Re: Counting matches

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Re^2: Counting matches by Nicpetbio23! (Acolyte) on May 29, 2017 at 14:08 UTC
Hi, I want to read the file Genomes_used_Hant.txt into an array and look for each element in the array in NRT2.txt and return a count. For example Gloin1 is at line 24 in the Genomes_used_Hant.txt: `Gloin1` [download] Below is an example of what is in the NRT2.txt file. `>Gloin1_46659 MVKLFARPLPIDP.... >Gloin1_30454 MIKLFDKPSKELS....` [download] I would like to return the following in an output file for each element in the array. Since this is not an exact match I expect I need to use a regex. `Gloin1: 2 occurrences in NRT2.txt` [download]	[reply] [d/l] [select]
Re^3: Counting matches by hippo (Archbishop) on May 29, 2017 at 15:08 UTC
Here is an SSCCE which matches your spec. Enjoy. `#!/usr/bin/env perl use strict; use warnings; use Test::More; my @hant = ('Gloin1'); my @counts = (2); plan tests => scalar @hant; my $nrt2 = <<EOT; >Gloin1_46659 MVKLFARPLPIDP.... >Gloin1_30454 MIKLFDKPSKELS.... EOT for my $pat (@hant) { my $matches = () = $nrt2 =~ /$pat/g; is ($matches, shift @counts, "Correct number of matches found for +$pat"); }` [download]	[reply] [d/l]
Re^4: Counting matches by Nicpetbio23! (Acolyte) on May 29, 2017 at 16:00 UTC
I think that is too specific. I want to count the occurrences of every element in Genomes_used_Hant.txt that occurs in NRT2.txt. Not just Gloin1 `Genomes_used_hant.txt Laesu1 Patat1 Hydru2 Armost1 Pacta12 VKMF3808 Gaegr1 Corca1 Artol1 Agabivarbur1 Uncre1 Armme11 Suidec1 Aspka11 MagorBR32 Bjead1 Gymlu1 CopciAmutBmut1 Thihy1 Aspgl1 Leugo1 Bacci1 Schoc1 Gloin1 ....ext` [download] NRT2.txt >ANRT2 MDFAKLLVASPEVNPNNRKALTIPVLNPFNTYGRVFFFSWFGFMLAFLSWYAFPPLLTVTIRDDLDMSQT +QIANSNIIALLATLLVRLICGPLCDRFGPRLVFIGLLLVGSIPTAMAGLVTSPQGLIALRFFIGILGGT +FVPCQVWCTGFFDKSIVGTANSLAAGLGNAGGGITYFVMPAIFDSLIRDQGLPAHKAWRVAYIVPFILI +VAAALGMLFTCDDTPTGKWSERHIWMKEDTQTASKGNIVDLSSGAQSSRPSGPPSIIAYAIPDVEKKGT +ETPLEPQSQAIGQFDAFRANAVASPSRKEAFNVIFSLATMAVAVPYACSFGSELAINSILGDYYDKNFP +YMGQTQTGKWAAMFGFLNIVCRPAGGFLADFLYRKTNTPWAKKLLLSFLGVVMGAFMIAMGFSDPKSEA +TMFGLTAGLAFFLESCNGAIFSLVPHVHPYANGIVSGMVGGFGNLGGIIFAIIFRYSHHDYARGIWILG +VISMAVFISVSWVRPVPKSQMRE >Metac1_3189 MGFNISLLWKTPMVDPINKKARSIPVLNVVDPYGRVFFFSWMGFMLGFWAWYTFPPLLTVTIKKDLHLSA +AEVANSNIVSLCATLLLRFVAGPLCDQFGSRRVYASLLLLGCLPVGLAPLVKTANGLYVSRFFIGILGA +TFVPCQVWCTGFFDKNIVGTANALSGGWGNAGGGITYFIMPAVFDSLVASQGMAPSKAWRVTFVVPLIC +LIACALGMLFLCPDTPLGSWEERSQKLQENLDQYSPTSTTAVNTPHILSEPPSRDVEKAEEFDEDSKFY +KQPSAISLSEAVAIAQAETVVKPSFKDSLPVMLSLQTLFHVATYSCSFGGELAVNSILSSYYKANFPHL +DQTKASNYAAIFGFLNFVTRPLGGVVADILYRMSGQNLWTKKAWITMAGLLSGALLIIVGKVDPSEANG +RDIGTMVGLVTVAAFFIEAGNGANFALVPHVYPAANGVLSGCTGGGGNLGGVVFAIIFRFIDHGSGYAT +ACWVIGVIHIAVNLAVCRIPPLPKGQVGGQ >MagorUS71_00075311 MGINVKFSDLYRAPEVNPITRKARSIPALNVINMYGRVFFFSWFGFMIAFWAWYTFPPLLTVTIRKDLNL +TAAEVANSNIVSLVATLFVRMVAGPLCDLWGSRVVFGGVLLVGAIPLGLAPLIQNATGLYVSRFFIGIL +GGAFVPCQVWSTGFFDKNVVGTANALTGGFGNAGGGITYFIMPAVFDSFVHRMGYTPGQAWRLTFVVPL +VMIIVTGVSLLLLCPDTPTGKWSERHMHAQQMVGQASTTDATNQDKIVDVPGSITDKGPNASNSSEGNS +FVEEKEKTRKEKDEQVGELLDAEAGRVIKSDDAAVQNTDTIAKPTFGESLRVMASPQTLVHVLTYFCSF +GGELAINAILSSYYLKNFPELGQTGASNYAAIFGFLNFITRPLGGVVSDLLYNAAGSGPRGLWLKKGWI +HVCGIATGALLILIGQLNPHHQPTMLGLVIFMAFFHEAGNGANFALIPHVHPHANGLVSGITGAGGNLG +GVVFAVVFRFVGGGTGYATGFWIIGIVHIAINIAMAWIKPLPKGQIGGY >Phchr2_2932727 MVYFPFARPQRSSVAPAETADALDTAAAAQIGHPEKLSLWERLTTVRINPANNKCTTLPILKLNNPYSIN +FHLSWLGFWVAFLSWFAFSPLVPEAVKNDLKLTQKQIGNSNIVSLCSTLLVRVIVGPLCDRFGPRKVMA +GLLIVGAIPSGLAGTVSSAQGLYVIRFFIGILGGTFVPCQAWTTAFYDTSIVGRANALVAGWGNSGGGF +TFIIMVALYDRLRSDGLSPHSAWRAAFAIVPVPILFFVAIITLLVGTDHPNGKWADRHKNAALVPAALT +DGSPRGSDDIEAIREIAPTQDGPKEKTENEKDAVNVDVTAVMPSRPPSIRQDSVPLTWKIALDVVLNPL +TWLPALAYMSSFGYELAIDANLANVYFGLYNKTKGFGQTRCGYIASIFGLLNVFSRPLGGYMGDVVYRR +WGVPGKKYLVLALGVLQGALSLAWGLYLDRHAASLAVVIVLMILTAAVDELGNGANFSLVPHCNPSSNG +VMTGIVGAMGNLGGVWFALMFRFQPSPFGKAFWIAGVVTMVTSVLLVVIRVPRK >Thiar1_121068 MGLKFHHLYASPEVNPASLKARSIPFFNPVDIYGRVFFFSWFGFMVAFWAWAAFPPLLTKVIQKELGLTP +AEVANSNIISPCAALLVRLVAGPLCDQFGPRIVFGGLLLVGSIPLGLAPLVHNAAGLYVSRFFIGILGG +AFVPCQVWSTGFFDKNIVGTANALAGGFGTAGGGITYFVMPAVYDAFVSYGHTAGEAWRLAFIVPLAVV +ITTGTALIVLCPDTPTGKWSERHLANSTPDDGSPSHNMTPANCSVIDVPGRITDKLPSPTAPSLSLSSR +QDPESGRQKPSEKNSHLANHKPMLDPESQLPIITLATAANTTKSEVVQKPTLSQAIRVAFSPQAIFHLL +TYMCSFGSELAINMIISSYYVKNFPSLSQTSAATFAALFGFQNFVTRPLGGVVSDLLYNYCGRSLWLKK +LWIVSCGVLAGVFLIVTGRLDPHGEGAMFGLVAVAGVFLQAGNGANFSLVPHVHPFANGILSGLTGAGG +NFGGVVFSVIFRFMDGGTNYAKGFWVIGVVNLVVCLGLSWIPPLPKGQVGGH >Thiar1_767720 MGFKPSDLWRTPEVNPVNKKARSVPILNPIDRHGRVFFFSWMGFMLAFWAWYTFPPLLSVTIKKDLNLTS +EEVANSNIVSLVATLLVRFAAGPLCDLLGSRKVFSLILLVGSIPIGLAPLIKDATGLYIIRFFIGILGG +SFVPCQVWCTGWFDKNVVGTANALSGGWGNAGGGITYFIMPAVYDSLVHRHGHTSGEAWRITFIVPLVC +LITCGLGLLFLCDDTPMGKWSDRHENVQQNLETQGISGKVVAITGNIADREPPSSSTSPSRAPSDIEKA +DPEKPKLTGDLTVTEAIETAQGETVVKPTFRDSLPVVFSLHALFHTATYACSFGGELAVNSILGAYYLK +NFPHLGQTNASNYAALFGFLNFVTRPLGGVVGDMLYNYFGRNLWLKKIWIHVCGLLTGALLILIGMLDP +HDLGTMVGLIVLMAVFHEAGNGANFALVPHVYPHANGVLSGLTGAGGNLGGVVFAIIFRYMDNGTNYAK +GFWVIGIMHIILNLAVCWIPPIPKGQIGGR >Micmi1_478558 MPAIFDHFVGHYKLSPHDAWRRAFFVPFAIIVGTAILMVVLCPDTPVGKWSERHEAVEANLRVIHEQGRH +VPQSSVVYGESTGASPADSTEKVDKLAITKDVEFGKGEVTEIDAEYAHEVIEKPSAKEIFKVFISPQTV +ALMACYFNSFGSELAINSVLGAYYLKNFPKLGQTSSGRWAAMFGLLNVYGRPLGGIISDIIYKYTKGNL +WAKKIWIHFLGVTMGVFMLAIGLANSHNQHTMIGLVAGLAFFMDASNGANFALVPHVHPQANGIVSGFV +GAVGNFGGVIGAIIFRYNVTNYGKSIWILGVIAIVMNLSVAWIRPIPKGQIGGR >Micmi1_311120 MGFNPAVLFKAPQVNPITKKARSIPILNPFNVYGRVFFFSWWGFMVAFLSWYAWSPLIGETIKADLKLTQ +AQIANSNILALVATLLVRCIAGPLCDKFGPRLVFAGVLLAGAVPTAFAFAIKNAAGLIVLRFFVGILGG +SFVPCQVWSTGFFDKNIVGTANSITGGFGNAGGGITYFVMPAIFDTFVNHYGMTKHKAWRMAFFVPFGM +IVGTAILMLLLTPDTPVGKWKDRHAAVEANLRAEHEAGRIIPHTGLGEAHHAHGPPLVLDDKKNDSTSD +VEHGTGEVVAVDTEYSHEVVMSPTFKEIVQIALSPQTLTLMACYFCSFGAELAINSILGAYYLKNFPKL +GQSGSGDWAAMFGLLNVVFRPMGGMMSDALYKFTGGKVWSKKILVHVMGVLMGMFMIIIGATDSHNRST +MVGLIAGLAFFLEAGNGANFGLVPHVHPYANGVVSGFTGASGNLGGIIGAIIFRYNGLHYGKSIWIFGI +IAIVLNLAVCWIRPVPKGQIGGR >Aspnid1_6363 MKPTQVLRLAVAAPDVNPQTRKARSIPVLNPFDLYGRVFFFSWIGFLVAFLSWYAFPPLLSVTIKKDLHM +SQDDVANSNIVALLGTFVMRFIAGPLCDRFGPRLVFVGLLICGAVPTAMAGLVTTPQGLIALRFFVGIL +GATFVPCQVWCTGFFDKNIVGTANSLAGGFGNAGGGITYFVMPAIYDSFVHDRGLTPHKAWRVSYIVPF +IIIVSIALAMLFTCPDTPTGKWADREKTSGQSIVDLSSTPNASSANSINISSDEKKAVHPEVTDSEAQV +HVRAGQIESSDAVIEAPTIKRYLSIALDPSALAVAVPYACSFGAELAINSILGAYYLLNFPLLGQTQSG +RWASMFGLVNVVFRPMGGFIADLIYARTNSVWAKKMWLVVLGLAMSGMAILIGFLDPHRESVMFGLVVL +MAFFIAASNGANFAIVPHVHPSANGIVSGIVGGMGNFGGIIFAIVFRYNGTQYHRSLWIIGFIILGCTL +FFSWVRPVPKQNH >Aspnid1_5705 MDFAKLLVASPEVNPNNRKALTIPVLNPFNTYGRVFFFSWFGFMLAFLSWYAFPPLLTVTIRDDLDMSQT +QIANSNIIALLATLLVRLICGPLCDRFGPRLVFIGLLLVGSIPTAMAGLVTSPQGLIALRFFIGILGGT +FVPCQVWCTGFFDKSIVGTANSLAAGLGNAGGGITYFVMPAIFDSLIRDQGLPAHKAWRVAYIVPFILI +VAAALGMLFTCDDTPTGKWSERHIWMKEDTQTASKGNIVDLSSGAQSSRPSGPPSIIAYAIPDVEKKGT +ETPLEPQSQAIGQFDAFRANAVASPSRKEAFNVIFSLATMAVAVPYACSFGSELAINSILGDYYDKNFP +YMGQTQTGKWAAMFGFLNIVCRPAGGFLADFLYRKTNTPWAKKLLLSFLGVVMGAFMIAMGFSDPKSEA +TMFGLTAGLAFFLESCNGAIFSLVPHVHPYANGIVSGMVGGFGNLGGIIFAIIFRYSHHDYARGIWILG +VISMAVFISVSWVRPVPKSQMRE >PenroP1_04323 MAPGFFKRLYVSPEINPSTHKAKSIPVLNPFDKYGRVFFFSWLGFMVAFLSWYAFPPLLNVTIKKDLKMT +QEDVANSNIVALLATLLVRFVAGPLCDRYGPRLVFVGLLLCGAIPTAMAGLVTGPKGLIALRFFIGILG +GTFVPCQVWCTGFFDKSIVGAANSLSGGWGNAGGGITYFVMPAVYDSLVQSRGIPSHKAWRIAYVIPFI +IITAVALCMLVLCEDTPTGKWSERNLWAKDSNGTTSAPNANIVDINSCTSSSGTMTPHNAATIDSEKKG +TQSPHVIDDTPATGQIDIFRQETVVSPTRREALNVAMSLSTMALAIPYACSFGSELAINSMLGSYYTEQ +FPHMSQTKSGQWAAMFGLLNVVCRPAGGLFGDLVYLYTGTAWSKKILIAFLGIGMGAFQLAIGLSNPST +EATMFGLVAGLAFFIEASNGANFALVPHVYPFANGIVSGIVGGLGNLGGIIFAIIFRYNGSNYGRSLWI +IGVISLATNLAVSWIRPIPKSQTLS >Pyrtt1_5571 MPFAISMLWSAPELNPYNKKARSIPVLNPVNKYGRVFFFSWLGFFIAFWSWYAFPPLLSKSIKADMHLSQ +DQIANSNIVALCATLLVRFIAGPMCDHFGPRITFASLLFAGAIPTALAGTAHNATGLYFIRFFVGILGG +TFVPCQVWTTGFYDKNVVGSANALVGGWGNSGGGITYFVMPVIYDSLKSNQGLSSHVAWRVSFIVPFVL +ISACAVALLLLTEDTPTGKWSERGVTVVSGDQPNQAGHSIVPTTGALDDKPSTAASLSSNDEKKYENTA +ADVETANGDVQIMDEVQHEVVVKPSLKEGLKVMFSLQTGALCAGYFCSFGGELAINSILGAYYLKNFPY +LGQTQSGRWAAMFGLLNVITRPLGGFIADLLYQTTGHNLWAKKLWINFVGIMTGVMCIIIGKLDPHNLS +EMIGLIALMAIFLEAGNGANFALVPHVHPHANGVLSGIVGATGNFGGIIFAIIFRYHKTNYSQVFWIIG +IMIIALNCAFIWVRPIPKNQIGGR >Sodal1_324937 MGLDYLWKAPEVNPINLKACRRFETTRKIQGCPANKLQQARSVPVLNPFNKYGAAFFFSWMGFMIAFWAW +YTFPPLLTVTIRDDLNLTPAQVANSNIVSLSSTLLMRLLAGPACDKFGSRLVFGGLLLLGALPVGLAPL +VQDATGLYISRFFIGVLGATFVPCQVWCTGFFDKNIVGTANALAGGWGNAGGGITYFVMPAVFDSFRDR +GYSPAVAWRLTFIVPLICIIVCGVGLILCCEDTPMGKWSDRHLHIQENLRNQGVEDATLVNVVNVPGGI +TDRPEPSPAPASADEERNSSTKSRKDESHFDAQAIDLSRAEMLETAQGETVAKPSLRDSLRVAVSPQTI +FHVLTYACSFGGELAINAILSSYYLKNFPHLGQTGASNWAAMFGFLNFVTRPLGGIVGDLLYNYVGRDL +WWKKGWIVLCGVATGVLLVLIGQLDPHHEPTMFGLIFLMAVFHEAGNGANFALVPHVHPAANGVLSGLT +GAGGNLGGVVFAIIFRFMDGGTDYAKGFWVIGCMHIGLNLLVSWIPPLPKGQIGGH >Aspfl1_27006 MDSVKLLFLSPEVNPSNRKARSIPILNPFDKYGRVYFFSWLGFMVAFLSWYAFPPLLTVTIRKDLKMTQP +EVANSNIVALLATLLVRFVAGPLCDRFGPRLVFIGLLLCGSIPTAMAGLVTNAQGLIALRFFVGILGGT +FVPCQVWCTGFFDKKIVGTANSLAAGWGNAGGGITYFVMPAIFDSLVHNQGLPAHKAWRVAYIVPFIII +VVIAVAMFFTCEDTPTGKWSERHLWAEETSRFEGNIVNINSGISSSHPSSPPSTTNIVADLEKKGNPSP +PESIAPMPGQLESLRTDTVVAPTFKEAMNVLLSLSTAAVAIPYACSFGAELAINSILGDFYAENFPYMG +QTKTGQWAAMFGLLNVICRPAGGFIADLLYRHTQSVWSKKILLSFLGVGMGAFQLALGFSNPKSEATMF +GLTAGLAFFLEACNGANFAVVPHVHPFANGIVSGAVGGMGNLGGIIFAIIFRYNGSHYARSLWIIGIIA +IAANLAVSWIRPVPRPQMV >Necha2_90170 MGFQIAHMWKAPEVNPISRKARSVPVLNPVDIYGRVFFFSWMGFMLAFWAWYTFPPLLTVTIKKDLHLTP +AQIANSNIVSLSATFFLRFITGPLCDQFGPRRVFAYLILLGCFPIGLAPLVKNATGLYISRFFIGILGA +TFVPCQVWCTGFFDKNIVGTANALAGGWGNAGGGITYFIMPAVFDSLVAHQGLTPSKAWRVTFIVPLIC +LIVCGVGMLLLCPDSPMGDWDDQAQQVRKNMEEHGVSTSDEITPVGTPDRSGSDEENSAGCEKDVKVGD +HEHSITRNEAMEIAQGEIVVKPSLKEALPVLYSPQTFFHVATYACSFGGELAINAVLSAYLKKNFPHLD +QTKASNYAAIFGFLNFVNRPLGGVIADILYNKFGRNLWLKKGWITVCGLLTGALLILIGRVNPAESNGG +TVGTFVGLIVLMSVFHEAGNGANFALVPHVHPFANGILSGLTGGGGNLGGVIFAIIFRFMNQGKDFAMG +FWVIGIIHIALNLAVCWIPPLPKGQVGGH >Conli1_4928 MGVNIKFTDLYKAPDVNPVNRKAHSIPALNPINMYGRVFFFSWFGFMIAFWAWYTFPPLLTVTIKADLHL +TPAQVANSNIVSLVATLFIRFVAGPLCDMYGPRRVFAGTLLVGALPLGLAPLIHNATGLYVSRFFIGIL +GGSFVPCQVWSTGFFDKNIVGTANALTGGFGNAGGGITYFIMPAVYDSFVHMGHTPHQSWRLTFIVPLI +MAIATGLSLLLLCPDTPMGKWSERHLHVQENLQLHGVAERVVDIPGGITDKATPSESHVSDGEEKKPVT +YDHEAALSKSEMIETAQGETIQKPTLREALPVIFSQQTAFHFLTYFCSFGGELAINAILSSYYLKNFPT +LGQTKASNWAAMFGFLNFVTRPLGGVVSDLLYNLAGRNLWLKKGWITTCGVATGALLILIGQLNSHHQS +TMYGLVALMAFFLEAGNGANFALVPHVHPFANGILSGVTGAGGNLGGVVFAVIFRFMGGGTNYAKAFWV +IGVIHIAMNLSVCWIRPLPKGQIGGH ...ext [download]	[reply] [d/l] [select]
Re^5: Counting matches by hippo (Archbishop) on May 29, 2017 at 16:04 UTC
Re^6: Counting matches by Nicpetbio23! (Acolyte) on May 29, 2017 at 17:07 UTC
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Re^5: Counting matches by poj (Abbot) on May 29, 2017 at 17:38 UTC
Re^6: Counting matches by Nicpetbio23! (Acolyte) on May 29, 2017 at 17:47 UTC
Re^6: Counting matches by Nicpetbio23! (Acolyte) on May 29, 2017 at 18:20 UTC
Some notes below your chosen depth have not been shown here
Re^5: Counting matches by AnomalousMonk (Archbishop) on May 29, 2017 at 19:19 UTC
Re^3: Counting matches by kcott (Archbishop) on May 30, 2017 at 06:53 UTC
Now that you've provided an indication of your data, a much better solution (than my earlier tentative suggestion) presents itself. Assuming you have a filehandle, e.g. `$matches_fh`, to your file of match data (`Genomes_used_Hant.txt` in your example); and another, e.g. `$fasta_fh`, to your fasta data (`NRT2.txt` in your example); you can capture the wanted counts like this: `my $alt = join '\|', reverse sort <$matches_fh>; my $re = qr{(?x: ^ > ( $alt ) )}; my %count; /$re/ && ++$count{$1} while <$fasta_fh>;` [download] The code you've presented, in a couple of your posts in this thread, use the 3-argument form of open with lexical filehandles: this is very good. You are not, however, checking for I/O errors: this is not good at all. The easiest method is to let Perl do this checking for you with the autodie pragma; the alternative is to do this yourself, as shown in the open documentation. In the test code below, I've used Inline::Files purely for convenience. The count information is in `%count`: you can format and output this however you want. `#!/usr/bin/env perl use strict; use warnings; use Data::Dump; use Inline::Files; my $alt = join '\|', reverse sort <MATCHES>; my $re = qr{(?x: ^ > ( $alt ) )}; my %count; /$re/ && ++$count{$1} while <FASTA>; dd \%count; __MATCHES__ Gloin1 XYZ1 XYZ XYZ12 __FASTA__ >Gloin1_1 unwanted data >XYZ_1 unwanted data >XYZ12_1 unwanted data >XYZ1_2 unwanted data >XYZ1_1 unwanted data >XYZ12_3 unwanted data >Gloin1_2 unwanted data >XYZ12_2 unwanted data` [download] Output: `{ Gloin1 => 2, XYZ => 1, XYZ1 => 2, XYZ12 => 3 }` [download] — Ken	[reply] [d/l] [select]
Re^3: Counting matches by johngg (Canon) on May 29, 2017 at 14:34 UTC
Something along these lines then: `use strict; use warnings; my $inputFile = q{/path/to/NRT2.txt}; open my $inputFH, q{<}, $inputFile or die qq{open: < $inputFile: $!\n}; my %occurs; while ( <$inputFH> ) { $occurs{ $1 } ++ if m{^>([^_]+)} } close $inputFH or die qq{close: < $inputFile: $!\n}; print qq{$_: $occurs{ $_ } occurrences in $inputFile\n} for sort keys %occurs;` [download] A more comprehensive example of your input file would be needed to be sure of the solution. Update: Too simplistic, ignore this as examples of both files are needed before making a stab at a solution. Cheers, JohnGG	[reply] [d/l]