFLSPDLELNSSSSHNTLRPAPRGSAQESAVRPRRMVEPLEDRRQENF
+FCGPPEKSYAKLVFMSTSSGSLWNLHAIHSMCRMEQDQIRSHTSFGALCQRTAANQCCPSWSLGNYLAV
+LSNRSSCLDTTQADAARTLALLRTCALYYHSGALVPSCLGPGQNKSPRCAQVPTKCSQSSAIYQLLHFL
+LDRDFLSPQTTDYQVPSLKYSLLFLPTPKGASLMDIYLDRLATPWGLADNYTSVTGMDLGLKQELLRHF
+LVQDTVYPLLALVAIFFGMALYLRSLFLTLMVLLGVLGSLLVAFFLYQVAFRMAYFPFVNLAALLLLSS
+VCANHTLIFFDLWRLSKSQLPSGGLAQRVGRTMHHFGYLLLVSGLTTSAAFYASYLSRLPAVRCLALFM
+GTAVLVHLALTLVWLPASAVLHERYLARGCARRARGRWEGSAPRRLLLALHRRLRGLRRAAAGTSRLLF
+QRLLPCGVIKFRYIWICWFAALAAGGAYIAGVSPRLRLPTLPPPGGQVFRPSHPFERFDAEYRQLFLFE
+QLPQGEGGHMPVVLVWGVLPVDTGDPLDPRSNSSLVRDPAFSASGPEAQRWLLALCHRARNQSFFDTLQ
+EGWPTLCFVETLQRWMESPSCARLGPDLCCGHSDFPWAPQFFLHCLKMMALEQGPDGTQDLGLRFDAHG
+SLAALVLQFQTNFRNSPDYNQTQLFYNEVSHWLAAELGMAPPGLRRGWFTSRLELYSLQHSLSTEPAVV
+LGLALALAFATLLLGTWNVPLSLFSVAAVAGTVLLTVGLLVLLEWQLNTAEALFLSASVGLSVDFTVNY
+CISYHLCPHPDRLSRVAFSLRQTSCATAVGAAALFAAGVLMLPATVLLYRKLGIILMMVKCVSCGFASF
+FFQSLCCFFGPEKNCGQILWPCAHLPWDAGTGDPGGEKAGRPRPGSVGGMPGSCSEQYELQPLARRRSP
+SFDTSTATSKLSHRPSVLSEDLQLHDGPCCSRPPPAPASPRELLLDHQAVFSQCPALQTSSPYKQAGPS
+PKTRARQDSQGEEAEPLPASPEAPAHSPKAKAADPPDGFCSSASTLEGLSVSDETCLSTSEPSARVPDS
+VGVSPDDLDDTGQPVLERGQLNGKRDTLWLALRETVYDPSLPASHHSSLSWKGRGGPGDGSPVVLPNSQ
+PDLPDVWLRRPSTHTSGYSS
>Q96HU8 | Homo sapiens (Human). | NCBI_TaxID=9606; | 199 |    Name=DIR
+AS2;
MPEQSNDYRVAVFGAGGVGKSSLVLRFVKGTFRESYIPTVEDTYRQVISCDKSICTLQITDTTGSHQFPA
+MQRLSISKGHAFILVYSITSRQSLEELKPIYEQICEIKGDVESIPIMLVGNKCDESPSREVQSSEAEAL
+ARTWKCAFMETSAKLNHNVKELFQELLNLEKRRTVSLQIDGKKSKQQKRKEKLKGKCVIM
>Q8N4W6 | Homo sapiens (Human). | NCBI_TaxID=9606; | 341 |    Name=DNA
+JC22;
MAKGLLVTYALWAVGGPAGLHHLYLGRDSHALLWMLTLGGGGLGWLWEFWKLPSFVAQANRAQGQRQSPR
+GVTPPLSPIRFAAQVIVGIYFGLVALISLSSMVNFYIVALPLAVGLGVLLVAAVGNQTSDFKNTLGSAF
+LTSPIFYGRPIAILPISVAASITAQRHRRYKALVASEPLSVRLYRLGLAYLAFTGPLAYSALCNTAATL
+SYVAETFGSFLNWFSFFPLLGRLMEFVLLLPYRIWRLLMGETGFNSSCFQEWAKLYEFVHSFQDEKRQL
+AYQVLGLSEGATNEEIHRSYQELVKVWHPDHNLDQTEEAQRHFLEIQAAYEVLSQPRKPWGSRR

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[reply]
[d/l]
        those sequences you don't see because they are in the file I'm parsing not what I posted otherwise I'd have to post the entire 3000 line file. my experience is pretty novice I've been working with perl for about 3 months but I have to write this code myself I don't have any other person's script that I'm editing to make it. It's a bit more complicated than what you gave me as a response in your code because If you match the first in the header, store it. If then on the next line iteration you have a match to the residues, print out the header and the match. If there's additional matches in the sequence, like the output shows, only print the name of the sequence once, but print out the other hits, like I've shown in the output. I can easily pull out all the sequences from the file or all the headers but I want to store the header only if the sequence(s) are present on the subsequent line then print them all at once. my issue is not with working with the regular expressions but more on deciding which kind of loop would be best suited for the task. Thank you and sorry about my posting etiquette.
[reply]

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