I aim analyzing the output and I found that the program is n't showing the output result from the start. I show any of the sequence randomly. I want program to show output starting from the first sequence but this is somewhat taking random sequence from the file.

this are the fasta sequences which are in fasta file. The problem is it is not showing result from the beginning.

>gi|226694487|sp|Q1DF98.2|ATPF_MYXXD RecName: Full=ATP synthase subuni
+t b; AltName: Full=ATP synthase F(0) sector subunit b; AltName: Full=
+ATPase subunit I; AltName: Full=F-type ATPase subunit b; Short=F-ATPa
+se subunit b
MFLPSVLAASNLVKVQPGLIFWTLVTFVIAAVVLKWKAWGPILSLVEEREKQIASSIESAKRERAEAEKL
LADQKTAIAEARREAAEMMRRNTQEMEKFREELMAKSRKEAEELKLSARREIDEQKAKAIAEVRSMAVDL
AMEVAGKLISERMDDSKQRALAEQFVQGLPLNSTSATGAVRRTA<br>

>gi|172046103|sp|Q1D4N0.2|LIPA_MYXXD RecName: Full=Lipoyl synthase; Al
+tName: Full=Lip-syn; Short=LS; AltName: Full=Lipoate synthase; AltNam
+e: Full=Lipoic acid synthase; AltName: Full=Sulfur insertion protein 
+LipA
MTETTRKPEWLKVRLPHGEGYERVKAIVKRTKLATVCEEARCPNIAECWGGGTATVMLMGEVCTRACRFC
HVKVGAPPPLDPMEPIHLAQAVKEMDLEYIVVTSVNRDDRPDGGASHFASAIRELRRESPRTIVEVLIPD
FKGVEKDLTTVAEAKPHVVAHNVETVERLTPTVRDRRAKYHQSLRVLEYLKNRPEGLYTKTSVMVGLGET
DAELEQTFKDLRDVGVDVLTLGQYLQPSQYHLRVERFVTPAQFEAYKTLAESYGFLYVASGPLVRSSYRA
AEFFMKGLMERERLERLG<br>

>gi|123374798|sp|Q1DDB3.1|KDSB_MYXXD RecName: Full=3-deoxy-manno-octul
+osonate cytidylyltransferase; AltName: Full=CMP-2-keto-3-deoxyoctulos
+onic acid synthase; Short=CKS; Short=CMP-KDO synthase
MQSCRTVAVIPARHASTRFPGKPLAIIAGRTMIEHVWRRCQEAQAFDEVWVATDDDRIRAAVEGFGGKAV
MTSPACATGTDRVAEVALGRPDIDIWVNVQGDEPLVDPATLQRLAGLFQDASVRMGTLVRPLEADEAASP
HVVKAVLALNGDALYFSRSLVPHVREPGTPVQRWGHIGLYGYRREVLLSLAKLAPTPLEDAEKLEQLRAL
EHGIPIRCAKVTSHTVAVDLPGDVEKVEALMRARGG<br>

>gi|123374766|sp|Q1DCG7.1|FMT_MYXXD RecName: Full=Methionyl-tRNA formy
+ltransferase
MSRPRIVFMGTPEFAVSSLAACFELGDVVAVVTQPDKPKGRGNTVTAPPVKELALSRGVPVLQPTKLRTP
PFAEELRQYAPDVCVVTAYGRILPKDLLELPTHGCVNVHGSLLPRFRGAAPIQWAIAHGDTETGVSLMVM
DEGLDTGPVLAMKRMAIAPDETSASLYPKLAALGGEVLREFLPAYLSGELKPVPQPSEGMVLAPIIEKDQ
GRLDFTKPAVELERRLRAFTPWPGAFTTLGGKLLKVHRAQARGGSGAPGTVLASGPDGIEVACGEGSLVL
LDLQPEGKRVMRAADFLQGHKLAPGSQPFVAG<br>

>gi|123374695|sp|Q1DAN7.1|SSRP_MYXXD RecName: Full=SsrA-binding protei
+n
MTSGGKSKGVGSEPGVRVIAENRRARFDYTVDEKVEAGLALTGSEVKSLRDGIANLSDAYALPKGDELFL
LNANIGSYKAASFFDHLPTRGRKLLMHRGEIDRWTAKVRERGYSIIPLVLYFRNGRAKVELGLCRGKTHE
DRRHDIKERETKREMDRAMRRR<br>

>gi|123374693|sp|Q1DAM1.1|PNP_MYXXD RecName: Full=Polyribonucleotide n
+ucleotidyltransferase; AltName: Full=Polynucleotide phosphorylase; Sh
+ort=PNPase
MLKKSVKIGESELSIEVGRLAKQADGSVVVRYGDTMLLVTAVSAREKKDIDFLPLTVEYQEKLYSAGRIP
GSYFKREGRLTEKETLASRLVDRSCRPLFPEGYAYETQIIASVISSDPENEGDIHGITGASAALWVSDIP
FDGPIAGIRVGRVGGQLVANPTAKQREQSDLDLVMAVSRKAIVMVEGGAEEVSEADMVAALDFGFTTAQP
ALDLQDELRRELNKQVRSFEKPAAVDEGLRAKVRELAMDGIKAGYGIKEKGARYEALGKTKKEALAKLKE
QLGDGYTPLVEKHAKAVVEDLKYEHMREMTVNGGRIGDRGHDVVRSITCEVGVLPRTHGSAVFTRGETQA
LVVTTLGTSDDEQRLEMLGGMAFKRFMLHYNFPPFSVNETKPLRGPGRREVGHGALAERALRNMVPKSES
FPYTVRLVSDILESNGSSSMASVCGGTLALMDAGVPLKAPVAGIAMGLVKEGDKIAILSDILGDEDHLGD
MDFKVCGTSKGITSIQMDIKITGLTTEIMSRALEQARQGRLHILGEMLKTLAESRKEISQYAPRITTIQI
RPEFIKNVIGPGGKVIKDIIARTGAAINIEDSGRVDIASANGEAVKAAIAMIQALTREAEIGKIYTGTVR
KIAEFGAFVELFPGTDGLIHISELSDKRVKSVSDVLNEGDEVLVKVVSIDKTGKIRLSRKEAMAERAAQQ
GAAAGEAAAQPAPAPTQPDAKA<br>

>gi|123374596|sp|Q1D8K2.1|SYM_MYXXD RecName: Full=Methionine--tRNA lig
+ase; AltName: Full=Methionyl-tRNA synthetase; Short=MetRS
MAERTLVTSALPYANGPLHIGHAVEYVQTDIYVRFLRSCGRDVVYFCADDTHGTPIELNAAKQGLKPEEF
IARFHEEHQRDFHDLDVRFDYFHSTNSPENRQYAELIYGRLKEKGDIERRNIEQTYCENDRRFLPDRFIK
GTCPNCKASDQYGDACEKCGKAYDPTDLIDARCALCGTPPVRKHSEHLFFKLSRHEDFLQDVLRKPGFIH
PGLATQLQGFFEKGLSDWDISRDGPYFGFAIPGETDKYFYVWLDAPIGYIATTEKWAKETGKAKSALDYW
SADADTRIIHFIGKDIVYFHALFWPAVLNVAGFHIPSEIKVHGHLMLNGEKMSKTRGTMVPVRDYLDQLD
PSYLRYFYAANLGPGVEDLDLNLKDFRQRVNGELVNNVGNLANRALSLLAGPLEKRLAPGRAEGPGRELV
EAALARVPEVRDAFDKLEYRSAIRVITEIASAANGFLQTAAPWAQVKKDAEVARADLSDAADVAYLLGAL
LAPVTPRLSEKLFAQLGAEPLTFQALEGAKYPLLDRSRPIGTPEPLLPRLEEERVNAIIKLPEGAAAPQA
AEARPAKGAKTEKKPAEAPAATQAAAPSAGAAESPGEIEYDDFAKVVLKAGKVLAAEKVQKADKLLKLTV
DVGEGSPRTIVSGIAEAFAPEALTGRNVVVVANLKPRKLKGIESRGMLLTAGPGGKELSLLDPGDVAPGS
EVK<br>

>gi|123374566|sp|Q1D7X3.1|GCSH_MYXXD RecName: Full=Glycine cleavage sy
+stem H protein
MADNIPGDLKYTREHEWARVQGTSVVVGVTQHAQESLGDVVYVELPKVGSTVTEGKQFGVIESTKAVSEL
YSPLTGKVVKVNDGLSDNPSTVNTDPYGAGWIVEIEPSDPKQVDGLMDAAAYTALLQNS<br>

>gi|123374515|sp|Q1D773.1|RL23_MYXXD RecName: Full=50S ribosomal prote
+in L23
MNLNDVIKGPLITEKLDKAREKFRQYSFIVDRKATKHDVARAVETLFKVTVEGVNTNIVRGKIKRVGRSI
GKRPNFKKAVVTLKQGDSIELFEGGAA<br>

>gi|123374507|sp|Q1D751.1|RS13_MYXXD RecName: Full=30S ribosomal prote
+in S13
MARIAGIDLPPNKRAVISLQYIYGIGNKSAQDIIAAAGIDPTTRTKDLTEEQARKIREIIEASYKVEGDL
RREVTMNIKRLMDLGCYRGLRHRKGLPVRGQRTHTNARTRKGPKRGIVRAKPAAPAR<br>

>gi|123374498|sp|Q1D6W9.1|PIMT_MYXXD RecName: Full=Protein-L-isoaspart
+ate O-methyltransferase; AltName: Full=L-isoaspartyl protein carboxyl
+ methyltransferase; AltName: Full=Protein L-isoaspartyl methyltransfe
+rase; AltName: Full=Protein-beta-aspartate methyltransferase; Short=P
+IMT
MGDWGRADYLSRHGIKDARVLEAIARLNRADFVPEDLREEASADSPLPIGHGQTISQPYVVALMTEALQL
QGDERVLEIGTGSGYQTALLSLLCREVYSVEIVPELAQSAREVLGRQGFENVSFREGDGSLGWPDQAPFD
AILAAAAPPDVPLQLLSQLKPGGRMIIPVGPRGGTQQLLRIQRALRPGEVPQVESLLSVRFVPMTGQPLS
QG<br>

>gi|123374481|sp|Q1D6N0.1|MNMA_MYXXD RecName: Full=tRNA-specific 2-thi
+ouridylase MnmA
MRVVVAMSGGVDSSAAAALLKEQGHEVIGITLRVWSYEGKATCGSCCSPDDIDDARAVAQTLGIPFYVAN
AEEIFQDRVINPFVQSYLGGRTPIPCVACNRDVKFNFLLKRARALGARLATGHYARVEEVDGRFVLRRAV
DAAKDQSYFLFTLGQDELRDILFPVGGMTKAEVRAVAERHGLVTSQKPESMEICFVPDGDYAGFVEKVAG
PQPAGDIVDTEGNVLGTHQGIHRYTVGQRKGLNLGGGEIRYVHRLEPETQRVVVGPAEGTGRDNFGLLQP
HWVDGPPPASQPVEVRIRHRHSGAQGRVHVSPHGLVSVKLDAPARAVTPGQAAVVYDQDRVLGGGWIV<b
+r>

>gi|123374426|sp|Q1D5J6.1|MUTS_MYXXD RecName: Full=DNA mismatch repair
+ protein MutS
MNEGAGAREIASLTPMMRQYMEVKALHPDSLLFFRLGDFYEMFFEDAVKASEILQITLTARSKGADKVPM
CGVPYHAARRYIGRLVSEGLKVAICEQVEEPGNGPGIVRREVTRVITPGMVLDEEVLEPQASNFLAAVSW
NDKGWGAALLEASTGEFMALEAPGIAELAESLSRVEPRELLVPDGKRDAPEVAQLLARLVRTPAVAEGEA
ASFEPTRAAGYLRSHFAVQSLSAFGLDDAPLAAGAAGAALRYLKDTQKTAAAHVDRLSRQERGGNLLMDE
SSRANLEVLRSLRDGGRKGSLLGVLDKTVTSLGARKLARWLASPLGSLPEIHARLDAVEELSGRSVWREE
LAGILKEVGDLERLCGRLSLGAGNARDLRALGLSLAQLPRVVAVLARCESPLLKSLTGPLSALPELAELL
SRAVAEEPPVTLKDGGMIRAGFHAELDKLVALSTSGKDLLLQIEQREKERTGISSLKVRYNKVFGYYLEV
TKSNLDRVPKDYIRKQTTVNSERFVTPELKEYEEQVLTAEERRCALEIQLFEELRAQVVSAAPRIRSAAE
AVATGDALLSFARCAAEYGYTRPEVDASVALSITAGRHPVVERMLGAGDSFVPNDVRLDPAEDAQLMVIT
GPNMAGKSTVMRQVALTALMAQAGSFVPAKAARIGLCDRIFTRVGAADNLARGQSTFMVEMTETSHILHH
ATNKSLIILDEIGRGTSTFDGLSIAWAVAEHLHDTVGARALFATHYHELVDLARERPRVKNLCVAVKEQN
GKVIFLRKLVPGGASRSYGIEVAKLAGLPPEVVGRARELLQNLESGELDDAGRPRVAVRQPQGGRRGAST
GQLGLFGMEPAQGGTGVTPAQQKALDALKGASIDRMTPLDALNLLAKLQRELE<br>

>gi|123374387|sp|Q1D4R3.1|NADD_MYXXD RecName: Full=Probable nicotinate
+-nucleotide adenylyltransferase; AltName: Full=Deamido-NAD(+) diphosp
+horylase; AltName: Full=Deamido-NAD(+) pyrophosphorylase; AltName: Fu
+ll=Nicotinate mononucleotide adenylyltransferase; Short=NaMN adenylyl
+transferase
MRPAVQVALLGGSFNPPHVGHLMAATYVHATQDVDEVWLMPSWQHPFGKQMEPFEHRVAMCDALCAETSG
WLKTSRIEQEPGLSGRTVDTLTLLVARHPDIRWSIIIGSDILRDLPHWKDFHRIEELSRVMVLNRAGYPA
PNTLGPPLAEVSSTLIRDLLARGEAPSDLVPARAIAYAREHGLYGLKRTP<br>

>gi|123374295|sp|Q1D375.1|YBEY_MYXXD RecName: Full=Endoribonuclease Yb
+eY
MSGARRGNGVRLRKGKLIPRDDGKRIEEFVGAATTSTDSASVARMLAPPGWSEPAQRPEFDEVVIVLTGE
LTIVVEGRRERISAGEVGLVPRGKRVVYRNDGQGACDYWSVCAPAFRPELAHMETPKPRVQENHVTIQVA
HGQGRDFARLLTTWARAYLVQLELSGVELSLSLVDDRAIRRLNRTWRKKDKATDVLSFPAGDLPKGTPGP
RPLGDVVISLDTAKRQAKEYGRTLESEMARYLAHGLLHLLGHDHERPRDAKRMAALEEQLLGERGMVADS
LQVDAKARRARSLM<br>

>gi|123374287|sp|Q1D339.1|PLSX_MYXXD RecName: Full=Phosphate acyltrans
+ferase; AltName: Full=Acyl-ACP phosphotransacylase; AltName: Full=Acy
+l-[acyl-carrier-protein]--phosphate acyltransferase; AltName: Full=Ph
+osphate-acyl-ACP acyltransferase
MRLVLDAMGGDHAPAAPVEGGVLFARAHPGHEVLLVGDEAKVAPLLGKLRPPSNLQVHHASEVVEMDEHA
STAFRRKRDSSLRVGFELVRDGRAEALVSAGNSGAVMAGGLLTLGRLPGVERPAIAALFPALKGGGRCLL
LDAGANVDCKPTHLAQFAVMGEAYVRARMGVARPRVAVLSNGEESSKGTPLTREASGLLRRSDLDFVGYV
EGKDLFSGEVQVVVTDGFTGNVVLKTSEGVGMGVIGMLRQAIERRGGLAEKVGAMLLQPALAGLRRVVDY
AEYGGAPLLGIQGVGIVAHGRSTPRALFNALGAALAMAEGGVQAELTRCIGRAAAWLPTHPKGKRATDAG
VSD<
[download]

Dude.

I'm not a code writing service.

Please read How do I post a question effectively?

This is very likely the last update I'll ever write for this. Ever.

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

my $file = $ARGV[0];
my @currentProtein;
my %protein;
open (FASTA, "<", $file) || die "Can't open $file\n";
my $fastaLine; 
my $protSequence;
my @fastaTag;
my @tagOrder;

while (<FASTA>) 
  {
    print STDERR "CURRENT: $_";
    chomp;
    if (($_ !~ /^>/) && ($_ =~ /\w/)) 
      {
        push (@currentProtein, $_);
      }
    if ((/^>/) || (eof))
      {
       
        if ((@currentProtein > 0) || (eof))
          {
            $protSequence = join("", @currentProtein);
            $protSequence =~ s/ //g;
            @fastaTag = split(" ", $fastaLine);
            $protein{$fastaTag[0]} = $protSequence; 
            push (@tagOrder, $fastaTag[0]);
            @currentProtein = ();
          }
         $fastaLine = $_ if $_ =~ /\w/; 
      }
   
    }
close FASTA;
for(@tagOrder)
    {
      my $count_of_acidic = 0;
      my $count_of_basic = 0;
      my $count_of_neutral = 0;
      my $aa;
      my $sequence = "$protein{$_}";

      $sequence =~ s/\s//g;
      my @prot=split("",$sequence); #splits string into an array
      #print " \nThe original PROTEIN file is:\n$sequence \n";

      while(@prot)
        {
          $aa = shift (@prot);
          if($aa =~/[DNEQ]/ig)
            {
              $count_of_acidic++;
            }
          if($aa=~/[KRH]/ig)
            {
               $count_of_basic++;
            }
          if($aa=~/[DNEQKRH]/ig)
            {
              $count_of_neutral++;
            }
      }
      print "\nName: $_\n";
      print "Number of acidic amino acids:".$count_of_acidic."\n";
      print "Number of basic amino acids:".$count_of_basic."\n";
      print "Number of neutral amino acids:".$count_of_neutral."\n";
    }
[download]