Re^3: Counting matches

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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
There is absolutely nothing preventing you from expanding the `@hant` and `@counts` arrays. Why do you suppose I set them up as arrays in the first place even though you had only given us one data point in your sample?	[reply] [d/l] [select]
Re^6: Counting matches by Nicpetbio23! (Acolyte) on May 29, 2017 at 17:07 UTC
`#!/usr/bin/env perl use strict; use warnings; use Test::More; use File::Slurp; #Counter.pl open my $handle, '<', "/home/nic/Desktop/5-27-17/Genomes_used_HANT.txt +"; chomp(my @HANT = <$handle>); close $handle; my @counts = (0,1,2,3,4,5,6,7,8,9,10); plan tests => scalar @hant; my $nrt2 = read_file("/home/nic/Desktop/5-27-17/NRT2.txt"); for my $hant (@HANT) { my $matches = () = my $nrt2 =~ /$hant/g; is ($matches, shift @counts, "Number of matches found for $hant"); }` [download] Ok, I tried this script and got the following error. "You said to perform 0 tests at Counter.pl line 13". What should I change? Sorry like I said I am new at writing perl scripts. My script might not make sense.lol	[reply] [d/l]
Re^7: Counting matches by shmem (Chancellor) on May 29, 2017 at 17:19 UTC
Re^8: Counting matches by Nicpetbio23! (Acolyte) on May 29, 2017 at 17:45 UTC
Some notes below your chosen depth have not been shown here
Re^5: Counting matches by poj (Abbot) on May 29, 2017 at 17:38 UTC
How big are the 2 files ? Try #!/usr/bin/env perl use strict; use warnings; my %count = (); my $dir = '/home/nic/Desktop/5-27-17/'; my $file1 = $dir.'Genomes_used_hant.txt'; open IN,'<',$file1 or die "Could not open $file1 : $!"; while (<IN>){ chomp; $count{$_} = 0; } close IN; my $file2 = $dir.'NRT2.txt'; my $n = 0; open IN,'<',$file2 or die "Could not open $file2 : $!"; while (my $line = <IN>){ if ($line =~ /^>(.*)_/){ ++$count{$1} if exists $count{$1}; } ++$n; } close IN; print "$n lines read from $file2\n\n"; for (sort keys %count){ if ($count{$_} > 0 ) { printf "%-15s count %d\n",$_,$count{$_}; } } [download] poj	[reply] [d/l]
Re^6: Counting matches by Nicpetbio23! (Acolyte) on May 29, 2017 at 17:47 UTC
Perfect!	[reply]
Re^6: Counting matches by Nicpetbio23! (Acolyte) on May 29, 2017 at 18:20 UTC
What does this line do/mean? `printf "%-15s count %d\n",$_,$count{$_};` [download]	[reply] [d/l]
Re^7: Counting matches by poj (Abbot) on May 29, 2017 at 18:49 UTC
Re^5: Counting matches by AnomalousMonk (Archbishop) on May 29, 2017 at 19:19 UTC
For those monks following along at home, please note that the sample `NRT2.txt` Fasta file given here has none of the genomes in the sample `Genomes_used_hant.txt` file! You'll have to roll your own sample data. Thank you, Nicpetbio23!. Give a man a fish: `<%-{-{-{-<`	[reply] [d/l] [select]