I have an AoA construct with four columns and many rows. Following is an example of data (input).
DQ556929 103480190 103480214 154943
DQ540839 103325247 103325275 2484
DQ566549 103322763 103322792 99
DQ699634 103322664 103322694 0
DQ544472 103322664 103322692 373
DQ709105 103322291 103322318 46
DQ705937 103322245 103322273 486
DQ699398 103321759 103321788 1211
DQ710151 103320548 103320577 692251
DQ548430 102628297 102628326 1
DQ558403 102628296 102628321 855795
DQ692476 101772501 101772529 481463
DQ544274 101291038 101291068 484047
DQ723982 100806991 100807020 1
DQ709023 100806990 100807020 3
DQ712307 100806987 100807014 0
DQ709654 100806987 100807012 571051
DQ707370 100235936 100235962 1481849
I want to group and write into a file all the row elements (sequentially).
Conditions are if column four values less than 1000 and minimum two values are next to each other, group them else if the value less than 1000 and lies between the values more than 1000 treat them as single and append separately in the same file and the values which are more than 1000 also write as a block but with out affecting the order of the 2nd and third column.
This file is output of my previous program, now for this I have tried implementing my hands but getting some weird results. Here is my chunk of code, but non functional. Guys I need just help if i am executing my logic well here, I am open for any comments as a beginner. And also correct me anywhere.
my #dataf= sort{ $a->[1]<=> $b->[1]} #data;
#dataf=reverse #dataf;
for(my $i>=0;$i<=$#Start;$i++)
{
print "$sortStart[$i]\n";
my $diff = $sortStart[$i] - $sortStart[$i+1];
$dataf[$i][3]= $diff;
# $IDdiff{$ID[$i]}=$diff;
}
#print Dumper(#dataf);
open (CLUST, ">> ./clustTest.txt" );
for (my $k=0;$k<=$#Start;$k++)
{
for (my $l=0;$l<=3;$l++)
{
# my $tempdataf = shift $dataf[$k][$l];
# print $tempdataf;
if ($dataf[$k][3]<=1000)
{
$flag = 1;
do
{
print CLUST"----- Cluster $clustNo -----\n";
print CLUST"$dataf[$k][$l]\t";
if ($dataf[$k][3]<=1000)
{
$flag1 = 1;
}else {$flag1=0;}
$clustNo++;
}until($flag1==0 && $data[$k][3] > 1000);
if($flag1==0 && $data[$k][3] > 1000)
{
print CLUST"Singlet \n";
print CLUST"$dataf[$k][$l]\t";
next;
}
#print CLUST"$dataf[$k][$l]\t"; ##IDdiff
}
print CLUST"\n";
}
}
Expected output in file:
Singlets
DQ556929 103480190 103480214 154943
DQ540839 103325247 103325275 2484
Cluster1
DQ566549 103322763 103322792 99
DQ699634 103322664 103322694 0
DQ544472 103322664 103322692 373
DQ709105 103322291 103322318 46
DQ705937 103322245 103322273 486
Singlets
DQ699398 103321759 103321788 1211
DQ710151 103320548 103320577 692251
DQ548430 102628297 102628326 1
DQ558403 102628296 102628321 855795
DQ692476 101772501 101772529 481463
DQ544274 101291038 101291068 484047
Cluster2
DQ723982 100806991 100807020 1
DQ709023 100806990 100807020 3
DQ712307 100806987 100807014 0
Singlets
DQ709654 100806987 100807012 571051
DQ707370 100235936 100235962 1481849
This seems to produce the expected output. I'm not sure I understood the specification correctly, so there might be errors and edge cases.
How it works: it remembers what kind of section it's currently outputting ($section, Singlet or Cluster). It accumulates lines in the #cluster array if they belong together, when an incompatible line arrives, the cluster is printed and a new one is started. If the cluster to print has only one member, it's treated as a singlet.
#!/usr/bin/perl
use warnings;
use strict;
my $section = q();
my #cluster;
my $cluster_count = 1;
sub output {
if (#cluster > 1) {
print "Cluster$cluster_count\n";
$cluster_count++;
} elsif (1 == #cluster) {
print $section = 'Singlet', "s\n" unless 'Singlet' eq $section;
}
print for #cluster;
#cluster = ();
}
my $last = 'INF';
while (<>) {
my ($id, $from, $to, $value) = split;
if ($value > 1000 || 1000 < abs($last - $from)) {
output();
} else {
$section = 'Cluster';
}
push #cluster, $_;
$last = $to;
}
output();
Related
I have some values and the roots that generate these values.
For example in the value-root format.
100-0
200-1
300-2
100-2
400-1
300-3
100-3
Now I need to create a Hash of arrays in Perl in the following format.
keys are 100, 200, 300, 400; and the values corresponding to each key are given below (same as the roots of the values).
100-0,2,3
200-1
300-2,3
400-1
I am giving the code I have written to achieve the same. But the value for each key is coming as nil.
Below part of the code is inside a loop in which it supplies different root numbers in each iteration in $root_num, As per the above example, they are 100, 200, 300, 400.
Root Number is 100, 200, 300 and 400 in each iteration.
my %freq_and_root;
my #HFarray = ();
my #new_array = ();
if(exists $freq_and_root{$freq_value})
{
#HFarray = #{ $freq_and_root{$freq_value} };
$new_array[0] = $root_num;
push(#HFarray,$new_array[0]);
$freq_and_root{$freq_value} = [#HFarray] ;
} else {
$new_array1[0] = $root_num;
$freq_and_root{$freq_value} = $new_array1[0];
}
Finally after the loop I am printing the hash as follows:
foreach ( keys %freq_and_root) {
print "$_ => #{$freq_and_root{$_}}\n";
}
Following is the output, I am missing the first item in every key-value
100-2 3
200-
300-3
400-
Also how can I post-process the hash so that roots are not repeated in the different key values and root should be there in the highest number key, Hash key values will be following in that case
100-0
200-
300-2 3
400-1
See if following code satisfies your requirements
use strict;
use warnings;
use feature 'say';
my %data;
while(<DATA>) { # walk through data
chomp; # snip eol
my($root,$value) = split '-'; # split into root and value
push #{$data{$root}}, $value; # fill 'data' hash with data
}
foreach my $root(sort keys %data) { # sort roots
say "$root - " . join ',', #{$data{$root}}; # output root and values
}
__DATA__
100-0
200-1
300-2
100-2
400-1
300-3
100-3
Output
100 - 0,2,3
200 - 1
300 - 2,3
400 - 1
I'm looping through multiple objects, but the loop stops before going to the next object.
Created a loop with condition. If condition is met, it calls a ReduceEdge() function. Problem is it will only iterate once and not go to the next object and repeat the procedure.
global proc ReduceEdge()
{
polySelectEdgesEveryN "edgeRing" 2;
polySelectEdgesEveryN "edgeLoop" 1;
polyDelEdge -cv on;
}
string $newSel[] = `ls -sl`;
for($i = 0; $i < size($newSel); $i++)
{
select $newSel[$i];
int $polyEval[] = `polyEvaluate -e $newSel[$i]`;
int $temp = $polyEval[0];
for($k = 0; $k < $temp; $k++)
{
string $polyInfo[] = `polyInfo -fn ($newSel[$i] + ".f[" + $k + "]")`;
$polyInfo = stringToStringArray($polyInfo[$i]," ");
float $vPosX = $polyInfo[2];
float $vPosY = $polyInfo[3];
float $vPosZ = $polyInfo[4];
if($vPosX == 0 && $vPosY == 0 && $vPosZ == 1.0)
{
select ($newSel[$i] + ".e[" + $k + "]");
ReduceEdge();
}
}
}
Expected results:
If I select 4 cylinders, all their edges will reduce by half the current amount.
Actual results:
When 4 cylinders are selected, only one reduces down to half the edges. The rest stay the same.
Since my comment did help you out, I'll try and give a more thorough explanation.
Your first loop (with $i) iterates over each object in your selection. This is fine.
Your second loop (with $k) iterates over the number of edges for the current object in the loop. So far, so good. Though, I'm wondering if it would be more correct to loop of the number of faces...
Now you ask for an array of all face normals of the face at index $k at object $i, with string $polyInfo[] = `polyInfo -fn ($newSel[$i] + ".f[" + $k + "]")`;.
If you try and print the size and values in $polyInfo, you'll realize you have an array with one element, which is the face normal of the particular face you queried just before. Therefore, it will always be element 0, and not $i, which would increases with every iteration.
I have made a Python/PyMEL version of the script, which may be nice for you to see.
import pymel.core as pm
import maya.mel as mel
def reduceEdge():
mel.eval('polySelectEdgesEveryN "edgeRing" 2;')
mel.eval('polySelectEdgesEveryN "edgeLoop" 1;')
pm.polyDelEdge(cv=True)
def reducePoly():
selection = pm.ls(sl=True)
for obj in selection:
for i, face in enumerate(obj.f):
normal = face.getNormal()
if (normal.x == 0.0 and normal.y == 0.0 and normal.z == 1.0):
pm.select(obj + '.e[' + str(i) + ']')
reduceEdge()
reducePoly()
Using Text::Table or Text::ANSITable, or something similar...
If I have a two-dimensional array (which represents a grid of data), where the first row can be the column headers, how can I apply that data and format it into a command line grid with columns.
Something like this: PERL : How to create table from an array?
Except that the number of rows and columns is variable depending on the array setup and needs to automatically output as such.
Thanks
You can use Text::Table to accomplish this, as it handles variable numbers of rows and columns. Although the documentation leaves a lot to be desired, you can usually look to the test files or examples to show you how the library should actually get used. I've adapted example.pl to illustrate this:
table.pl
#!/usr/bin/perl
use strict;
use warnings;
use utf8;
use Text::Table;
binmode STDOUT, ':utf8';
my ($rows, $cols) = #ARGV;
$rows ||= 5;
$cols ||= 7;
my #cols = map { "column " . $_} ( 1..$cols );
my $sep = \'│';
my $major_sep = \'║';
my $tb = Text::Table->new($sep, " Number ", $major_sep,
(map { +(" $_ ", $sep) } #cols)
);
my $num_cols = #cols;
for my $row (1..$rows) {
$tb->load([ "row $row", map { "r$row,c$_" } ( 1..$cols ) ]);
}
my $make_rule = sub {
my ($args) = #_;
my $left = $args->{left};
my $right = $args->{right};
my $main_left = $args->{main_left};
my $middle = $args->{middle};
return $tb->rule(
sub {
my ($index, $len) = #_;
return ('─' x $len);
},
sub {
my ($index, $len) = #_;
my $char =
( ($index == 0) ? $left
: ($index == 1) ? $main_left
: ($index == $num_cols+1) ? $right
: $middle
);
return $char x $len;
},
);
};
my $start_rule = $make_rule->(
{
left => '┌',
main_left => '╥',
right => '┐',
middle => '┬',
}
);
my $mid_rule = $make_rule->(
{
left => '├',
main_left => '╫',
right => '┤',
middle => '┼',
}
);
my $end_rule = $make_rule->(
{
left => '└',
main_left => '╨',
right => '┘',
middle => '┴',
}
);
print $start_rule, $tb->title,
(map { $mid_rule, $_, } $tb->body()), $end_rule;
output
perl table.pl 3 5
┌────────╥──────────┬──────────┬──────────┬──────────┬──────────┐
│ Number ║ column 1 │ column 2 │ column 3 │ column 4 │ column 5 │
├────────╫──────────┼──────────┼──────────┼──────────┼──────────┤
│row 1 ║r1,c1 │r1,c2 │r1,c3 │r1,c4 │r1,c5 │
├────────╫──────────┼──────────┼──────────┼──────────┼──────────┤
│row 2 ║r2,c1 │r2,c2 │r2,c3 │r2,c4 │r2,c5 │
├────────╫──────────┼──────────┼──────────┼──────────┼──────────┤
│row 3 ║r3,c1 │r3,c2 │r3,c3 │r3,c4 │r3,c5 │
└────────╨──────────┴──────────┴──────────┴──────────┴──────────┘
While modules offer easier control and features, if you only need to print it out as a grid
use warnings;
use strict;
use feature 'say';
my #ary = ([1..3], [10..12], [100..102]);
foreach my $row (#ary) {
printf "%7.3f ", $_ for #$row;
say ''
}
Prints
1.000 2.000 3.000
10.000 11.000 12.000
100.000 101.000 102.000
Choose your specifier (%7.3f above) accordingly to what data you have. See sprintf
If the first row is headers, shift it off of the array and print with the same width but using %s
my #ary = ([qw(one two three)], [1..3], [10..12], [100..102]);
printf "%7s ", $_ for #{shift #ary};
say '';
foreach my $row (#ary) {
printf "%7.3f ", $_ for #$row;
say ''
}
This prints the same as above but with (aligned) column names in the first row.
If "grid of data" means numeric data, then the code can discover whether there is a header line, with a reasonable assumption that the first line contains something non-numeric
use List::Util qw(any);
my $have_header = any { /[^0-9.+-]/ } #{$ary[0]};
what also assumes the absence of NaN and 1e02 or such on the first line (can be checked).
Better yet, use looks_like_number from Scalar::Util
use List::Util qw(any);
use Scalar::Util qw(looks_like_number);
my $have_header = any { not looks_like_number($_) } #{$ary[0]};
This uses Perl's internal sense of what a number is, and accounts for NaN and exponential notation, among other things.
If the program needs to find out the width of columns, or they differ a lot, there is more to do for a nice output since we need the maximum width of each column.
use warnings;
use strict;
use feature 'say';
use List::Util qw(max);
my $file = shift #ARGV || 'data.txt';
open my $fh, '<', $file or die "Can't open $file: $!";
my #ary = map { [ split ] } <$fh>;
my #maxw = (1) x #{$ary[0]};
for my $r (#ary) {
for (0..$#$r) {
my $len = length $r->[$_];
$maxw[$_] = $len if $len > $maxw[$_]
}
};
my $hdr = shift #ary;
printf "%$maxw[$_]s ", $hdr->[$_] for 0..$#$hdr;
say '';
for my $i (0..$#ary) {
printf "%-$maxw[$_].2f ", $ary[$i]->[$_] for 0..$#{$ary[$i]};
say '';
}
This expects numbers, except for the header. A few other reasonable assumptions are made.
With input data.txt file used to populate the array
one two three
1.12 1.1 12
1.00 10.00 102.00
the program prints
one two three
1.12 1.10 12.00
1.00 10.00 102.00
If there is a reason to "underline" the column names print this line right after headers
say join(" ", map { '-'x$maxw[$_] } 0..$#$hdr);
(However, tables are generally most readable when free of extra decorations.)
Note. If the numbers are computed in the program those scalars are used as numbers and the length of the string representing them in print should be queried as length sprintf "%s", $num. When they are read from a file they are taken as strings, what is used above for simplicity.
Note for another refinement. The above uses (fixed) 2 decimal places. That can be changed, if needed, so to first count the number of decimal places in input and print out accordingly. However, it is probably more sensible to decide on the uniform width, or at least fix the maximum width. (One doesn't want an accidental column with 16 decimal places, most useless!)
I'm trying to filter an array of a delimited text file in my program. The array from this text file looks like this:
YCL049C 1 511.2465 0 0 MFSK
YCL049C 2 4422.3098 0 0 YLVTASSLFVALT
YCL049C 3 1131.5600 0 0 DFYQVSFVK
YCL049C 4 1911.0213 0 0 SIAPAIVNSSVIFHDVSR
YCL049C 5 774.4059 0 0 GVAMGNVK
..
.
and the code I have for this section of the program is:
my #msfile_filtered;
my $msline;
foreach $msline (#msfile) {
my ($name, $pnum, $m2c, $charge, $missed, $sequence) = split (" ", $msline);
if (defined $amino) {
if ($amino =~ /$sequence/i) {
push (#msfile_filtered, $msline);
}
}
else {
push (#msfile_filtered, $msline);
}
}
$amino will just be a letter that will be input by the user, and corresponds to the last field $sequence. It is not essential that the user actually inputs $amino, so I need to duplicate this array and keep it unchanged if this is the case (hence the else statement). At the minute the #msfile_filtered array is empty, but I am unsure why, any ideas?
EDIT: just to clarify, there is only one space between each field, I copy and pasted this from notpad++, so extra spaced were added. The file itself will only have one space between fields.
Thanks in advance!
The regex that tries to find matching rows is backwards. To find a needle in a haystack, you need to write $haystack =~ /needle/, not the other way around.
Also, to simplify your logic, if $amino is undef, skip the loop entirely. I would rewrite your code as follows:
if (defined $amino)
{
foreach $msline (#msfile)
{
my ($name, $pnum, $m2c, $charge, $missed, $sequence) = split(" ", $msline);
push #msfile_filtered, $msline if ($sequence =~ /$amino/i);
}
} else
{
#msfile_filtered = #msfile;
}
You could simplify this further down to a single grep statement, but that begins to get hard to read. An example of such a line might be:
#msfile_filtered =
defined $amino
? grep { ( split(" ", $_ ) )[5] =~ /$amino/i } #msfile
: #msfile;
The split is should take more than one whitespaces, and the regex vars are vice versa.
First debug to check that values are correct after the split.
Also, you must swap your regex variables like this:
if ($sequence =~ /$amino/i) {
Now you're checking if $amino contains $sequence, which obviously it doesn't
I am a Perl newbie, stuck with another bioinformatics problem that requires some help and input.
The problem in brief:
I have a file, which has over 40,000 unique DNA sequences. By unique, I mean unique sequence id. I am attaching a portion of it at the end of my post to help you show what it looks like.
I need to divide each of the 40,000 sequences into 3 parts. So if a particular sequence is 999 character long, each of the 3 parts would have 333 characters.
I need to look for the following pattern through each of the 3 individual parts:
$gpat = [G]{3,5};
$npat = [A-Z]{1,25};
$pattern = $gpat.$npat.$gpat.$npat.$gpat.$npat.$gpat;
If $pattern appears in the first of the 3 parts, increase the counter of 'beginning', if $pattern occurs in the 2nd of the 3 parts, increase counter of 'middle' and lastly if the $pattern appears in the 3rd part, increase counter of 'end'.
Print the counters of 'beginning','middle' and 'end' i.e basically summation of 'beginning','middle','end' for each of the sequences.
Say in 1st sequence, the values are like '2','5','3' respectively and in 2nd sequence, the values are '4','1','6', the final count should be '7,6,9'.
The issues I am having:
If a particular sequence is split into 3 parts, potential $pattern is lost. eg say on a sequence like :
gggatgtcgatgcatggggatgcatcgatgcggggactagctagcgggatgctacgatggggatgatgataatatcgcggcgcatatatgctagtctatatatta
a split into 3 parts produces following 3 sub-parts,each of 35 character length:
gggatgtcgatgcatggggatgcatcgatgcgggg
actagctagcgggatgctacgatggggatgatgat
aatatcgcggcgcatatatgctagtctatatatta
Hence, $pattern gets split into the first 2 parts. Is there anyway to say "If $pattern begins in 1st part and ends in 2nd part", increase count of "beginning" ?
##UPDATE## The following issue has been resolved thanks to the code suggested by Cupidvogel
2.How do I divide a sequence into 3 parts if its length is not divisible by 3? I tried using int, but then the last part is 1-2
characters short.
The following is the code I have written so far.
It reads in the file, displays the header name and sequence, the length into which each sequence will be divided and finally the sequence split into 3 parts which works fine provided the sequence length is divisible by 3, for those which aren't, the final 3rd part is 1-2 characters short.
#Take Filename from user
print "Please enter file name : ";
$in =<>;
chomp $in;
open (FASTA,"$in") or die ;
while (<FASTA>)
{
$/=">";
#array = split '\n', $_;
$header=shift #array; # Header of the fasta sequence
print "\n\nNext sequence: \n";
print $header,"\n";
$seq= join '', #array; # sequence
$seq=~s/\s//g;
$seq=~s/\*//g;
$seq=~s/>//g;
print $seq,"\n\n";
$num = int(length($seq)/3);
#arr = unpack("A$num A$num A*",$seq);
print " New method gives this :", #arr;
print "\nThe first element is :", $arr[0];
print "\nThe second element is :",$arr[1];
print "\nThe third element is :",$arr[2] ;
#The following lines of code were originally written to split...
#...the sequence into 3 parts, albeit unsuccessfully
#my $split = (length $seq)/3;
#print $split,"\n\n";
#my $int = int $split;
#print $int,"\n\n";
#my #array2 = $seq =~ /(.{$int})/g;
#print join (" ", #array2),"\n\n";
#print $array2[0],"\n",$array2[1],"\n",$array2[2];
}
exit;
I have been trying the code I have written so far with the following sample file : sample.fa
>ABC_123 2
atgtcgatcgatcggcgggcatgcgcgcgcggatg
atatatagcgcgcgctatatagcgcgactctacgc
atgctgctgactagctatagtcgctgactgcgcgt
gggaaaaagggcccgggccccgttttggggatcta
ggggatagctgatgctagcatgcatgctgactgca
>DEF_456 4
gggatgtcgatgcatggggatgcatcgatgcgggg
actagctagcgggatgctacgatggggatgatgat
aatatcgcggcgcatatatgctagtctatatatta
>GHI_789 1
atagctgctagtcgatcggcgcgggtatcgatcgg
ggatcgatcgatcggggatcgatcgggggatcgat
The actual input file looks like the following:
>NR_037701 1
aggagctatgaatattaatgaaagtggtcctgatgcatgcatattaaaca
tgcatcttacatatgacacatgttcaccttggggtggagacttaatattt
aaatattgcaatcaggccctatacatcaaaaggtctattcaggacatgaa
ggcactcaagtatgcaatctctgtaaacccgctagaaccagtcatggtcg
gtgggctccttaccaggagaaaattaccgaaatcactcttgtccaatcaa
agctgtagttatggctggtggagttcagttagtcagcatctggtggagct
gcaagtgttttagtattgtttatttagaggccagtgcttatttagctgct
agagaaaaggaaaacttgtggcagttagaacatagtttattcttttaagt
gtagggctgcatgacttaacccttgtttggcatggccttaggtcctgttt
gtaatttggtatcttgttgccacaaagagtgtgtttggtcagtcttatga
cctctattttgacattaatgctggttggttgtgtctaaaccataaaaggg
aggggagtataatgaggtgtgtctgacctcttgtcctgtcatggctggga
actcagtttctaaggtttttctggggtcctctttgccaagagcgtttcta
ttcagttggtggaggggacttaggattttatttttagtttgcagccaggg
tcagtacatttcagtcacccccgcccagccctcctgatcctcctgtcatt
cctcacatcctgtcattgtcagagattttacagatatagagctgaatcat
ttcctgccatctcttttaacacacaggcctcccagatctttctaacccag
gacctacttggaaaggcatgctgggtctcttccacagactttaagctctc
cctacaccagaatttaggtgagtgctttgaggacatgaagctattcctcc
caccaccagtagccttgggctggcccacgccaactgtggagctggagcgg
gagggaggagtacagacatggaattttaattctgtaatccagggcttcag
ttatgtacaacatccatgccatttgatgattccaccactccttttccatc
tcccagaagcctgctttttaatgcccgcttaatattatcagagccgagcc
tggaatcaaactgcctctttcaaaacctgccactatatcctggctttgtg
acctcagccaagttgcttgactattctcagtctcagtttctgcacctgtc
aaatagggtttatgttaacctaactttcagggctgtcaggattaaatgag
catgaaccacataaaatgtttggtgtatagtaagtgtacagtaaatactt
ccattatcagtccctgcaattctatttttcttccttctctacacagcccc
tgtctggctttaaaatgtcctgccctgctttttatgagtggataccccca
gccctatgtggattagcaagttaagtaatgacactcagagacagttccat
ctttgtccataacttgctctgtgatccagtgtgcatcactcaaacagact
atctcttttctcctacaaaacagacagctgcctctcagataatgttgggg
gcataggaggaatgggaagcccgctaagagaacagaagtcaaaaacagtt
gggttctagatgggaggaggtgtgcgtgcacatgtatgtttgtgtttcag
gtcttggaatctcagcaggtcagtcacattgcagtgtgtcgcttcacctg
gctccctcttttaaagattttccttccctctttccaactccctgggtcct
ggatcctccaacagtgtcagggttagatgccttttatgggccacttgcat
tagtgtcctgatagaggcttaatcactgctcagaaactgccttctgccca
ctggcaaagggaggcaggggaaatacatgattctaattaatggtccaggc
agagaggacactcagaatttcaggactgaagagtatacatgtgtgtgatg
gtaaatgggcaaaaatcatcccttggcttctcatgcataatgcatgggca
cacagactcaaaccctctctcacacacatacacatatacattgttattcc
acacacaaggcataatcccagtgtccagtgcacatgcatacacgcacaca
ttcccttcctaggccactgtattgctttcctagggcatcttcttataaga
caccagtcgtataaggagcccaccccactcatctgagcttatcaaccaat
tacattaggaaagactgtatttcctagtaaggtcacattcagtagtactg
agggttgggacttcaacacagctttttgggggatcataattcaacccatg
acagccactgagattattatatctccagagaataaatgtgtggagttaaa
aggaagatacatgtggtacaaggggtggtaaggcaagggtaaaaggggag
ggaggggattgaactagacacagacacatgagcaggactttggggagtgt
gttttatatctgtcagatgcctagaacagcacctgaaatatgggactcaa
tcattttagtccccttctttctataagtgtgtgtgtgcggatatgtgtgc
tagatgttcttgctgtgttaggaggtgataaacatttgtccatgttatat
aggtggaaagggtcagactactaaattgtgaagacatcatctgtctgcat
ttattgagaatgtgaatatgaaacaagctgcaagtattctataaatgttc
actgttattagatattgtatgtctttgtgtccttttattcatgaattctt
gcacattatgaagaaagagtccatgtggtcagtgtcttacccggtgtagg
gtaaatgcacctgatagcaataacttaagcacacctttataatgacccta
tatggcagatgctcctgaatgtgtgtttcgagctagaaaatccgggagtg
gccaatcggagattcgtttcttatctataatagacatctgagcccctggc
ccatcccatgaaacccaggctgtagagaggattgaggccttaagttttgg
gttaaatgacagttgccaggtgtcgctcattagggaaaggggttaagtga
aaatgctgtataaactgcatgatgtttgcaggcagttgtggttttcctgc
ccagcctgccaccaccgggccatgcggatatgttgtccagcccaacacca
caggaccatttctgtatgtaagacaattctatccagcccgccacctctgg
actccctcccctgtatgtaagccctcaataaaaccccacgtctcttttgc
tggcaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
aaa
>NM_198399 1
aacagattttaactctgaaaagccatttccagtgtctatagactattgtg
agcctggagaagtagcatttagttgggatagcttcactagagctgcctgc
caaagacttccttccacaggatcttgtcgcaccagcaactgacaggagct
tgggagctcgggagcttgggagagggcttatgtttttaataatgtagctg
tcagttcgaagcctggaaatgttgaccctcaaagggcataaaatcttgtt
attttaatttgcatctgggagaatgtctgagcaaggagacctgaatcagg
caatagcagaggaaggagggactgagcaggagacggccactccagagaac
ggcattgttaaatcagaaagtctggatgaagaggagaaactggaactgca
gaggcggctggaggctcagaatcaagaaagaagaaaatccaagtcaggag
caggaaaaggtaaactgactcgcagccttgctgtctgtgaggaatcttct
gccagaccaggaggtgaaagtcttcaggatcagactctctgaaaactgca
aatggaaaggaattcaaaagaatttagattaaaagttaaataaaaagtag
gcacagtagtgctgaattttcctcaaaggctctcttttgataaggctgaa
ccaaatataatcccaagtatcctctctccttccttgttggagatgtctta
cctctcagctccccaaaatgcacttgcctataagaaacacaattgctggt
tcatatgaaacttaggaaatagtgaataaggtgcatttaactttggagaa
atacttttatggctttggtggagatttctcaatactgcaaaagttgtcca
gaaatgaatctgagctgatggtgactttaagttaatattattaatatatc
actgcatatttttacccttatttttgctccttacagcaagattagtaggt
tataaaaatttaaatttaaacaaaattatttcatgacaaaatgggaaact
tcacatcatacttatttttgtttgcctttcaggcatcatattagctttta
taaaaaatggtcttgctgctgaaattgtacttattttatcagaggctggg
tgcagtcaagacaaaagtaaaatggtttacctgagcccaggggagggaaa
attgattaagatatcattatttttgtttggtttggttttgcttttttcct
cttactttaattgaaatactctgaattcccctcatggaaacagagagcat
tgagagcactttctttaaaaggaccaaaaataaattcctaatagattttg
tcctaagagagtgtttttttttctagcatcattttctttacatgccactc
atgtcataaggcatggacaggctatctttcagtggccattactatgtttc
gtacacatgctttattttacttgggctctgagaaatgtgtggctttcctt
cagcattttatttgtgcttctctttttaatggagattgaaaagggagaat
aatgtgaatatcacggcttatattattaaatgttgattgatggcttgtaa
tgtactgcacacaatatatgttaactctgcagaatgacagaccctgggag
aagtaatgccccagttgtcccccactcctaatgccaggcagagaaggaca
gcctttatagacttaatctgctttttgtcccatttgacaaggtaccagga
ggaaattttttaagggatcaactgtatcacagtgcccactctggacctaa
gtctagtgtatccatacaattggtgcagagaaataaggtgtaaatggtgc
tttgttcctgctggttccaagctcagaaaccaagactagctttgtaggag
agaatgagagcctgcaagcctctctttggattggctgaggagtggtggga
gcagggggttgatagaaaacatccagacacacatataagcaagtggccgt
gctacctttttagagaataaagaaacagacttttgagtttatatgcaatg
ccttcattaggtaccaccggcacttacaaaatgtgcggactgaatcccag
agaacactggcagatgtatacagtatatggattgtatcgcttccccaatg
tttgtaaattcacagtatttggaaaactgccttcattttccagtgtggga
aaaactcttgctacctgtattacttgatctcagacccatacctgatggtt
cagtctgtccttaagttaaaagaattttgcttttctaatgttatactatt
tacctgtcagtgtattactgcaacttgaatcactcttttactgttgttgg
atataaacttatcctgtaccaatgtatttattaacacttgtattttatta
ttgagcatatcaataaaaatattaaaaaataacagattgttttttaccaa
aaaaaaaaaaaaa
>NR_026816 1
caacccactctctgtgctatgacttcattactctttcccagcccagccct
gggcaagccccttacgaagtctcaggctacctggatgaccaccctttctt
atgatgctgcaaggagggcaggtgggcagagccccgtgcatcctgggctc
aggccagggacccaagagcttgggagaagctggttctcagactgaaggcc
agagcccagcaccttgtcaccatcccggggagcatcatggcacacaacaa
ccagagccaaggctacagctagagagttgactcctctatttgagattgac
aggcctcggaagtcaaaataagtggtttcctagaccgggtcgagagcaag
tctctattggtcccaactgagttttttcagctggtttttcaaccaaacag
cacctcatctcccagtgaggggaagggaaggctgggctgagagcagcaag
gctgctcatctcacctctccccacccagccatgccagccgcctcacctgg
tggggagaggtgggcctcacctgggtcccctggcagtgctctgtgaaggg
tcttgacattgcactgtaataataaaggtgtgtgtgaagtatcaaaaaaa
>NR_027917 1
atgaagatgattgagcagcacaatcaggaatacagggaagggaaacacag
cttcacaatggccatgaacgcctttggagaaatgaccagtgaagaattca
ggcaggtggtgaatggctttcaaaaccagaagcacaggaaggggaaagtg
ctccaggaacctctgcttcatgacatccgcaaatctgtggattggagaga
gaaaggctacgtgactcctgtgaaggatcagtgcagctggggctctgtaa
ggacagatgttaggaaaactgagaaactagtttcactgagtgtgcagacc
tggtggactgctctaggcttcaaggcaatgttggctgcatttttggagaa
ccattattttgcttccagtatgttgccgacaatggaggcctggactctga
ggaatccttttcatatgaagaaaagctctggagactggaaagtccaaggt
cacagaggtgcatctggtgagagccttcttgctagtggggaatctcagca
gagtcctgaggtggcacagtattctgggaagcatcaagtgcagtgtcatc
ttatcgaggaggctctgcagatgctaagtggtggggatgaggatcacgat
gaagacaaatggccccatgacatgaggaatcatctggctggagaggccca
ggtgtag
>NR_002777 3
cttgtcctttcagaagatcagagacaagtgatatctgtgccaatttggcc
ttttcagtgttataattatggtgtcttgggatcccaatatttctcctaat
gtttccctgatgtgatactttgagagcccaggatgccagtacaataattg
aaattcacaaatgtctggtatcttgtccctcgtgccccatatattatctg
tggtttcggagagctcacttgtctcttatcttcagaaatgacagcacatg
aaatgttgtttggagccactgtcacatcaactgtagaaaaattaacaggt
cagctaagggatataatgtaactttatttgtgatatgagagaaatcttga
taaagacttgagagaaaactgggaggaaccttgtttagaagttataagga
ggggtaagttatgtgtgtcttggaaggagaatcataaatcttaaaacatg
agcctaatagagaacataaaattctaaaagataaagataataataatgat
aagccgcagggtggcttatgataatgtgacttctccttaccccagtagcg
tcggacatctgtcagctctgaaatgataaaaatgcacaatattgaataca
aacaaaggagtcagcactgaaattcattttctctccagattagggaaaga
gtaggtatgccctatggtagggcagtaaattgctgaatgatgagatgaaa
cagccacctagccatttcccattaaatataatcccatcagcagcagacaa
tatctatcctcccctatcccctctatccatatttggaaactgcaccctct
tccctatttagcaccctaacaccacttgaattccataaccctgttgttga
tctagctctcctcacctctaaacacttctagcattcctttcagatcagga
gctcgaaacactctcctttgattttttggaaaagtttctggcttcttcaa
ggtcacgttctccgtcctaagaattaaaaaaaaaaaaaaaaacttccaaa
cctttgaccttgtgtccgtggaacacccctgacttcctatcatttcaacc
cattgaggcacttgaactctcttcttggggatcctgagaagggagagtgc
aaactcttgaccctggaggcaaacaaaatgttctcatgtttgccttccca
cttactttctgtgagaacgtgggaagatcttaacctctcagaagcacagt
ttcttccttctaaaatgaaataattaacctctccctgtctacattcttaa
actcataggacataaaaaaaaaaaaaa
>NR_033769 1
ggcctctggcgggcctccagccagttagaccatttgactaggacgtgtgc
agctcagccagccacagaactggaatttttcaggagcagggggagcatgg
agtttggactttgctgagcaactgaagtggagcgcagagcttgctcgctt
aggagagggcagcatggatggcaaacaagggggcatggatgggagcaagc
ccacggggccaagagactctcctgacaccaggcttctttcaaacccattg
atgggtgattctgtgtctgattggtctcctatgcctgaagctgcaatcta
cggacatcagctgtctctgaggaacctcatcagccacgggtggcttgtga
acatcatcatggcagatcatgtttccccactccatgaagcctgtctcaga
ggtcatccctctcgtgtaaagattttattaaagcatggagctcaggtgaa
tggcgtgacaacagactggcacactccactgtttaatgtttgtatcagca
gcagctgggattatgcttctgcagcatggagccagcgttcaacctgagag
tgatctggcatcccccgtccatgaagctgctaggagaggccacgtggagt
gtgtcgactctcttacagcttataggggcaaaaatgaccataacatcagc
cacgtgggcacttcactgtatttggcttgtgaaaaccagcagatagcctg
tgtcaagaagcttctggagtcaggagcagacctgaacccagggagaggtt
ccccacttcatgcagtggccttcatgaaggccctcatgaaggattcccca
cttcatgcagtggccaggacagccagtgaagagctggcctgcctgctcat
ggattttggagcagacacccaggccaagaatgctgaaggcaaatgtcatg
tggagctggtgcctccagagagccctttgatccagctcttcttggagaga
gaagggcccccttcttttgatgcagttatgcctagaaatcagaagggctt
tggaatccagcagcatcataagataaccaaagtcgtcctcccagaggatc
tgaaatggtttctcctacatctttgtatgtatcaatggaatggattcaca
aacaatgtgaaaacattattgagtgttgtagccactagaattttaaaatc
aagttaggtttatagagtttgactagttttttcgattagatttgtattag
ttataaatttgttcatagagtttgactaattttttcgattagatttgtat
ttgttaaactctgaagccagagtttaaacacactgcatacgtttgtatga
ttagttagaaggcatgaagacttttttccctgcttggagactgtctaaaa
taacagctattgttttgcatatccactgcaggccaagcactttcagcatc
atctaattcagccctcacagcaactgggtcaatctgtccaatttcccagg
gcaaggatagaggagtcagattcaaatacaggttttctgacgttaactta
tgtgatgatttgatcaaagcaggattttccagcatcactatccttgttcc
atctctgctatatgggaatgaaaataaagaaatgtatttcaaaaaaataa
aaagaaaagaaaaacagagacggtc
>NM_016326 3
atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc
ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg
cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac
gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag
tgtgaaaggccacgtgaagatgctgcggctggtgtttgcacttgtgacag
cagtatgctgtcttgccgacggggcccttatttaccggaagcttctgttc
aatcccagcggtccttaccagaaaaagcctgtgcatgaaaaaaaagaagt
tttgtaattttatattactttttagtttgatactaagtattaaacatatt
tctgtattcttccacatattttctgcagttattttaactcagtataggag
ctagaggaagagatttccgaagtctgcaccccgcgcagagcactactgta
acttccaagggagcgctgggagcagcgggatcgggttttccggcacccgg
gcctgggtggcagggaagaatgtgccgggatccgcctcagggatctttga
atctctttactgcctggctggccggcagctccg
>NM_181641 2
atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc
ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg
cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac
gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag
tgtgaaaggccacgtgaagatgctgcggctggcactaactgtgacatcta
tgaccttttttatcatcgcacaagcccctgaaccatatattgttatcact
ggatttgaagtcaccgttatcttatttttcatacttttatatgtactcag
acttgatcgattaatgaagtggttattttggcctttgcttgtgtttgcac
ttgtgacagcagtatgctgtcttgccgacggggcccttatttaccggaag
cttctgttcaatcccagcggtccttaccagaaaaagcctgtgcatgaaaa
aaaagaagttttgtaattttatattactttttagtttgatactaagtatt
aaacatatttctgtattcttccacatattttctgcagttattttaactca
gtataggagctagaggaagagatttccgaagtctgcaccccgcgcagagc
actactgtaacttccaagggagcgctgggagcagcgggatcgggttttcc
ggcacccgggcctgggtggcagggaagaatgtgccgggatccgcctcagg
gatctttgaatctctttactgcctggctggccggcagctccg
>NM_001144931 1
gtttccgttcctctgcccgccatgccgttcctagagctgcacacgaattt
ccccgccaaccgagtgcccgcggggctggagaaacggctgtgcgccgtcg
ctgcctccatcttgggcaaacctgcagaccttgtgaacgtgacggtacgg
ccgggcctggccagggcgctgagcgggtccaccgagccctgcgcgcagct
gtccatctcctccatcggcgtagtgggcaccgccgaggacaaccgcagcc
acagtgcccacttctttgagtttctcaccaaggagctagccctgggccag
gaccggtgcgcaggggtagtaggcccggaatattattctaaaacacaatc
agagtactccattcctgctaacagtttaaagccaaacacctaggcaggcc
atttaggcttctgaatgactgggtcttgaccaggagagctgctgtctagg
ttttctcttcctgaccagttcctcaagagaaatgcaaaactagtgattaa
cagtaagagtcaggcagggcgcggtggctcacgcctgtaatcccagcact
ttgggaggccgag
>NR_029429 1
ggacaccaccccaaaatttcctagtcctctttgatacgggttcctccaat
ctgtagctgccctccatctactgccagagccaagtctgctccaatcacaa
caggttcaatcccagcctgtcctccaccttcagaaacgatggacaaacct
atggactatcctatgggagtggcagcctgagtgtgttcctgggctatgac
actgtgactgttcataacatcgttgtcaataaccaggagtttggcctgag
tgagaatgagcccagcgaccccttttactattcagactttgacgggatcc
tgggaatggcctacccaaacatggcagaggggaattcccctacagtaatg
caggggatgctgcagcagagccagcttactcagcccgtcttcagcttcta
cttcacctgccagccaacccgccagtattgtggagagctcatccttggag
gtgtggaccccaactttattctggtcagatcatctggacccctgtcagcc
cgtaactgtactggcagattgccatcgaggaatttgccatcggtaaccag
gccactggcttgtgctctgagggttgccaggccattgtggataccgagac
cttcctgc
>NR_026551 1
tgtggcctgagaggacggccaggactggccagaaaagagagggacgtggc
taaacgtgagggggcgtggccaagatggccgcgtgcgggatcctcgggta
ccgggagcgaacgaggaggttctggctcagtgcatccactctgggagagc
gtggacctggttcctgggggcgatcgccagtcacccatcaacattcggtg
gagggacagtgtttatgatcccggcttaaaaccactgaccatctcttatg
acccagccacctgcctccacgtctggaataatgggtactctttcctcgtg
gaatttgaagattctacagataaatcagctgcacttagtgcattggaacg
cagtcaaatttgaaaactttgaggatgcagcactggaagaaaatggtttg
gctgtgataggagtatttttaaagatttcggaaacttctggcagcccagt
gtctactggaaggcccaagccgcttgccagaaagctgcgccccgcccaaa
agcactgggttctgcagtccaggcccttcctcagctcccaggtccaggag
aactgcaaggtcacctacttccacaggaagcactgggtccgcatccggcc
cctccgcaccactcctcccagctgggactacacccgcatctgcatccaga
gagagatggtccccgcccgcatccgcgtcctgagagagatggtccccgag
gcctggaggtgctttcccaacaggctgccgctgctgagcaacatcaggcc
tgatttctccaaggctcccctggcctacgtgaagcggtggctttggaccg
cccgccacccccacagcctgtccgcagcctggtgaccgtgaaaatcgccc
cgccagagagcagaggaagcccgacgcccaggccatctgccttcaggtct
gtgatgagaaacggagtggcctgttccgttgtgcccaggtctaggccgct
gagcagagccctcactcccaggcagagttgtctgaatccttcct
>NM_181640 2
atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc
ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg
cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac
gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag
tgtgaaaggccacgtgaagatgctgcggctggatattatcaactcactgg
taacaacagtattcatgctcatcgtatctgtgttggcactgataccagaa
accacaacattgacagttggtggaggggtgtttgcacttgtgacagcagt
atgctgtcttgccgacggggcccttatttaccggaagcttctgttcaatc
ccagcggtccttaccagaaaaagcctgtgcatgaaaaaaaagaagttttg
taattttatattactttttagtttgatactaagtattaaacatatttctg
tattcttccacatattttctgcagttattttaactcagtataggagctag
aggaagagatttccgaagtctgcaccccgcgcagagcactactgtaactt
ccaagggagcgctgggagcagcgggatcgggttttccggcacccgggcct
gggtggcagggaagaatgtgccgggatccgcctcagggatctttgaatct
ctttactgcctggctggccggcagctccg
>NM_016951 3
atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc
ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg
cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac
gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag
tgtgaaaggccacgtgaagatgctgcggctggcactaactgtgacatcta
tgaccttttttatcatcgcacaagcccctgaaccatatattgttatcact
ggatttgaagtcaccgttatcttatttttcatacttttatatgtactcag
acttgatcgattaatgaagtggttattttggcctttgcttgatattatca
actcactggtaacaacagtattcatgctcatcgtatctgtgttggcactg
ataccagaaaccacaacattgacagttggtggaggggtgtttgcacttgt
gacagcagtatgctgtcttgccgacggggcccttatttaccggaagcttc
tgttcaatcccagcggtccttaccagaaaaagcctgtgcatgaaaaaaaa
gaagttttgtaattttatattactttttagtttgatactaagtattaaac
atatttctgtattcttccacatattttctgcagttattttaactcagtat
aggagctagaggaagagatttccgaagtctgcaccccgcgcagagcacta
ctgtaacttccaagggagcgctgggagcagcgggatcgggttttccggca
cccgggcctgggtggcagggaagaatgtgccgggatccgcctcagggatc
tttgaatctctttactgcctggctggccggcagctccg
>NR_002773 1
cagcaccacaccaggaccctccagaggctgtgagaaacatcctgcaccca
ggtcctctctatctgtttatcattgtctattttgtattctgcattcagaa
ccaagagcctgaagacgacccaggagctttagctatggctgtcttcatta
ttttgtccctgtttagtgttctggtgacaggcatgggtgaaggtggggct
gggagtgagaaaggaggtgagagggaatgtaagctgaaccagcttcccca
ttgcccctccgtatctcccagtgcccagccttggacacaccctggccaga
gccagctgtttgcagacctgagccgagaggagctgacggctgtgatgcgc
tttctgacccagcagctggggccagggctggtggatgcagcccaggccca
gccctcggacaactgtgtcttctcagtggagttgcagctgcctcccaagg
ctgcagccctggctcacttggacagggggagccccccacctgcccgggag
gcactggccatcgtcttctttggcaggcaaccccagcccaacgtgagtga
gctggtggtggggccactgcctcacccctcctacatgcgggacgtgactg
tggagcgtcatggaggccccctgccctatcaccgacgccccatgttgttc
caagagtacctggacatagaccagatgatcttcgacagagagctgcccca
ggcttctgggcttctccatcactgttgcttctacaagcgccggggacgga
acctggtgacaatgaccacggctccccgtggtctgcaatcaggggaccgg
gccacctagtttggcctctactacaacatctcgggcgctgggttcttcct
gcaccacgtgggcttggagctgctagtgaaccacaaggcccttgaccctg
cccgctggactatccagaaggtgttctatcaaggccgctactatgacagc
ctggcccagctggaggcccagtttgaggccggcctggtgaatgtggtgct
gatcccagacaatggcacaggtgggtcctggtccctgaagtcccctgtgc
ccccgggtccagctccccctctgcagttccatccccaaggcccccgcttc
agtgtccagggaagtcgagtggcctcctcactgtggactttctcctttgg
cctcggagcattcagtggcccaaggatctttgacgttcccttccaagggg
agagggtggcctatgaagtcagtgtccaggcggccttggccatctatgga
ggcaattctccttctgctctacgaagccggtacatagatagtggctttgg
cttgggccacttctccacgcccctgacccatggggtggactgcccctacc
tggccacctacgtggactggcacttcctttttgagtcccaggccgccaag
acaatacgcgatgccttttgtatatttgaacagaaccagggcctccccct
gcggcgacaccactcagatctctactcccactactttgggggccttgcgg
aaacggtgctggtcatcagatctgtgtctactatgctcaactatgactat
gtgtgggatatggtcttccaccctaatggggccatagaaatcagactcca
caccaccggctacatcagctcagcattcccctttggtgctgcccagaggt
atggaaacaaagtttcagagcacaccctgggcacggtccacacccacagc
gcccacttcaaggtggacctggatgtagcaggtaaggcatcctggcagag
gcaaaagtgctggaggggtgagctgaagtctccatgcctagctttaaaag
ttttcgttgggctgggagcagtagcttatgcctgtaagcccaacactttg
ggagactgaggggggtggatcacttgaggtcaggagttcaaaaccagcct
ggccaacatggcgaaatcctgtctgtactaaaaatacaaaaattagctgg
gcatgggtatgctgtaatcctagctactcgggaggctgaggcaggagaat
cacttgaatctgggagtcagaggttgcagtgagctgagattgagccactg
cactccatcctgcgtgactgaac
>NR_037806 1
attcccagtcacccactcactcagaaagccgggagtcatcggacaccttg
ctggtcagaggtcctgggggtggttttgaaccatcagagcttggactttt
ctgacttccccagcaaggatcttcccacttcctgctccctgtgttcccac
cctccagtgttggcacaggcccacccctggctccaccagagccagaagca
gaggtagaatcaggcgggccccgggctgcactccgagcagtgttcctggc
catctttgctactttcctagagaacccggctgttgccttaaatgtgtgag
agggacttggccaaggcaaaagctggggagatgccagtgacaacatacag
ttcatgactaggtttaggaattgggcactgagaaaattctcaatatttca
gagagtccttcccttatttgggactcttaacacggtatcctcgctagttg
gttttaagggaaacactctgctcctgggtgtgagcagaggctctggtctt
gccctgtggtttgactctccttagaaccaccgcccaccagaaacataaag
gattaaaatcacactaataacccctggatggtcaatctgataataggatc
agatttacgtctaccctaattcttaacattgcagctttctctccatctgc
agattattcccagtctcccagtaacacgtttctacccagatcctttttca
tttccttaagttttgatctccgtcttcctgatgaagcaggcagagctcag
aggatcttggcatcacccaccaaagttagctgaaagcagggcactcctgg
ataaagcagcttcactcaactctggggaatgctaccattttttttccaaa
gtagaaaggaagcacttctgagccagtgaccactgaaagatgaacactct
tcctgatcctctcctctagaattcatctcctcctgctagcagccgcgtcc
tggaggagcagcggatggggaatccattctgtttcttcctggtgtttagg
aagttgccccacacacagattgccccgatgtccaaccagaagaagtgaaa
ctgctgctgggtctggagaggtgaagacccgtggccagcttctgttgttg
ccatcggccattgctttttgttcgcttgcttttggttttgcaagaagagc
ggcctctgtctctgatctgcttcaaatcatcattccatcagtgacagaag
tggctgttccatcagtggtcgcagccagttcagctcctgcatccatcccc
aagtgttctgagtggaatttgaggcctccccaaccacctaccaaaaaagg
agggtgaaatgaaaggaagaagaaaaactcagcattctttcctctgacaa
agagtaaaacgacaaggaatatcggcctgaattctcttcccaagaagaaa
gaaagcacaccaacgcaggcatttgtcttctgtccatggtgctgaagttt
attcactttcaaaccactttcagtaacagcaaattctttagaaaaggaaa
atacagggaaagggataaacctcactgacttggaggaaatcaagaggagt
gagcacagcatcagaaagccccctggccccagactgcacccgctttcctg
gccctaccttgaaatccatcaggtctgcgttggacacggcattgtacatg
ggattagctctg
Any help and input would be deeply appreciated.
Thank you for taking the time to go through my problem!
Rather than splitting the sequence into three parts, the way I see this working is to find all occurrences of $pattern in the complete sequence and determine in which third the pattern starts.
The built-in variable $-[0] contains the offset of the start of the most recent successful match.
The code below does what I think you want. It works by accumulating each sequence (which ends either when a new sequence ID is found or the end of file is reached) and passing it to the process_seq subroutine.
The subroutine takes the length of the sequence and caclulates the offset of the end of each third of the string. The idiomatic sprintf '%.0f', $value is used to round fractional values to the nearest character position.
The #counts array is adjusted for each occurrence of $regex in the sequence. The element of #counts to be incremented is established by comparing the starting position of the match in $-[0] with the end offset of each of the three segments of the sequence.
Once each sequence has been processed the values in #counts are accumulated into #totals to give overall figures for all sequences.
The output of the program when using your sample data is shown. The grand total is (9, 1, 6).
use strict;
use warnings;
my $gpat = '[G]{3,5}';
my $npat = '[A-Z]{1,25}';
my $pattern = $gpat.$npat.$gpat.$npat.$gpat.$npat.$gpat;
my $regex = qr/$pattern/i;
open my $fh, '<', 'sequences.txt' or die $!;
my ($id, $seq);
my #totals = (0, 0, 0);
while (<$fh>) {
chomp;
if (/^>(\w+)/) {
process_seq($seq) if $id;
$id = $1;
$seq = '';
print "$id\n";
}
elsif ($id) {
$seq .= $_;
process_seq($seq) if eof;
}
}
print "Total: #totals\n";
sub process_seq {
my $sequence = shift;
my $length = length $sequence;
my #offsets = map {sprintf '%.0f', $length * $_ / 3} 1..3;
my #counts = (0, 0, 0);
while ($sequence =~ /$regex/g) {
my $place = $-[0];
for my $i (0..2) {
next if $place >= $offsets[$i];
$counts[$i]++;
last;
}
}
print "#counts\n\n";
$totals[$_] += $counts[$_] for 0..2;
}
output
NR_037701
0 0 1
NM_198399
1 0 0
NR_026816
1 0 1
NR_027917
0 0 0
NR_002777
0 0 0
NR_033769
1 0 0
NM_016326
1 0 1
NM_181641
1 0 1
NM_001144931
0 0 0
NR_029429
0 1 0
NR_026551
1 0 0
NM_181640
1 0 1
NM_016951
1 0 1
NR_002773
1 0 0
NR_037806
0 0 0
Total: 9 1 6
I lifted Borodin's process_seq function but used Bio:SeqIO to read in the file sequence by sequence, an advantage over manually reading line by line and the logic to determine various processing. I believe those advantages are:
Code that has been developed and tested by many others
Whenever possible, if output is done via the Bio::SeqIO module, the result file can then be read using Bio::SeqIO read (next_seq) method.
Other reasons I can't think of now :-)
I imagine the BioPerl package of Bio Genetic code modules must be overwhelming to a biologist beginning programming. He might not be willing to try to dig out the information he needs to begin building a program. BioPerl wiki is a good starting place, especially the Howto section, and then there's a how to for beginners and others. You'll find code examples which are mostly(?) helpful. Bio::Seq has some good code examples in the beginning and is where most of the general sequence functions are. Also, for input/output, the Bio::SeqIO module is used and it has examples at the beginning of it's manual.
#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;
my $gpat = '[G]{3,5}';
my $npat = '[A-Z]{1,25}';
my $pattern = $gpat.$npat.$gpat.$npat.$gpat.$npat.$gpat;
my $regex = qr/$pattern/i;
my $in = Bio::SeqIO->new ( -file => "fasta_dat.txt",
-format => 'fasta');
my #totals;
while ( my $seq = $in->next_seq() ) {
process($seq);
}
print "Totals: ";
print "#totals\n";
sub process {
my $seq = shift;
my #offset = map {sprintf '%.0f', $seq->length * $_ / 3} 1..3;
my $sequence = $seq->seq;
my #count = (0,0,0);
while ($sequence =~ /$regex/g) {
my $place = $-[0];
for my $i (0 .. 2) {
next if $place >= $offset[$i];
$count[$i]++;
last;
}
}
print $seq->id, "\n#count\n";
$totals[$_] += $count[$_] for 0 .. $#count;
}