Perl Lecture 4 - Loops and Filehandles
while, for, foreach

Reading: Deitel 3.7->, Deitel 4.6, Deitel 5.1, 5.2, 5.3, Deitel 10.3 -> 10.7

What is a loop?
foreach loops
The *$_* (dollar underscore) variable
The for Loop
Loops - *map* and *grep*
Nested Loops
Escaping from loops : next, last
Filehandles
$_ as the default input variable
Input from a file
Writing to a file
Input record seperator
Exercises

What is a loop?

So far we have gone from programs with a single flow of execution (Lecture 1) and with decision points (Lecture 2).

What we have lacked to far is the ability to do repetition

while loops

program 1
#!/usr/local/bin/perl # sum.pl - adds a list of numbers
print "Enter a list of numbers, seperated by spaces:\n"; $line = <STDIN>;
# use the split function to break the line # up into an array of numbers @numbers = split( ' ', $line );
# initialize the running total to zero $sum = 0;
while ( @numbers ) { # execute loop until array is empty
# get the next number from the array $number = shift @numbers;
# increment the running total $sum += $number; print "Current Running total is $sum\n";
}
print "\n\nThe sum of your numbers is: $sum\n";
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% perl sum.pl Enter a list of numbers, seperated by spaces: 4 3 77 21 Current Running total is 4 Current Running total is 7 Current Running total is 84 Current Running total is 105 The sum of your numbers is: 105

How does this work?

A while loop is composed of a test condition and a block of code.

the block of code is executed so long as the test condition evaluates to true.

while ( test condition ) { statements }

foreach loops

program 2
# print_bases.pl $i = 1; foreach $base ( 'A', 'C', 'G', 'T' ) { print "base $i = $base\n"; $i++; }
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this outputs:

base 1 = A base 2 = C base 3 = G base 4 = T

the structure of this command is

foreach loop variable ( list ) { statements }

Here is an example from the Deitel book:

program 3
#!/usr/local/bin/perl # square_array.pl # # Using foreach to iterate over an array.
@array = ( 1 .. 10 ); # create array containing 1-10
foreach $number ( @array ) { # for each element in @array $number **= 2; # square the value }
print "@array\n"; # display the results
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this outputs:
1 4 9 16 25 36 49 64 81 100

The $_ (dollar underscore) variable

Perl has reserved a number of variable names which have special meaning.

program 4
# seq_lengths.pl @seqs = qw( AATGG CAAT GCGTTAAC ATATATATATATA ); foreach ( @seqs ) { $seq_length = length($_); print "sequence = $_ length = $seq_length\n"; }
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this outputs:

program 5
sequence = AATGG length = 5 sequence = CAAT length = 4 sequence = GCGTTAAC length = 8 sequence = ATATATATATATA length = 13
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If we don't give foreach a loop variable, the special scalar variable $_ is used instead.

Whether you make use of these special variables is up to you and your own style of programming. Some people find this style leads to more succinct, condensed programs. some people (myself included) like this style because it appeals to their laziness - less typing. On the other hand, some people detest this style of programming and say it leads to ugly code that is difficult to read.

The for Loop

program 6
# for_loop.pl for ( $i = 0 ; $i < 10; $i++ ) { print "the value of \$i is $i\n"; }
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the value of $i is 0 the value of $i is 1 the value of $i is 2 the value of $i is 3 the value of $i is 4 the value of $i is 5 the value of $i is 6 the value of $i is 7 the value of $i is 8 the value of $i is 9

program 7
# forloop_decrement.pl for ( $i = 10 ; $i > -10; $i -= 2 ) { print "the value of \$i is $i\n"; }
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the value of $i is 10 the value of $i is 8 the value of $i is 6 the value of $i is 4 the value of $i is 2 the value of $i is 0 the value of $i is -2 the value of $i is -4 the value of $i is -6 the value of $i is -8

make sure you get the test condition right - if you say less than are you sure you mean less than and not less than or equal to

Loops - map and grep

map

program 8
# map_example.pl - prints the numbers 1 to 100 @numbers = (1, 2, 3, 4, 5); @numbers_squared = map { $_ * $_ } @numbers; print "number = @numbers \n"; # 1 2 3 4 5 print "squared = @numbers_squared \n"; # 1 4 9 16 25
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grep

program 9
# grep_example.pl - filters expect values
# initialize an array of blast expect values @expect_values = (0, 3.1e-20, 1.2e-17, 4.7e-5, 0.098, 1.2);
# set an arbitrary threshold $threshold = 1e-5;
# loop through all values filtering ones that meet threshold @passed = grep { $_ < $threshold } @expect_values;
print scalar(@passed), " hits passed the threshold\n"; # 3 print "values = @passed \n"; # 0 3.1e-20 1.2e-17
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Nested Loops

program 10
# nested_loop.pl
for ( my $x = 0; $x < 10; $x++ ) { for ( my $y = 0; $y < 10; $y++ ) { print "$x * $y = ", ( $x * $y ), "\n"; } }
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Always indent your code so that you know which statement block each line of code belongs to.

Escaping from loops : next, last

Reading: Deitel 5.6

All the following examples are from the Deitel book:

program 11
# using_next.pl foreach ( 1 .. 10 ) { if ( $_ == 5 ) { $skipped = $_; # store skipped value next; # skip remaining code in loop only if $_ is 5 } print "$_ "; } print "\n\nUsed 'next' to skip the value $skipped.\n";
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last

program 12
# using_last.pl foreach ( 1 .. 10 ) { if ( $_ == 5 ) { $number = $_; # store current value before loop ends last; # jump to end of foreach structure } print "$_ "; } print "\n\nUsed 'last' to terminate loop at $number.\n";
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redo

program 13
# using_redo.pl $number = 1; while ( $number <= 5 ) { if ( $number <= 10 ) { print "$number "; ++$number; redo; # Continue loop without testing ( $number <= 5 ) } } print "\nStopped when \$number became $number.\n";
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1 2 3 4 5 6 7 8 9 10 Stopped when $number became 11.

Block Labels (optional)

It is possible to label statement blocks to have greater control over program flow. While this is unecessary, some people prefer this style.

Described in Deitel 5.9

Filehandles

we have already encountered the standard input filehandle STDIN

recall -

program 14
#!/usr/local/bin/perl # echo.pl
$line = <STDIN>; print "echo:$line";
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this program reads a line of input from the user's terminal, and writes back the line.

STDIN is the name of a special Filehandle that is for reading input from the command line

The next program reads in multiple lines and prints them all
program 15
#!/usr/local/bin/perl # echo2.pl
# keeps echoing back what the user types while ( $line = <STDIN> ) { print "echo:$line"; }
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$_ as the default input variable

program 16
#!/usr/local/bin/perl # echo3.pl
# keeps echoing back what the user types while ( <STDIN> ) { print "echo:$_"; }
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Here is another example:

program 17
#!/usr/local/bin/perl # wc.pl - imitates unix wc (word count) program
$lines = 0; $words = 0; $characters = 0; while ( <> ) {
$lines++;
@words = split(' ', $_); $words += scalar(@words);
$characters += length($_);
} print " $lines $words $characters\n";
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The empty angle brackets <> inidicate input should either be from files specified on the command line, or from standard input.

you can use the program this way (with a pipe):
% cat myfile | wc.pl

or this way:
% wc.pl myfile

Input from a file

program 18
#!/usr/local/bin/perl # sort.pl - sorts the lines in a file alphabetically
# open a file and assign the filehandle F open(F, "myfile.txt") or die("can't open myfile.txt: $!\n");
# read in the whole file into an array of lines @lines = (); while(<F>) { push(@lines, $_); } close(F); # close the filehandle
# sort the lines @lines = sort @lines;
# print out the lines, now sorted foreach (@lines) { print; # means the same as print $_; }
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Notice the construct in the first line of code; this is a common construct in perl programs. If the open function returns FALSE, indicating the file could not be opened, then the program dies/exits with a meaningful message.

Let's create a file then sort it using our program:

% cat > myfile.txt frizzle zen abacus quibble jellybean % sort.pl abacus frizzle jellybean quibble zen

Writing to a file

program 19
# filewrite.pl open(F, ">output.txt") or die( "cannot write to output.txt : $!\n"); print F "Hello World!\n"; close(F);
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appending

program 20
open(F, ">>output.txt"); print F "Goodbye world!\n"; close(F);
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% cat output.txt Hello World! Goodbye world!

Input record seperator

So far we have been reading in files (or user input) one line at a time.

the construct
program 21
while ( $line = <F> ) { # do something here }
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Loops through the filehandle F, each time reading in all the characters up to and including the newline character \n

What if we want to split up a file using a different seperator?

This is where some of perl's more unusual features become extremely useful and powerful. The next program reads in a series of genbank records, with each record divided using the double-forwardslash. It asks the user for a record number and prints that record.

See the appendix for a test dataset

program 22
#!/usr/local/bin/perl # genbank_fetch.pl
$/ = "//"; # genbank record seperator
print "What record number do you want to fetch?\n"; my $record = <STDIN>; chomp $record;
$current_record = 1; while ( <> ) { chomp; print if $record == $current_record; $current_record++; }
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To download a test genbank file click here

We can modify the above program, using our knowledge of regular expressions and pattern matching:

program 23
#!/usr/local/bin/perl # genbank_filter.pl - filters a file of genbank entries
$/ = "//"; # genbank record seperator
$filter = shift @ARGV; # get filter pattern from user
while ( <> ) { print if /$filter/s; # only print record if it matches pattern }
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Try running this program on a file of genbank entries, filtering by organism:

% cat test.genbank | genbank_filter.pl "Homo sapiens"

or by gene name:
% cat test.genbank | genbank_filter.pl "beta-globin"

or multiple filters using your knowledge of unix pipes:

% cat test.genbank | genbank_filter.pl "Homo sapiens" | genbank_filter.pl "beta-globin"

Exercises

Write a program to loop through a file of sequences, and give the count of the number of sequences containing EcoRI sites.

Assume a sequence file of one line per sequence.

Extend the program to give a count for each of the restriction enzymes in this hash:

program 24
%re_lookup = ( 'Eco47III'=> 'AGCGCT', 'EcoRI' => 'GAATTC', 'HindIII' => 'AAGCTT', );
(notice that we exclude all enzymes that have Ns / purines/ pyramidines to match)
You should write the program in such a way that it is easy to extend with other restriction enzymes (again focusing only on ones with A/C/G/T recognition) just by changing the hash.

if you wrote the medline lookup program in the last set of exercises, extend this to read it's data from a file.
otherwise, extend the restriction enzyme count program above to read the restriction enzyme sequences from a file.

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Appendix - data

Here is an example file of 5 GenBank entries for using in some of the programs above.

You can also download this by clicking here

LOCUS DDU63596 310 bp DNA INV 14-MAY-1999 DEFINITION Dictyostelium discoideum Tdd-4 transposable element flanking sequence, clone p427/428 right end. ACCESSION U63596 NID g2393749 KEYWORDS . SOURCE Dictyostelium discoideum. ORGANISM Dictyostelium discoideum Eukaryota; Dictyosteliida; Dictyostelium. REFERENCE 1 (bases 1 to 310) AUTHORS Wells,D.J. TITLE Tdd-4, a DNA transposon of Dictyostelium that encodes proteins similar to LTR retroelement integrases JOURNAL Nucleic Acids Res. 27 (11), 2408-2415 (1999) REFERENCE 2 (bases 1 to 310) AUTHORS Wells,D.J. and Welker,D.L. TITLE Dictyostelium discoideum Tdd-4 transposable element, right end flanking sequence from clone p427/428 JOURNAL Unpublished REFERENCE 3 (bases 1 to 310) AUTHORS Wells,D.J. and Welker,D.L. TITLE Direct Submission JOURNAL Submitted (11-JUL-1996) Biology, Utah State Univ., Logan, UT 84322-5305, USA FEATURES Location/Qualifiers source 1..310 /organism="Dictyostelium discoideum" /strain="AX4" /db_xref="taxon:44689" clone="p427428" misc_feature 5.12 /note="Fuzzy location" misc_feature J00194:(100..202),1..245,300..422 /note="Location partly in another entry" BASE COUNT 118 a 46 c 67 g 79 t ORIGIN 1 gtgacagttg gctgtcagac atacaatgat tgtttagaag aggagaagat tgatccggag 61 taccgtgata gtattttaaa aactatgaaa gcgggaatac ttaatggtaa actagttaga 121 ttatgtgacg tgccaagggg tgtagatgta gaaattgaaa caactggtct aaccgattca 181 gaaggagaaa gtgaatcaaa agaagaagag tgatgatgaa tagccaccat tactgcatac 241 tgtagccctt acccttgtcg caccattagc cattaataaa aataaaaaat tatataaaaa 301 ttacacccat // LOCUS DDU63595 83 bp DNA INV 14-MAY-1999 DEFINITION Dictyostelium discoideum Tdd-4 transposable element flanking sequence, clone p427/428 left end. ACCESSION U63595 NID g2393748 KEYWORDS . SOURCE Dictyostelium discoideum. ORGANISM Dictyostelium discoideum Eukaryota; Dictyosteliida; Dictyostelium. REFERENCE 1 (bases 1 to 83) AUTHORS Wells,D.J. TITLE Tdd-4, a DNA transposon of Dictyostelium that encodes proteins similar to LTR retroelement integrases JOURNAL Nucleic Acids Res. 27 (11), 2408-2415 (1999) REFERENCE 2 (bases 1 to 83) AUTHORS Wells,D.J. and Welker,D.L. TITLE Dictyostelium discoideum Tdd-4 transposable element, left end flanking sequence from clone p427/428 JOURNAL Unpublished REFERENCE 3 (bases 1 to 83) AUTHORS Wells,D.J. and Welker,D.L. TITLE Direct Submission JOURNAL Submitted (11-JUL-1996) Biology, Utah State Univ., Logan, UT 84322-5305, USA FEATURES Location/Qualifiers source 1..83 /organism="Dictyostelium discoideum" /strain="AX4" /db_xref="taxon:44689" clone="p427428" BASE COUNT 31 a 16 c 12 g 24 t ORIGIN 1 ttcgaaggat atctcaaggc agttaataat tactatgatg attgtaaaat attccaaagt 61 ttcccagacc caccaataat gac // LOCUS HUMBDNF 918 bp DNA PRI 31-OCT-1994 DEFINITION Human brain-derived neurotrophic factor (BDNF) gene, complete cds. ACCESSION M37762 VERSION M37762.1 GI:179402 KEYWORDS neurotrophic factor. SOURCE Human DNA. ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 918) AUTHORS Jones,K.R. and Reichardt,L.F. TITLE Molecular cloning of a human gene that is a member of the nerve growth factor family JOURNAL Proc. Natl. Acad. Sci. U.S.A. 87 (20), 8060-8064 (1990) MEDLINE 91045937 COMMENT Draft entry and computer-readable sequence for [Proc. Natl. Acad. Sci. U.S.A. (1990) In press] kindly submitted by K.R.Jones, 13-AUG-1990. FEATURES Location/Qualifiers source 1..918 /organism="Homo sapiens" /db_xref="taxon:9606" /dev_stage="adult" sig_peptide 76..123 /gene="NTF3" /note="G00-125-917; putative" /product="brain-derived neurotrophic factor" CDS 76..819 /gene="BDNF" /note="putative" /codon_start=1 /db_xref="GDB:G00-125-916" /product="brain-derived neurotrophic factor" /protein_id="AAA51820.1" /db_xref="GI:179403" /translation="MTILFLTMVISYFGCMKAAPMKEANIRGQGGLAYPGVRTHGTLE SVNGPKAGSRGLTSLADTFEHVIEELLDEDQKVRPNEENNKDADLYTSRVMLSSQVPL EPPLLFLLEEYKNYLDAANMSMRVRRHSDPARRGELSVCDSISEWVTAADKKTAVDMS GGTVTVLEKVPVSKGQLKQYFYETKCNPMGYTKEGCRGIDKRHWNSQCRTTQSYVRAL TMDSKKRIGWRFIRIDTSCVCTLTIKRGR" gene 76..816 /gene="NTF3" /map="12p13" gene 76..819 /gene="BDNF" /map="11p13" mat_peptide 124..816 /gene="NTF3" /note="G00-125-917; putative" /product="brain-derived neurotrophic factor" BASE COUNT 269 a 192 c 237 g 220 t ORIGIN 1 ggtgaaagaa agccctaacc agttttctgt cttgtttctg ctttctccct acagttccac 61 caggtgagaa gagtgatgac catccttttc cttactatgg ttatttcata ctttggttgc 121 atgaaggctg cccccatgaa agaagcaaac atccgaggac aaggtggctt ggcctaccca 181 ggtgtgcgga cccatgggac tctggagagc gtgaatgggc ccaaggcagg ttcaagaggc 241 ttgacatcat tggctgacac tttcgaacac gtgatagaag agctgttgga tgaggaccag 301 aaagttcggc ccaatgaaga aaacaataag gacgcagact tgtacacgtc cagggtgatg 361 ctcagtagtc aagtgccttt ggagcctcct cttctctttc tgctggagga atacaaaaat 421 tacctagatg ctgcaaacat gtccatgagg gtccggcgcc actctgaccc tgcccgccga 481 ggggagctga gcgtgtgtga cagtattagt gagtgggtaa cggcggcaga caaaaagact 541 gcagtggaca tgtcgggcgg gacggtcaca gtccttgaaa aggtccctgt atcaaaaggc 601 caactgaagc aatacttcta cgagaccaag tgcaatccca tgggttacac aaaagaaggc 661 tgcaggggca tagacaaaag gcattggaac tcccagtgcc gaactaccca gtcgtacgtg 721 cgggccctta ccatggatag caaaaagaga attggctggc gattcataag gatagacact 781 tcttgtgtat gtacattgac cattaaaagg ggaagatagt ggatttatgt tgtatagatt 841 agattatatt gagacaaaaa ttatctattt gtatatatac ataacagggt aaattattca 901 gttaagaaaa aaataatt // LOCUS NT_010368 161485 bp DNA CON 16-NOV-2000 DEFINITION Homo sapiens chromosome 15 working draft sequence segment, complete sequence. ACCESSION NT_010368 VERSION NT_010368.1 GI:11433101 KEYWORDS HTG. SOURCE human. ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 161485) AUTHORS International Human Genome Project collaborators. TITLE Toward the complete sequence of the human genome JOURNAL Unpublished COMMENT GENOME ANNOTATION REFSEQ: NCBI contigs are derived from assembled genomic sequence data. They may include both draft and finished sequence. COMPLETENESS: not full length. FEATURES Location/Qualifiers source 1..310 /organism="Homo sapiens" /db_xref="taxon:9606" /chromosome="15" source order(1..100,251..300,300..310) /note="Doctored from Accession AC011224 sequenced by Whitehead Institute for Biomedical Research" /organism="Homo sapiens" /db_xref="taxon:9606" /clone="RP11-10K20" variation 244 /replace="T" /replace="A" /db_xref="dbSNP:140670" ORIGIN 1 gtgacagttg gctgtcagac atacaatgat tgtttagaag aggagaagat tgatccggag 61 taccgtgata gtattttaaa aactatgaaa gcgggaatac ttaatggtaa actagttaga 121 ttatgtgacg tgccaagggg tgtagatgta gaaattgaaa caactggtct aaccgattca 181 gaaggagaaa gtgaatcaaa agaagaagag tgatgatgaa tagccaccat tactgcatac 241 tgtagccctt acccttgtcg caccattagc cattaataaa aataaaaaat tatataaaaa 301 ttacacccat // LOCUS HUMBETGLOA 3002 bp DNA PRI 26-AUG-1994 DEFINITION Human haplotype C4 beta-globin gene, complete cds. ACCESSION L26462 VERSION L26462.1 GI:432453 KEYWORDS beta-globin. SOURCE Homo sapiens DNA. ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 3002) AUTHORS Fullerton,S.M., Harding,R.M., Boyce,A.J. and Clegg,J.B. TITLE Molecular and population genetic analysis of allelic sequence diversity at the human beta-globin locus JOURNAL Proc. Natl. Acad. Sci. U.S.A. 91 (5), 1805-1809 (1994) MEDLINE 94173918 FEATURES Location/Qualifiers source 1..3002 /organism="Homo sapiens" /db_xref="taxon:9606" /haplotype="C4" /note="sequence found in a Melanesian population" variation replace(111,"t") variation replace(263,"t") /note="Rsa I polymorphism" variation replace(273,"c") variation replace(286..287,"") /note="2 bp insertion of AT" variation replace(288,"t") variation replace(295..296,"") /note="1 bp deletion of C or 2 bp deletion of CT" variation replace(347,"c") variation replace(476,"t") variation replace(500,"c") CDS join(866..957,1088..1310,2161..2289) /codon_start=1 /product="beta-globin" /protein_id="AAA21100.1" /db_xref="GI:532506" /translation="MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFE SFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPE NFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH" exon <866..957 /number=1 variation replace(874,"c") intron 958..1087 /number=1 exon 1088..1310 /number=2 intron 1311..2160 /number=2 variation replace(1326,"g") /note="Ava II polymorphism" variation replace(1384,"g") variation replace(1391,"t") variation replace(1976,"t") exon 2161..>2289 /number=3 variation replace(2522,"c") variation replace(2602,"a") variation replace(2604,"c") variation replace(2760,"t") /note="Hinf I polymorphism" variation replace(2913,"g") BASE COUNT 810 a 601 c 599 g 992 t ORIGIN 1 acctcctatt tgacaccact gattacccca ttgatagtca cactttgggt tgtaagtgac 61 tttttattta tttgtatttt tgactgcatt aagaggtctc tagtttttta cctcttgttt 121 cccaaaacct aataagtaac taatgcacag agcacattga tttgtattta ttctattttt 181 agacataatt tattagcatg catgagcaaa ttaagaaaaa caacaacaaa tgaatgcata 241 tatatgtata tgtatgtgtg tacatataca catatatata tatatatatt ttttcttttc 301 ttaccagaag gttttaatcc aaataaggag aagatatgct tagaactgag gtagagtttt 361 catccattct gtcctgtaag tattttgcat attctggaga cgcaggaaga gatccatcta 421 catatcccaa agctgaatta tggtagacaa aactcttcca cttttagtgc atcaacttct 481 tatttgtgta ataagaaaat tgggaaaacg atcttcaata tgcttaccaa gctgtgattc 541 caaatattac gtaaatacac ttgcaaagga ggatgttttt agtagcaatt tgtactgatg 601 gtatggggcc aagagatata tcttagaggg agggctgagg gtttgaagtc caactcctaa 661 gccagtgcca gaagagccaa ggacaggtac ggctgtcatc acttagacct caccctgtgg 721 agccacaccc tagggttggc caatctactc ccaggagcag ggagggcagg agccagggct 781 gggcataaaa gtcagggcag agccatctat tgcttacatt tgcttctgac acaactgtgt 841 tcactagcaa cctcaaacag acaccatggt gcatctgact cctgaggaga agtctgccgt 901 tactgccctg tggggcaagg tgaacgtgga tgaagttggt ggtgaggccc tgggcaggtt 961 ggtatcaagg ttacaagaca ggtttaagga gaccaataga aactgggcat gtggagacag 1021 agaagactct tgggtttctg ataggcactg actctctctg cctattggtc tattttccca 1081 cccttaggct gctggtggtc tacccttgga cccagaggtt ctttgagtcc tttggggatc 1141 tgtccactcc tgatgctgtt atgggcaacc ctaaggtgaa ggctcatggc aagaaagtgc 1201 tcggtgcctt tagtgatggc ctggctcacc tggacaacct caagggcacc tttgccacac 1261 tgagtgagct gcactgtgac aagctgcacg tggatcctga gaacttcagg gtgagtctat 1321 gggacccttg atgttttctt tccccttctt ttctatggtt aagttcatgt cataggaagg 1381 ggataagtaa cagggtacag tttagaatgg gaaacagacg aatgattgca tcagtgtgga 1441 agtctcagga tcgttttagt ttcttttatt tgctgttcat aacaattgtt ttcttttgtt 1501 taattcttgc tttctttttt tttcttctcc gcaattttta ctattatact taatgcctta 1561 acattgtgta taacaaaagg aaatatctct gagatacatt aagtaactta aaaaaaaact 1621 ttacacagtc tgcctagtac attactattt ggaatatatg tgtgcttatt tgcatattca 1681 taatctccct actttatttt cttttatttt taattgatac ataatcatta tacatattta 1741 tgggttaaag tgtaatgttt taatatgtgt acacatattg accaaatcag ggtaattttg 1801 catttgtaat tttaaaaaat gctttcttct tttaatatac ttttttgttt atcttatttc 1861 taatactttc cctaatctct ttctttcagg gcaataatga tacaatgtat catgcctctt 1921 tgcaccattc taaagaataa cagtgataat ttctgggtta aggcaatagc aatatctctg 1981 catataaata tttctgcata taaattgtaa ctgatgtaag aggtttcata ttgctaatag 2041 cagctacaat ccagctacca ttctgctttt attttatggt tgggataagg ctggattatt 2101 ctgagtccaa gctaggccct tttgctaatc atgttcatac ctcttatctt cctcccacag 2161 ctcctgggca acgtgctggt ctgtgtgctg gcccatcact ttggcaaaga attcacccca 2221 ccagtgcagg ctgcctatca gaaagtggtg gctggtgtgg ctaatgccct ggcccacaag 2281 tatcactaag ctcgctttct tgctgtccaa tttctattaa aggttccttt gttccctaag 2341 tccaactact aaactggggg atattatgaa gggccttgag catctggatt ctgcctaata 2401 aaaaacattt attttcattg caatgatgta tttaaattat ttctgaatat tttactaaaa 2461 agggaatgtg ggaggtcagt gcatttaaaa cataaagaaa tgaagagcta gttcaaacct 2521 tgggaaaata cactatatct taaactccat gaaagaaggt gaggctgcaa acagctaatg 2581 cacattggca acagccctga tgcatatgcc ttattcatcc ctcagaaaag gattcaagta 2641 gaggcttgat ttggaggtta aagttttgct atgctgtatt ttacattact tattgtttta 2701 gctgtcctca tgaatgtctt ttcactaccc atttgcttat cctgcatctc tcagccttga 2761 ctccactcag ttctcttgct tagagatacc acctttcccc tgaagtgttc cttccatgtt 2821 ttacggcgag atggtttctc ctcgcctggc cactcagcct tagttgtctc tgttgtctta 2881 tagaggtcta cttgaagaag gaaaaacagg ggtcatggtt tgactgtcct gtgagccctt 2941 cttccctgcc tcccccactc acagtgaccc ggaatctgca gtgctagtct cccggaacta 3001 tc //

Chris Mungall cjm@fruitfly.org

Berkeley Drosophila Genome Project

Date: Fri May 25 09:25:37 2001