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Re: Re: Selecting a random number, and back calculating to chromosome and contig!

by Sameet (Beadle)
on Apr 30, 2004 at 18:01 UTC ( [id://349470]=note: print w/replies, xml ) Need Help??


in reply to Re: Selecting a random number, and back calculating to chromosome and contig!
in thread Selecting a random number, and back calculating to chromosome and contig!

I will try to do this. Actually this hash business sort of tricky. i actually tried to avoid it!! but i can see that using hashes is probably the best option i have got. I will look into it and get back as soon as possible
Thank you for all the help
Sameet


Update
Hi,
I did a lookup table as you had suggested but it still has become a huge file (now huge is subjective i know :-) ), but it is something like 650+ lines of code for the look-up hash itself. I will test it and again get back if i have more doubts or need more help.
Thank you again for all the help!


Update 2
Acutally the file from which i am downloading these values come from a standard data format an html file, where length of each contig is given. What i am trying to do it is make those contigs into periods and then map the given random number where it would fall.
. What i want to know are there any HTML parsers avialable, if yes, (I am sure they are but I am at a loss which one to use! :-( ), how to go about using them.
Regards


UPDATE3
I have done what you had asked. But it gives me following error
Argument "NT_077988.2" isn't numeric in sort at newhumangenomelookup.p
+l line 736.
Argument "contig" isn't numeric in sort at newhumangenomelookup.pl lin
+e 736.
Argument "NT_024498.12" isn't numeric in sort at newhumangenomelookup.
+pl line 736.
Argument "NT_030737.8" isn't numeric in sort at newhumangenomelookup.p
+l line 736.
Argument "NT_077627.2" isn't numeric in sort at newhumangenomelookup.p
+l line 736.
Argument "NT_079485.1" isn't numeric in sort at newhumangenomelookup.p
+l line 736.
Argument "NT_035608.1" isn't numeric in sort at newhumangenomelookup.p
+l line 736.
Argument "NT_077911.1" isn't numeric in sort at newhumangenomelookup.p
+l line 736.
Argument "NT_023736.16" isn't numeric in sort at newhumangenomelookup.
+pl line 736.
Argument "Y" isn't numeric in sort at newhumangenomelookup.pl line 736
+.
Argument "NT_077931.2" isn't numeric in sort at newhumangenomelookup.p
+l line 736.
Argument "NT_011903.10" isn't numeric in sort at newhumangenomelookup.
+pl line 736.
Argument "NT_011295.10" isn't numeric in sort at newhumangenomelookup.
+pl line 736.

[download]
I have given here just a part of the error that i got as output. Can you give me some hints as to what is going wrong
I am giving my new code here
#!/usr/bin/perl

use strict;
use warnings;
#use Statististics::ChiSquare;

#my %chr_cont_pos;
my $chromosome;
my $contig;
my $number = 1;
my @numbers;

my $max = 3070805846;

#print "How many random sequences need to be generated\?\n";
#$number = <STDIN>;

for ( 1 .. $number ) {
    my $rnd = "";
    my $div = "1";
    for ( 0 .. length($max)/3 ) {
        $rnd .= sprintf( "%03d", int( rand( 1000 ) ) );
        $div .= "000";
    }
    my $return = int( $max * $rnd / $div );
    push (@numbers, $return);
    print "@numbers";
    print "\n";
#   print "$return\n";
}



my %chr_cont_pos = (
   167280 => (chromosome => 1, contig =>'NT_077402.1'),
   217280 => (chromosome => 1, contig =>'Gap'),
   257582 => (chromosome => 1, contig =>'NT_077911.1'),
   357582 => (chromosome => 1, contig =>'Gap'),
   511231 => (chromosome => 1, contig =>'NT_077912.1'),
   561231 => (chromosome => 1, contig =>'Gap'),
   852347 => (chromosome => 1, contig =>'NT_034471.3'),
   902347 => (chromosome => 1, contig =>'Gap'),
   1225930 => (chromosome => 1, contig =>'NT_077913.2'),
   1275930 => (chromosome => 1, contig =>'Gap'),
   1467952 => (chromosome => 1, contig =>'NT_077914.2'),
   1567952 => (chromosome => 1, contig =>'Gap'),
   1841751 => (chromosome => 1, contig =>'NT_077915.1'),
   1891751 => (chromosome => 1, contig =>'Gap'),
   2426208 => (chromosome => 1, contig =>'NT_004350.16'),
   2476208 => (chromosome => 1, contig =>'Gap'),
   3606565 => (chromosome => 1, contig =>'NT_004321.15'),
   3666565 => (chromosome => 1, contig =>'Gap'),
   5096724 => (chromosome => 1, contig =>'NT_004547.16'),
   5156724 => (chromosome => 1, contig =>'Gap'),
   5532487 => (chromosome => 1, contig =>'NT_077919.2'),
   5582487 => (chromosome => 1, contig =>'Gap'),
   12700941 => (chromosome => 1, contig =>'NT_021937.16'),
   12750941 => (chromosome => 1, contig =>'Gap'),
   12935532 => (chromosome => 1, contig =>'NT_077382.2'),
   12985532 => (chromosome => 1, contig =>'Gap'),
   15767341 => (chromosome => 1, contig =>'NT_004873.15'),
   15817341 => (chromosome => 1, contig =>'Gap'),
   16506739 => (chromosome => 1, contig =>'NT_077920.2'),
   16556739 => (chromosome => 1, contig =>'Gap'),
   17765618 => (chromosome => 1, contig =>'NT_030584.10'),
   17815618 => (chromosome => 1, contig =>'Gap'),
   18616225 => (chromosome => 1, contig =>'NT_077921.1'),
   18666225 => (chromosome => 1, contig =>'Gap'),
   23664943 => (chromosome => 1, contig =>'NT_004610.16'),
   23714943 => (chromosome => 1, contig =>'Gap'),
   25079605 => (chromosome => 1, contig =>'NT_077383.3'),
   25129605 => (chromosome => 1, contig =>'Gap'),
   25308668 => (chromosome => 1, contig =>'NT_077922.2'),
   25358668 => (chromosome => 1, contig =>'Gap'),
   25443479 => (chromosome => 1, contig =>'NT_077384.1'),
   25493479 => (chromosome => 1, contig =>'Gap'),
   28348206 => (chromosome => 1, contig =>'NT_037485.3'),
   28498206 => (chromosome => 1, contig =>'Gap'),
   29559071 => (chromosome => 1, contig =>'NT_004538.15'),
   29564071 => (chromosome => 1, contig =>'Gap'),
   34675916 => (chromosome => 1, contig =>'NT_004511.16'),
   34725916 => (chromosome => 1, contig =>'Gap'),
   37706847 => (chromosome => 1, contig =>'NT_079482.1'),
   37806847 => (chromosome => 1, contig =>'Gap'),
   74597419 => (chromosome => 1, contig =>'NT_032977.6'),
   74602419 => (chromosome => 1, contig =>'Gap'),
   87542284 => (chromosome => 1, contig =>'NT_026943.13'),
   87592284 => (chromosome => 1, contig =>'Gap'),
   91268979 => (chromosome => 1, contig =>'NT_004686.16'),
   91273979 => (chromosome => 1, contig =>'Gap'),
   103228563 => (chromosome => 1, contig =>'NT_028050.13'),
   103278563 => (chromosome => 1, contig =>'Gap'),
   108252779 => (chromosome => 1, contig =>'NT_029860.11'),
   108302779 => (chromosome => 1, contig =>'Gap'),
   115380796 => (chromosome => 1, contig =>'NT_019273.16'),
   115430796 => (chromosome => 1, contig =>'Gap'),
   120043537 => (chromosome => 1, contig =>'NT_004754.15'),
   140333537 => (chromosome => 1, contig =>'Gap'),
   140529125 => (chromosome => 1, contig =>'NT_077387.2'),
   140579125 => (chromosome => 1, contig =>'Gap'),
   140744983 => (chromosome => 1, contig =>'NT_022052.2'),
   140794983 => (chromosome => 1, contig =>'Gap'),
   140974431 => (chromosome => 1, contig =>'NT_077988.2'),
   141024431 => (chromosome => 1, contig =>'Gap'),
   141135329 => (chromosome => 1, contig =>'NT_022071.12'),
   141185329 => (chromosome => 1, contig =>'Gap'),
   141387038 => (chromosome => 1, contig =>'NT_077930.1'),
   141537038 => (chromosome => 1, contig =>'Gap'),
   141939137 => (chromosome => 1, contig =>'NT_077389.2'),
   141989137 => (chromosome => 1, contig =>'Gap'),
   142115614 => (chromosome => 1, contig =>'NT_077931.2'),
   142165614 => (chromosome => 1, contig =>'Gap'),
   142292877 => (chromosome => 1, contig =>'NT_077932.2'),
   142342877 => (chromosome => 1, contig =>'Gap'),
   142513546 => (chromosome => 1, contig =>'NT_077933.1'),
   142563546 => (chromosome => 1, contig =>'Gap'),
   143562310 => (chromosome => 1, contig =>'NT_004434.16'),
   143612310 => (chromosome => 1, contig =>'Gap'),
   143893842 => (chromosome => 1, contig =>'NT_034398.4'),
   143943842 => (chromosome => 1, contig =>'Gap'),
   144932957 => (chromosome => 1, contig =>'NT_034400.2'),
   145382957 => (chromosome => 1, contig =>'Gap'),
   145723885 => (chromosome => 1, contig =>'NT_077936.2'),
   145873885 => (chromosome => 1, contig =>'Gap'),
   146046674 => (chromosome => 1, contig =>'NT_079483.1'),
   146096674 => (chromosome => 1, contig =>'Gap'),
   146316987 => (chromosome => 1, contig =>'NT_034401.5'),
   146366987 => (chromosome => 1, contig =>'Gap'),
   146676227 => (chromosome => 1, contig =>'NT_034403.3'),
   146726227 => (chromosome => 1, contig =>'Gap'),
   150716960 => (chromosome => 1, contig =>'NT_032962.5'),
   150766960 => (chromosome => 1, contig =>'Gap'),
   158631905 => (chromosome => 1, contig =>'NT_079484.1'),
   158681905 => (chromosome => 1, contig =>'Gap'),
   168140884 => (chromosome => 1, contig =>'NT_004668.16'),
   168190884 => (chromosome => 1, contig =>'Gap'),
   185883273 => (chromosome => 1, contig =>'NT_004487.16'),
   185933273 => (chromosome => 1, contig =>'Gap'),
   200700752 => (chromosome => 1, contig =>'NT_004671.15'),
   200750752 => (chromosome => 1, contig =>'Gap'),
   203100676 => (chromosome => 1, contig =>'NT_034410.5'),
   203550676 => (chromosome => 1, contig =>'Gap'),
   203570592 => (chromosome => 1, contig =>'NT_079485.1'),
   203620592 => (chromosome => 1, contig =>'Gap'),
   220275984 => (chromosome => 1, contig =>'NT_021877.16'),
   220325984 => (chromosome => 1, contig =>'Gap'),
   220748437 => (chromosome => 1, contig =>'NT_077939.1'),
   220798437 => (chromosome => 1, contig =>'Gap'),
   227054016 => (chromosome => 1, contig =>'NT_004559.11'),
   227104016 => (chromosome => 1, contig =>'Gap'),
   229358920 => (chromosome => 1, contig =>'NT_021973.16'),
   229408920 => (chromosome => 1, contig =>'Gap'),
   232233360 => (chromosome => 1, contig =>'NT_004433.16'),
   232283360 => (chromosome => 1, contig =>'Gap'),
   244737553 => (chromosome => 1, contig =>'NT_004836.15'),
   244742553 => (chromosome => 1, contig =>'Gap'),
   244752602 => (chromosome => 1, contig =>'NT_077941.1'),
   244757602 => (chromosome => 1, contig =>'Gap'),
   245572688 => (chromosome => 1, contig =>'NT_031730.8'),
   245622688 => (chromosome => 1, contig =>'Gap'),
   245826842 => (chromosome => 1, contig =>'NT_077390.2'),
   245876842 => (chromosome => 1, contig =>'Gap'),
   246047941 => (chromosome => 1, contig =>'NT_032968.6'),
247265993 => (chromosome => 2, contig =>'NT_022327.13'),
247266993 => (chromosome => 2, contig =>'Gap'),
247575678 => (chromosome => 2, contig =>'NT_033000.6'),
247675678 => (chromosome => 2, contig =>'Gap'),
249091763 => (chromosome => 2, contig =>'NT_022221.10'),
249191763 => (chromosome => 2, contig =>'Gap'),
250617892 => (chromosome => 2, contig =>'NT_022139.12'),
250717892 => (chromosome => 2, contig =>'Gap'),
251185545 => (chromosome => 2, contig =>'NT_022270.12'),
251235545 => (chromosome => 2, contig =>'Gap'),
262315376 => (chromosome => 2, contig =>'NT_005334.14'),
262390376 => (chromosome => 2, contig =>'Gap'),
267181543 => (chromosome => 2, contig =>'NT_015926.13'),
267206543 => (chromosome => 2, contig =>'Gap'),
335580521 => (chromosome => 2, contig =>'NT_022184.13'),
335730521 => (chromosome => 2, contig =>'Gap'),
336127800 => (chromosome => 2, contig =>'NT_032994.5'),
337127800 => (chromosome => 2, contig =>'Gap'),
337858868 => (chromosome => 2, contig =>'NT_034508.2'),
340858868 => (chromosome => 2, contig =>'Gap'),
343453317 => (chromosome => 2, contig =>'NT_026970.9'),
343603317 => (chromosome => 2, contig =>'Gap'),
355773213 => (chromosome => 2, contig =>'NT_022171.13'),
355915213 => (chromosome => 2, contig =>'Gap'),
356085715 => (chromosome => 2, contig =>'NT_079502.1'),
356086715 => (chromosome => 2, contig =>'Gap'),
356775592 => (chromosome => 2, contig =>'NT_034485.4'),
356925592 => (chromosome => 2, contig =>'Gap'),
357285344 => (chromosome => 2, contig =>'NT_077407.2'),
357435344 => (chromosome => 2, contig =>'Gap'),
373064259 => (chromosome => 2, contig =>'NT_022135.13'),
373079759 => (chromosome => 2, contig =>'Gap'),
377499701 => (chromosome => 2, contig =>'NT_005079.12'),
377649701 => (chromosome => 2, contig =>'Gap'),
395941068 => (chromosome => 2, contig =>'NT_005058.14'),
396041068 => (chromosome => 2, contig =>'Gap'),
480254221 => (chromosome => 2, contig =>'NT_005403.14'),
480404221 => (chromosome => 2, contig =>'Gap'),
486090923 => (chromosome => 2, contig =>'NT_005120.14'),
486091923 => (chromosome => 2, contig =>'Gap'),
487044077 => (chromosome => 2, contig =>'NT_022173.11'),
487194077 => (chromosome => 2, contig =>'Gap'),
489156899 => (chromosome => 2, contig =>'NT_005416.11'),
489267899 => (chromosome => 2, contig =>'Gap'),
489463899 => (chromosome => 2, contig =>'NT_037540.2'),
489498899 => (chromosome => 3, contig =>'Gap'),
555430112 => (chromosome => 3, contig =>'NT_022517.16'),
555690112 => (chromosome => 3, contig =>'Gap'),
579889654 => (chromosome => 3, contig =>'NT_022459.13'),
584289654 => (chromosome => 3, contig =>'Gap'),
684819915 => (chromosome => 3, contig =>'NT_005612.14'),
684839915 => (chromosome => 3, contig =>'Gap'),
686070686 => (chromosome => 3, contig =>'NT_005535.15'),
686170686 => (chromosome => 3, contig =>'Gap'),
688752949 => (chromosome => 3, contig =>'NT_029928.11'),
690123617 => (chromosome => 3, contig =>'Gap'),
691531001 => (chromosome => 4, contig =>'NT_037622.3'),
691582001 => (chromosome => 4, contig =>'Gap'),
692618452 => (chromosome => 4, contig =>'NT_037623.4'),
692768452 => (chromosome => 4, contig =>'Gap'),
693950714 => (chromosome => 4, contig =>'NT_006081.16'),
694100714 => (chromosome => 4, contig =>'Gap'),
698052744 => (chromosome => 4, contig =>'NT_006051.16'),
698202744 => (chromosome => 4, contig =>'Gap'),
699049142 => (chromosome => 4, contig =>'NT_006307.15'),
699199142 => (chromosome => 4, contig =>'Gap'),
721686568 => (chromosome => 4, contig =>'NT_006316.15'),
721836568 => (chromosome => 4, contig =>'Gap'),
722813154 => (chromosome => 4, contig =>'NT_022794.9'),
722872154 => (chromosome => 4, contig =>'Gap'),
730317193 => (chromosome => 4, contig =>'NT_016297.15'),
730337193 => (chromosome => 4, contig =>'Gap'),
739378100 => (chromosome => 4, contig =>'NT_006238.10'),
739528100 => (chromosome => 4, contig =>'Gap'),
739699276 => (chromosome => 4, contig =>'NT_037645.2'),
742699276 => (chromosome => 4, contig =>'Gap'),
749773728 => (chromosome => 4, contig =>'NT_022853.14'),
749923728 => (chromosome => 4, contig =>'Gap'),
759630014 => (chromosome => 4, contig =>'NT_022778.14'),
759780014 => (chromosome => 4, contig =>'Gap'),
761907858 => (chromosome => 4, contig =>'NT_077444.2'),
762082858 => (chromosome => 4, contig =>'Gap'),
766012307 => (chromosome => 4, contig =>'NT_006216.14'),
766087307 => (chromosome => 4, contig =>'Gap'),
829003188 => (chromosome => 4, contig =>'NT_016354.16'),
829153188 => (chromosome => 4, contig =>'Gap'),
858257986 => (chromosome => 4, contig =>'NT_016606.16'),
858407986 => (chromosome => 4, contig =>'Gap'),
881845576 => (chromosome => 4, contig =>'NT_022792.16'),
881915576 => (chromosome => 5, contig =>'Gap'),
899428971 => (chromosome => 5, contig =>'NT_023089.13'),
899438971 => (chromosome => 5, contig =>'Gap'),
928296718 => (chromosome => 5, contig =>'NT_006576.14'),
931296718 => (chromosome => 5, contig =>'Gap'),
950691591 => (chromosome => 5, contig =>'NT_006431.13'),
950696591 => (chromosome => 5, contig =>'Gap'),
951580958 => (chromosome => 5, contig =>'NT_078018.1'),
951680958 => (chromosome => 5, contig =>'Gap'),
951901629 => (chromosome => 5, contig =>'NT_034819.3'),
952001629 => (chromosome => 5, contig =>'Gap'),
952437517 => (chromosome => 5, contig =>'NT_078019.1'),
952537517 => (chromosome => 5, contig =>'Gap'),
973565777 => (chromosome => 5, contig =>'NT_006713.13'),
973605777 => (chromosome => 5, contig =>'Gap'),
979483779 => (chromosome => 5, contig =>'NT_023148.12'),
979506779 => (chromosome => 5, contig =>'Gap'),
1020706150 => (chromosome => 5, contig =>'NT_034772.5'),
1020711150 => (chromosome => 5, contig =>'Gap'),
1037012813 => (chromosome => 5, contig =>'NT_029289.10'),
1037016913 => (chromosome => 5, contig =>'Gap'),
1058858971 => (chromosome => 5, contig =>'NT_023133.11'),
1058863971 => (chromosome => 5, contig =>'Gap'),
1062860498 => (chromosome => 5, contig =>'NT_077451.3'),
1062865498 => (chromosome => 6, contig =>'Gap'),
1072060226 => (chromosome => 6, contig =>'NT_034880.3'),
1072110226 => (chromosome => 6, contig =>'Gap'),
1120994993 => (chromosome => 6, contig =>'NT_007592.13'),
1121044993 => (chromosome => 6, contig =>'Gap'),
1121687500 => (chromosome => 6, contig =>'NT_033172.4'),
1124737500 => (chromosome => 6, contig =>'Gap'),
1124985923 => (chromosome => 6, contig =>'NT_033948.3'),
1125035923 => (chromosome => 6, contig =>'Gap'),
1158536639 => (chromosome => 6, contig =>'NT_007299.12'),
1158736639 => (chromosome => 6, contig =>'Gap'),
1220432445 => (chromosome => 6, contig =>'NT_025741.13'),
1220482445 => (chromosome => 6, contig =>'Gap'),
1230615721 => (chromosome => 6, contig =>'NT_007422.12'),
1230665721 => (chromosome => 6, contig =>'Gap'),
1232896979 => (chromosome => 6, contig =>'NT_007302.12'),
1233046979 => (chromosome => 6, contig =>'Gap'),
1233772074 => (chromosome => 6, contig =>'NT_007583.11'),
1233806074 => (chromosome => 7, contig =>'Gap'),
1234070738 => (chromosome => 7, contig =>'NT_029998.6'),
1234220738 => (chromosome => 7, contig =>'Gap'),
1281714278 => (chromosome => 7, contig =>'NT_007819.14'),
1281754278 => (chromosome => 7, contig =>'Gap'),
1283884454 => (chromosome => 7, contig =>'NT_030008.6'),
1283924454 => (chromosome => 7, contig =>'Gap'),
1290501747 => (chromosome => 7, contig =>'NT_033968.5'),
1290551747 => (chromosome => 7, contig =>'Gap'),
1291604602 => (chromosome => 7, contig =>'NT_023629.12'),
1294604602 => (chromosome => 7, contig =>'Gap'),
1294860784 => (chromosome => 7, contig =>'NT_023603.5'),
1294910784 => (chromosome => 7, contig =>'Gap'),
1295100921 => (chromosome => 7, contig =>'NT_077528.1'),
1295150921 => (chromosome => 7, contig =>'Gap'),
1307899887 => (chromosome => 7, contig =>'NT_007758.10'),
1308149887 => (chromosome => 7, contig =>'Gap'),
1372562799 => (chromosome => 7, contig =>'NT_007933.13'),
1372587799 => (chromosome => 7, contig =>'Gap'),
1387434448 => (chromosome => 7, contig =>'NT_007914.13'),
1387534448 => (chromosome => 7, contig =>'Gap'),
1388270780 => (chromosome => 7, contig =>'NT_034885.3'),
1388350780 => (chromosome => 7, contig =>'Gap'),
1392317592 => (chromosome => 7, contig =>'NT_007741.12'),
1399779651 => (chromosome => 8, contig =>'NT_023736.16'),
1399879651 => (chromosome => 8, contig =>'Gap'),
1404416944 => (chromosome => 8, contig =>'NT_077531.3'),
1404516944 => (chromosome => 8, contig =>'Gap'),
1413947817 => (chromosome => 8, contig =>'NT_030737.8'),
1413965217 => (chromosome => 8, contig =>'Gap'),
1421988386 => (chromosome => 8, contig =>'NT_023666.16'),
1422054486 => (chromosome => 8, contig =>'Gap'),
1430172695 => (chromosome => 8, contig =>'NT_007995.13'),
1430272695 => (chromosome => 8, contig =>'Gap'),
1436173855 => (chromosome => 8, contig =>'NT_008251.14'),
1439173855 => (chromosome => 8, contig =>'Gap'),
1440465004 => (chromosome => 8, contig =>'NT_023678.15'),
1440525004 => (chromosome => 8, contig =>'Gap'),
1478274240 => (chromosome => 8, contig =>'NT_008183.17'),
1478398340 => (chromosome => 8, contig =>'Gap'),
1478968702 => (chromosome => 8, contig =>'NT_078037.2'),
1479056002 => (chromosome => 8, contig =>'Gap'),
1527745378 => (chromosome => 8, contig =>'NT_008046.14'),
1527763578 => (chromosome => 8, contig =>'Gap'),
1535911131 => (chromosome => 8, contig =>'NT_028251.11'),
1536091831 => (chromosome => 8, contig =>'Gap'),
1536389885 => (chromosome => 8, contig =>'NT_008127.15'),
1536489885 => (chromosome => 8, contig =>'Gap'),
1537747881 => (chromosome => 8, contig =>'NT_023684.16'),
1537754981 => (chromosome => 8, contig =>'Gap'),
1538626411 => (chromosome => 8, contig =>'NT_037704.4'),
1578062137 => (chromosome => 9, contig =>'NT_008413.16'),
1578112137 => (chromosome => 9, contig =>'Gap'),
1578258280 => (chromosome => 9, contig =>'NT_078040.1'),
1578308280 => (chromosome => 9, contig =>'Gap'),
1578617010 => (chromosome => 9, contig =>'NT_078041.1'),
1578667010 => (chromosome => 9, contig =>'Gap'),
1578742056 => (chromosome => 9, contig =>'NT_078042.2'),
1578792056 => (chromosome => 9, contig =>'Gap'),
1578966899 => (chromosome => 9, contig =>'NT_079528.1'),
1579016899 => (chromosome => 9, contig =>'Gap'),
1579526470 => (chromosome => 9, contig =>'NT_078043.2'),
1579576470 => (chromosome => 9, contig =>'Gap'),
1579641608 => (chromosome => 9, contig =>'NT_078044.1'),
1579691608 => (chromosome => 9, contig =>'Gap'),
1579986252 => (chromosome => 9, contig =>'NT_078045.1'),
1580036252 => (chromosome => 9, contig =>'Gap'),
1580239143 => (chromosome => 9, contig =>'NT_079529.1'),
1580289143 => (chromosome => 9, contig =>'Gap'),
1580334967 => (chromosome => 9, contig =>'NT_078047.2'),
1580384967 => (chromosome => 9, contig =>'Gap'),
1580647758 => (chromosome => 9, contig =>'NT_078048.2'),
1580697758 => (chromosome => 9, contig =>'Gap'),
1580707340 => (chromosome => 9, contig =>'NT_078049.1'),
1580757340 => (chromosome => 9, contig =>'Gap'),
1580938987 => (chromosome => 9, contig =>'NT_078077.2'),
1580988987 => (chromosome => 9, contig =>'Gap'),
1581191068 => (chromosome => 9, contig =>'NT_078051.2'),
1581241068 => (chromosome => 9, contig =>'Gap'),
1581329894 => (chromosome => 9, contig =>'NT_079530.1'),
1581379894 => (chromosome => 9, contig =>'Gap'),
1581510018 => (chromosome => 9, contig =>'NT_078052.2'),
1581560018 => (chromosome => 9, contig =>'Gap'),
1581702823 => (chromosome => 9, contig =>'NT_079531.1'),
1581752823 => (chromosome => 9, contig =>'Gap'),
1582353148 => (chromosome => 9, contig =>'NT_078053.2'),
1582403148 => (chromosome => 9, contig =>'Gap'),
1582663206 => (chromosome => 9, contig =>'NT_078055.2'),
1582668206 => (chromosome => 9, contig =>'Gap'),
1582832632 => (chromosome => 9, contig =>'NT_078057.1'),
1582882632 => (chromosome => 9, contig =>'Gap'),
1582969772 => (chromosome => 9, contig =>'NT_079532.1'),
1601169772 => (chromosome => 9, contig =>'Gap'),
1601329311 => (chromosome => 9, contig =>'NT_078058.1'),
1601379311 => (chromosome => 9, contig =>'Gap'),
1601585440 => (chromosome => 9, contig =>'NT_078059.2'),
1601635440 => (chromosome => 9, contig =>'Gap'),
1601808540 => (chromosome => 9, contig =>'NT_078061.1'),
1601858540 => (chromosome => 9, contig =>'Gap'),
1601876173 => (chromosome => 9, contig =>'NT_078062.1'),
1601926173 => (chromosome => 9, contig =>'Gap'),
1602347829 => (chromosome => 9, contig =>'NT_078063.2'),
1602497829 => (chromosome => 9, contig =>'Gap'),
1602658559 => (chromosome => 9, contig =>'NT_078064.1'),
1602708559 => (chromosome => 9, contig =>'Gap'),
1602903050 => (chromosome => 9, contig =>'NT_078065.2'),
1602953050 => (chromosome => 9, contig =>'Gap'),
1603111512 => (chromosome => 9, contig =>'NT_079533.1'),
1603161512 => (chromosome => 9, contig =>'Gap'),
1603382139 => (chromosome => 9, contig =>'NT_078066.2'),
1603432139 => (chromosome => 9, contig =>'Gap'),
1603666676 => (chromosome => 9, contig =>'NT_078067.2'),
1603716676 => (chromosome => 9, contig =>'Gap'),
1603891441 => (chromosome => 9, contig =>'NT_078068.1'),
1603941441 => (chromosome => 9, contig =>'Gap'),
1604150045 => (chromosome => 9, contig =>'NT_078069.1'),
1604200045 => (chromosome => 9, contig =>'Gap'),
1604623746 => (chromosome => 9, contig =>'NT_078070.1'),
1604673746 => (chromosome => 9, contig =>'Gap'),
1604868998 => (chromosome => 9, contig =>'NT_078071.2'),
1604918998 => (chromosome => 9, contig =>'Gap'),
1625357836 => (chromosome => 9, contig =>'NT_023935.16'),
1625407836 => (chromosome => 9, contig =>'Gap'),
1626076124 => (chromosome => 9, contig =>'NT_023932.16'),
1626126124 => (chromosome => 9, contig =>'Gap'),
1626461235 => (chromosome => 9, contig =>'NT_079534.1'),
1626511235 => (chromosome => 9, contig =>'Gap'),
1626596615 => (chromosome => 9, contig =>'NT_079535.1'),
1626646615 => (chromosome => 9, contig =>'Gap'),
1632294721 => (chromosome => 9, contig =>'NT_008476.14'),
1632344721 => (chromosome => 9, contig =>'Gap'),
1667075516 => (chromosome => 9, contig =>'NT_008470.16'),
1667125516 => (chromosome => 9, contig =>'Gap'),
1670271648 => (chromosome => 9, contig =>'NT_035014.3'),
1670421648 => (chromosome => 9, contig =>'Gap'),
1670960538 => (chromosome => 9, contig =>'NT_008554.15'),
1671160538 => (chromosome => 9, contig =>'Gap'),
1671337271 => (chromosome => 9, contig =>'NT_030058.3'),
1671350271 => (chromosome => 9, contig =>'Gap'),
1673202625 => (chromosome => 9, contig =>'NT_019501.12'),
1673232625 => (chromosome => 9, contig =>'Gap'),
1674084776 => (chromosome => 9, contig =>'NT_024000.15'),
1674184776 => (chromosome => 9, contig =>'Gap'),
1674998456 => (chromosome => 9, contig =>'NT_023929.16'),
1675012456 => (chromosome => 10, contig =>'Gap'),
1680589566 => (chromosome => 10, contig =>'NT_077567.3'),
1680639566 => (chromosome => 10, contig =>'Gap'),
1692977137 => (chromosome => 10, contig =>'NT_077569.2'),
1693027137 => (chromosome => 10, contig =>'Gap'),
1713821297 => (chromosome => 10, contig =>'NT_008705.15'),
1713871297 => (chromosome => 10, contig =>'Gap'),
1714157397 => (chromosome => 10, contig =>'NT_024133.4'),
1716637397 => (chromosome => 10, contig =>'Gap'),
1716829149 => (chromosome => 10, contig =>'NT_079540.1'),
1716879149 => (chromosome => 10, contig =>'Gap'),
1720709426 => (chromosome => 10, contig =>'NT_033985.6'),
1720859426 => (chromosome => 10, contig =>'Gap'),
1721391415 => (chromosome => 10, contig =>'NT_031847.7'),
1721441415 => (chromosome => 10, contig =>'Gap'),
1721692615 => (chromosome => 10, contig =>'NT_037750.1'),
1721842615 => (chromosome => 10, contig =>'Gap'),
1722105922 => (chromosome => 10, contig =>'NT_077570.1'),
1722255922 => (chromosome => 10, contig =>'Gap'),
1722419153 => (chromosome => 10, contig =>'NT_077571.1'),
1722569153 => (chromosome => 10, contig =>'Gap'),
1723488595 => (chromosome => 10, contig =>'NT_030772.9'),
1723538595 => (chromosome => 10, contig =>'Gap'),
1725480469 => (chromosome => 10, contig =>'NT_017696.14'),
1725530469 => (chromosome => 10, contig =>'Gap'),
1725741904 => (chromosome => 10, contig =>'NT_035036.2'),
1725791904 => (chromosome => 10, contig =>'Gap'),
1755904517 => (chromosome => 10, contig =>'NT_008583.16'),
1755914517 => (chromosome => 10, contig =>'Gap'),
1798941603 => (chromosome => 10, contig =>'NT_030059.11'),
1798991603 => (chromosome => 10, contig =>'Gap'),
1800223586 => (chromosome => 10, contig =>'NT_037753.4'),
1800273586 => (chromosome => 10, contig =>'Gap'),
1800442328 => (chromosome => 10, contig =>'NT_033224.4'),
1800492328 => (chromosome => 10, contig =>'Gap'),
1803188925 => (chromosome => 10, contig =>'NT_035040.4'),
1803238925 => (chromosome => 10, contig =>'Gap'),
1807854260 => (chromosome => 10, contig =>'NT_008818.15'),
1807864260 => (chromosome => 10, contig =>'Gap'),
1808110383 => (chromosome => 10, contig =>'NT_025835.11'),
1808160383 => (chromosome => 10, contig =>'Gap'),
1809266168 => (chromosome => 10, contig =>'NT_024040.14'),
1809316168 => (chromosome => 10, contig =>'Gap'),
1809938715 => (chromosome => 10, contig =>'NT_017795.16'),
1809988715 => (chromosome => 10, contig =>'Gap'),
1810035671 => (chromosome => 10, contig =>'NT_079541.1'),
1810085671 => (chromosome => 11, contig =>'Gap'),
1811176040 => (chromosome => 11, contig =>'NT_035113.5'),
1811236040 => (chromosome => 11, contig =>'Gap'),
1860090541 => (chromosome => 11, contig =>'NT_009237.16'),
1860130541 => (chromosome => 11, contig =>'Gap'),
1860854637 => (chromosome => 11, contig =>'NT_035086.3'),
1861134637 => (chromosome => 11, contig =>'Gap'),
1861637989 => (chromosome => 11, contig =>'NT_035158.2'),
1864637989 => (chromosome => 11, contig =>'Gap'),
1878899478 => (chromosome => 11, contig =>'NT_033903.6'),
1878949478 => (chromosome => 11, contig =>'Gap'),
1879512950 => (chromosome => 11, contig =>'NT_078088.2'),
1879562950 => (chromosome => 11, contig =>'Gap'),
1897448202 => (chromosome => 11, contig =>'NT_033927.6'),
1897462202 => (chromosome => 11, contig =>'Gap'),
1905999536 => (chromosome => 11, contig =>'NT_008984.16'),
1906029536 => (chromosome => 11, contig =>'Gap'),
1944518625 => (chromosome => 11, contig =>'NT_033899.6'),
1944534625 => (chromosome => 12, contig =>'Gap'),
1951577918 => (chromosome => 12, contig =>'NT_009759.15'),
1951650918 => (chromosome => 12, contig =>'Gap'),
1979266586 => (chromosome => 12, contig =>'NT_009714.16'),
1980661586 => (chromosome => 12, contig =>'Gap'),
2019288902 => (chromosome => 12, contig =>'NT_029419.10'),
2019538902 => (chromosome => 12, contig =>'Gap'),
2052354836 => (chromosome => 12, contig =>'NT_019546.15'),
2052411836 => (chromosome => 12, contig =>'Gap'),
2064887060 => (chromosome => 12, contig =>'NT_009775.14'),
2064949060 => (chromosome => 12, contig =>'Gap'),
2065412571 => (chromosome => 12, contig =>'NT_009487.15'),
2065562571 => (chromosome => 12, contig =>'Gap'),
2074899288 => (chromosome => 12, contig =>'NT_009755.16'),
2075043288 => (chromosome => 12, contig =>'Gap'),
2075718070 => (chromosome => 12, contig =>'NT_035243.4'),
2075763070 => (chromosome => 12, contig =>'Gap'),
2076537004 => (chromosome => 12, contig =>'NT_024477.12'),
2076537016 => (chromosome => 12, contig =>'Gap'),
2093355016 => (chromosome => 13, contig =>'Gap'),
2161095341 => (chromosome => 13, contig =>'NT_024524.13'),
2161145341 => (chromosome => 13, contig =>'Gap'),
2186589011 => (chromosome => 13, contig =>'NT_009952.14'),
2186989011 => (chromosome => 13, contig =>'Gap'),
2188811010 => (chromosome => 13, contig =>'NT_027140.6'),
2188911010 => (chromosome => 13, contig =>'Gap'),
2189095066 => (chromosome => 13, contig =>'NT_077627.2'),
2189195066 => (chromosome => 13, contig =>'Gap'),
2189564996 => (chromosome => 13, contig =>'NT_024498.12'),
2207634996 => (chromosome => 14, contig =>'Gap'),
2294826212 => (chromosome => 14, contig =>'NT_026437.10'),
2313086212 => (chromosome => 15, contig =>'Gap'),
2314485958 => (chromosome => 15, contig =>'NT_037852.4'),
2314585958 => (chromosome => 15, contig =>'Gap'),
2314920037 => (chromosome => 15, contig =>'NT_077631.1'),
2315020037 => (chromosome => 15, contig =>'Gap'),
2315888774 => (chromosome => 15, contig =>'NT_078094.1'),
2315938774 => (chromosome => 15, contig =>'Gap'),
2319493824 => (chromosome => 15, contig =>'NT_026446.12'),
2319537824 => (chromosome => 15, contig =>'Gap'),
2319962080 => (chromosome => 15, contig =>'NT_078095.1'),
2320063080 => (chromosome => 15, contig =>'Gap'),
2321133722 => (chromosome => 15, contig =>'NT_010280.16'),
2321233722 => (chromosome => 15, contig =>'Gap'),
2321651711 => (chromosome => 15, contig =>'NT_078096.2'),
2321751711 => (chromosome => 15, contig =>'Gap'),
2375371676 => (chromosome => 15, contig =>'NT_010194.16'),
2375431676 => (chromosome => 15, contig =>'Gap'),
2377530453 => (chromosome => 15, contig =>'NT_077661.2'),
2377590453 => (chromosome => 15, contig =>'Gap'),
2391097739 => (chromosome => 15, contig =>'NT_010274.15'),
2391119739 => (chromosome => 15, contig =>'Gap'),
2395082868 => (chromosome => 15, contig =>'NT_035325.5'),
2397726727 => (chromosome => 16, contig =>'NT_037887.3'),
2397741727 => (chromosome => 16, contig =>'Gap'),
2403719588 => (chromosome => 16, contig =>'NT_010552.13'),
2403737088 => (chromosome => 16, contig =>'Gap'),
2423714261 => (chromosome => 16, contig =>'NT_010393.14'),
2423719261 => (chromosome => 16, contig =>'Gap'),
2429568676 => (chromosome => 16, contig =>'NT_024812.10'),
2429668676 => (chromosome => 16, contig =>'Gap'),
2430237106 => (chromosome => 16, contig =>'NT_078099.2'),
2430337106 => (chromosome => 16, contig =>'Gap'),
2431449757 => (chromosome => 16, contig =>'NT_024773.11'),
2441249757 => (chromosome => 16, contig =>'Gap'),
2442736327 => (chromosome => 16, contig =>'NT_035363.3'),
2442752327 => (chromosome => 16, contig =>'Gap'),
2446132552 => (chromosome => 16, contig =>'NT_010505.14'),
2446137552 => (chromosome => 16, contig =>'Gap'),
2468140708 => (chromosome => 16, contig =>'NT_010498.14'),
2468150708 => (chromosome => 16, contig =>'Gap'),
2480413029 => (chromosome => 16, contig =>'NT_024797.14'),
2480419029 => (chromosome => 16, contig =>'Gap'),
2483186701 => (chromosome => 16, contig =>'NT_019609.11'),
2483196701 => (chromosome => 16, contig =>'Gap'),
2483249193 => (chromosome => 16, contig =>'NT_077677.2'),
2483269193 => (chromosome => 16, contig =>'Gap'),
2485119800 => (chromosome => 16, contig =>'NT_010542.14'),
2485157800 => (chromosome => 17, contig =>'Gap'),
2485454654 => (chromosome => 17, contig =>'NT_024972.7'),
2485501176 => (chromosome => 17, contig =>'Gap'),
2486229360 => (chromosome => 17, contig =>'NT_035414.4'),
2486479360 => (chromosome => 17, contig =>'Gap'),
2504401543 => (chromosome => 17, contig =>'NT_010718.14'),
2504421543 => (chromosome => 17, contig =>'Gap'),
2506848446 => (chromosome => 17, contig =>'NT_030843.7'),
2506948446 => (chromosome => 17, contig =>'Gap'),
2507528370 => (chromosome => 17, contig =>'NT_024862.13'),
2510528370 => (chromosome => 17, contig =>'Gap'),
2519941198 => (chromosome => 17, contig =>'NT_010799.14'),
2520041198 => (chromosome => 17, contig =>'Gap'),
2521670467 => (chromosome => 17, contig =>'NT_078100.1'),
2521770467 => (chromosome => 17, contig =>'Gap'),
2526841160 => (chromosome => 17, contig =>'NT_010755.14'),
2526941160 => (chromosome => 17, contig =>'Gap'),
2551734762 => (chromosome => 17, contig =>'NT_010783.14'),
2551824762 => (chromosome => 17, contig =>'Gap'),
2563263380 => (chromosome => 17, contig =>'NT_010641.14'),
2563416380 => (chromosome => 17, contig =>'Gap'),
2565519506 => (chromosome => 17, contig =>'NT_024871.11'),
2565584506 => (chromosome => 17, contig =>'Gap'),
2566860066 => (chromosome => 17, contig =>'NT_010663.14'),
2582258953 => (chromosome => 18, contig =>'NT_010859.13'),
2583622951 => (chromosome => 18, contig =>'Gap'),
2617171189 => (chromosome => 18, contig =>'NT_010966.13'),
2617218189 => (chromosome => 18, contig =>'Gap'),
2637292388 => (chromosome => 18, contig =>'NT_025028.13'),
2637320388 => (chromosome => 18, contig =>'Gap'),
2640708863 => (chromosome => 18, contig =>'NT_025004.13'),
2640730863 => (chromosome => 18, contig =>'Gap'),
2642975205 => (chromosome => 18, contig =>'NT_010879.14'),
2642986205 => (chromosome => 19, contig =>'Gap'),
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2650277209 => (chromosome => 19, contig =>'Gap'),
2651568403 => (chromosome => 19, contig =>'NT_077812.2'),
2651573403 => (chromosome => 19, contig =>'Gap'),
2667398827 => (chromosome => 19, contig =>'NT_011295.10'),
2675398827 => (chromosome => 19, contig =>'Gap'),
2706781856 => (chromosome => 19, contig =>'NT_011109.15'),
2706836856 => (chromosome => 20, contig =>'Gap'),
2733096425 => (chromosome => 20, contig =>'NT_011387.8'),
2736096425 => (chromosome => 20, contig =>'Gap'),
2736330764 => (chromosome => 20, contig =>'NT_025215.4'),
2737330764 => (chromosome => 20, contig =>'Gap'),
2742394370 => (chromosome => 20, contig =>'NT_028392.4'),
2742414370 => (chromosome => 20, contig =>'Gap'),
2767396660 => (chromosome => 20, contig =>'NT_011362.8'),
2767411488 => (chromosome => 20, contig =>'Gap'),
2768558698 => (chromosome => 20, contig =>'NT_030871.1'),
2768585748 => (chromosome => 20, contig =>'Gap'),
2768621574 => (chromosome => 20, contig =>'NT_035608.1'),
2768771574 => (chromosome => 20, contig =>'Gap'),
2770473724 => (chromosome => 20, contig =>'NT_011333.5'),
2780402346 => (chromosome => 21, contig =>'Gap'),
2780683724 => (chromosome => 21, contig =>'NT_029490.3'),
2783733724 => (chromosome => 21, contig =>'Gap'),
2812335840 => (chromosome => 21, contig =>'NT_011512.9'),
2812365840 => (chromosome => 21, contig =>'Gap'),
2812595426 => (chromosome => 21, contig =>'NT_030187.1'),
2812618534 => (chromosome => 21, contig =>'Gap'),
2813997188 => (chromosome => 21, contig =>'NT_030188.3'),
2814017188 => (chromosome => 21, contig =>'Gap'),
2817449821 => (chromosome => 21, contig =>'NT_011515.10'),
2817449928 => (chromosome => 21, contig =>'Gap'),
2831879928 => (chromosome => 22, contig =>'Gap'),
2832114154 => (chromosome => 22, contig =>'NT_011516.5'),
2832116054 => (chromosome => 22, contig =>'Gap'),
2832522332 => (chromosome => 22, contig =>'NT_028395.2'),
2832672332 => (chromosome => 22, contig =>'Gap'),
2836333913 => (chromosome => 22, contig =>'NT_011519.10'),
2836383913 => (chromosome => 22, contig =>'Gap'),
2859562126 => (chromosome => 22, contig =>'NT_011520.9'),
2859612126 => (chromosome => 22, contig =>'Gap'),
2860417283 => (chromosome => 22, contig =>'NT_011521.2'),
2860460283 => (chromosome => 22, contig =>'Gap'),
2861995285 => (chromosome => 22, contig =>'NT_011522.4'),
2862082285 => (chromosome => 22, contig =>'Gap'),
2864639370 => (chromosome => 22, contig =>'NT_011523.9'),
2864689370 => (chromosome => 22, contig =>'Gap'),
2864903871 => (chromosome => 22, contig =>'NT_030872.2'),
2864962871 => (chromosome => 22, contig =>'Gap'),
2865992965 => (chromosome => 22, contig =>'NT_011525.5'),
2866056965 => (chromosome => 22, contig =>'Gap'),
2866347471 => (chromosome => 22, contig =>'NT_019197.3'),
2866387471 => (chromosome => 22, contig =>'Gap'),
2866826900 => (chromosome => 22, contig =>'NT_011526.5'),
2866863900 => (chromosome =>'X', contig =>'Gap'),
2866950463 => (chromosome =>'X', contig =>'NT_078115.2'),
2867050463 => (chromosome =>'X', contig =>'Gap'),
2867816636 => (chromosome =>'X', contig =>'NT_028413.7'),
2867916636 => (chromosome =>'X', contig =>'Gap'),
2868540343 => (chromosome =>'X', contig =>'NT_033330.6'),
2868740343 => (chromosome =>'X', contig =>'Gap'),
2870121761 => (chromosome =>'X', contig =>'NT_025302.12'),
2870221761 => (chromosome =>'X', contig =>'Gap'),
2902958029 => (chromosome =>'X', contig =>'NT_011757.13'),
2903008029 => (chromosome =>'X', contig =>'Gap'),
2909413492 => (chromosome =>'X', contig =>'NT_079573.1'),
2909463492 => (chromosome =>'X', contig =>'Gap'),
2915717879 => (chromosome =>'X', contig =>'NT_011568.13'),
2915767879 => (chromosome =>'X', contig =>'Gap'),
2918139605 => (chromosome =>'X', contig =>'NT_011638.12'),
2918239605 => (chromosome =>'X', contig =>'Gap'),
2924375703 => (chromosome =>'X', contig =>'NT_011630.14'),
2927375703 => (chromosome =>'X', contig =>'Gap'),
2942247181 => (chromosome =>'X', contig =>'NT_011669.14'),
2942297181 => (chromosome =>'X', contig =>'Gap'),
2947538635 => (chromosome =>'X', contig =>'NT_079574.1'),
2947588635 => (chromosome =>'X', contig =>'Gap'),
2973597811 => (chromosome =>'X', contig =>'NT_011651.14'),
2973647811 => (chromosome =>'X', contig =>'Gap'),
2979088821 => (chromosome =>'X', contig =>'NT_025319.14'),
2979158821 => (chromosome =>'X', contig =>'Gap'),
2980564422 => (chromosome =>'X', contig =>'NT_028405.9'),
2980614422 => (chromosome =>'X', contig =>'Gap'),
2981293292 => (chromosome =>'X', contig =>'NT_011565.6'),
2981313292 => (chromosome =>'X', contig =>'Gap'),
2989904419 => (chromosome =>'X', contig =>'NT_077819.3'),
2989954419 => (chromosome =>'X', contig =>'Gap'),
3009027846 => (chromosome =>'X', contig =>'NT_011786.14'),
3009107846 => (chromosome =>'X', contig =>'Gap'),
3012743675 => (chromosome =>'X', contig =>'NT_011681.13'),
3012793675 => (chromosome =>'X', contig =>'Gap'),
3014514811 => (chromosome =>'X', contig =>'NT_019686.8'),
3014584811 => (chromosome =>'X', contig =>'Gap'),
3017892829 => (chromosome =>'X', contig =>'NT_011726.11'),
3017942829 => (chromosome =>'X', contig =>'Gap'),
3019839999 => (chromosome =>'X', contig =>'NT_025965.12'),
3019939999 => (chromosome =>'X', contig =>'Gap'),
3020519291 => (chromosome =>'X', contig =>'NT_025307.14'),
3020556291 => (chromosome =>'Y', contig =>'Gap'),
3020642854 => (chromosome =>'Y', contig =>'NT_079581.1'),
3020742854 => (chromosome =>'Y', contig =>'Gap'),
3021509027 => (chromosome =>'Y', contig =>'NT_079582.1'),
3021609027 => (chromosome =>'Y', contig =>'Gap'),
3022232734 => (chromosome =>'Y', contig =>'NT_079583.1'),
3022432734 => (chromosome =>'Y', contig =>'Gap'),
3022813941 => (chromosome =>'Y', contig =>'NT_079584.1'),
   3029137202 => (chromosome =>'Y', contig =>'NT_011896.8'),
   3029187202 => (chromosome =>'Y', contig =>'Gap'),
   3030277140 => (chromosome =>'Y', contig =>'NT_011878.8'),
   3033327140 => (chromosome =>'Y', contig =>'Gap'),
   3043265903 => (chromosome =>'Y', contig =>'NT_011875.10'),
   3043315903 => (chromosome =>'Y', contig =>'Gap'),
   3048261650 => (chromosome =>'Y', contig =>'NT_011903.10'),
   3070261650 => (chromosome =>'Y', contig =>'Gap'),
   3070359945 => (chromosome =>'Y', contig =>'NT_025975.2'),
   3070409945 => (chromosome =>'Y', contig =>'Gap'),
   3070475575 => (chromosome =>'Y', contig =>'NT_025441.2'),
   3070805846 => (chromosome =>'Y', contig =>'NT_079585.1'),
);

NUMBER: foreach $number (@numbers) {
        foreach my $key (sort { $a <=> $b } keys %chr_cont_pos) {
                  if ($number < $key) {
                       $chromosome = $chr_cont_pos{$key}{chromosome};
                       $contig     = $chr_cont_pos{$key}{contig};
                     #do whatever processing here; I'll just print

                 print "chromosome = $chromosome, contig = $contig\n";
             next NUMBER;
              }
       }
}

[download]
Sameet

Replies are listed 'Best First'.
Re: Re: Re: Selecting a random number, and back calculating to chromosome and contig!
by biosysadmin (Deacon) on Apr 30, 2004 at 20:12 UTC
    It looks like you wrote your if/else statements by cutting and pasting each statement, and then modifying each individual statement. While this may feel like real work, it's really not an efficient use of your time. If you ever wanted to modify this program, it would be very difficult to do because of its length. Developing with repetitive code is also prone to typos and other sorts of little errors, as you can see by the conig/contig typos that are in your code. By using a better data structure like thor proposes, you can avoid making minute modifications to repetitive pieces of code (like your if/else statement) and concentrate more on developing your program.

    Another idea that you may look into as you learn more is by representing your data and operations on this data in the form of objects. For a reference, check out this short example on OO programming in Perl.

    As you develop your code more and more, you may want to begin abstracting your useful code into subroutines. Here's an example that relies on thor's hash-based data structure shown above: 

    sub print_contig_information {
 my $number = shift;
 foreach my $key (sort { $a <=> $b } keys %master) {
      if ($number < $key) {
         my $chromosome = $master{$key}{chromosome};
         my $contig     = $master{$key}{contig};
         #do whatever processing here; I'll just print

         print "chromosome = $chromosome, contig = $contig\n";
      }
   }
}

    [download]
    By modularizing your code every way, you avoid having to change the methodology of changing your code in many places every time you'd like to modify your program.

    Hope that this helps. :)

[reply]
[d/l]
      HI,
      I have tried doing this, but i keep on getting error messages saying tht the "chromosome" is not numeric to be sorted. It also gives the same error for some contigs. Is there a way around

      Sameet
[reply]

        You're problem is in the way you initalize %chr_cont_pos. You use parentheses '()' for the inner hashes when you should be using braces '{}'. Refer to perlref for more info.

[reply]

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