Re^4: Counting matches

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]

Comment on Re^4: Counting matches Select or Download Code

Replies are listed 'Best First'.
Re^5: Counting matches by hippo (Bishop) 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 $hant"); }` [download] Ok, I tried this script and got the following error. "You said to perform 0 tests at Counter.pl line 13". What should I change? Sorry like I said I am new at writing perl scripts. My script might not make sense.lol	[reply] [d/l]
Re^7: Counting matches by shmem (Chancellor) on May 29, 2017 at 17:19 UTC
This: `chomp(my @HANT = <$handle>); ... plan tests => scalar @hant;` [download] Perl is case sensitive, unless otherwise stated for details. `@HANT` and `@hant` are different arrays. perl -le'print map{pack c,($-++?1:13)+ord}split//,ESEL'	[reply] [d/l] [select]
Re^8: Counting matches by Nicpetbio23! (Acolyte) on May 29, 2017 at 17:45 UTC
Re^9: Counting matches by shmem (Chancellor) on May 29, 2017 at 20:37 UTC
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 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
it formats the print output, see printf and sprintf %-15s a string 15 characters minimum width left justified %d signed integer	[reply]
Re^6: Counting matches by Nicpetbio23! (Acolyte) on May 29, 2017 at 17:47 UTC
Perfect!	[reply]
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]


Think about Loose Coupling
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