perl - extracting fasta sequences based on position -


i newbie perl. still learning.

i have file in fasta format. extract sequences spanning particular position. example, position 200 300

>contig[0001] tgcatcaaaagctgaaaatatgtagtcgagaagtcatttcgagaaattgacgttttaagt ttcggtttccaaattcaaccggatgtatcttcgccaataattgtcagcagttagaatttc tttcaacattatgaagccctttttatatattttgattctgcatcaaaagctgaaaatatg tagtcttgaagtcatttcgagaaatcgacgttttaagtttctgtttccaaattcaaacgg atgtatcttcgccaataattgtcagaagttagaatttctttcaacattatgaagcccttt ttatatattttgattctgcatcaaaagctgaaaatgtgtagtctcgaagtcatttcgaga aattgacgttttaagtttctgtttccaaattcaaacggatgtatcttcgccaataattgt cagaagttagaatttctttcaacattatgaagccctttttacatattttgaccctgcatc aaaagctgaaaatatgtagtctcgaagtcattttgagaagttagaatttctttcaacatt atgaagccctttttatatattttgattctgcatcaaaagctgaaaatatgtagtctcgaa gtcwtttcragaaattgacgttttaagtttctgtttccaaattcaaacggatgtatcttc gccaataattgtcagaagttagaatttctttcaacattatgaagccctttttatatattt tgactctgcatcaaaagctgaaaatatgtagtctcgaagtcatttcgagaaattgacgtt

i extract sequences position 200–300 sequence contig[0001]. output be:

>contig[0001]_200-300 agaaatcgacgttttaagtttctgtttccaaattcaaacggatgtatcttcgccaataatt gtcagaagttagaatttctttcaacattatgaagcccttt

i have 500 sequences in fasta file , have required postions in tab delimited file containing id start end.

it great if me on this.

thank help.i not sure can give file containing info regarding positions.

newbie

one way. content of script.pl:

#!/usr/bin/env perl  use warnings; use strict;  ($adn, $l, $header);  while ( <> ) {      chomp;      ## first line known, header, print , process next one.     if ( $. == 1 ) {          printf qq|%s_%s\n|, $_, q|200-300|;         next;     }         ## concat adn while not found header.     if ( '>' ne substr $_, 0, 1 ) {          if ( ! $l ) { $l = length }         $adn .= $_;          if ( ! eof ) { next }     }        else {         $header = sprintf qq|%s_%s\n|, $_, q|200-300|;     }         ## extract range 200-300 , insert newlines set same length of      ## line before.     $s = substr $adn, 199, 100;     $s =~ s/(.{$l})/$1\n/g;     printf qq|%s\n|, $s;      undef $adn;      ## if not end of file, print header of following adn.     if ( ! eof ) { print $header } }

run like:

perl script.pl infile

that yields:

>contig[0001]_200-300 agaaatcgacgttttaagtttctgtttccaaattcaaacggatgtatcttcgccaataat tgtcagaagttagaatttctttcaacattatgaagccctt

Comments

Post a Comment

Popular posts from this blog

jquery - How can I dynamically add a browser tab? -

since using iframes house external pages are, accounts "not preferred method" , disallowed sites (flickr, one), want dynamically generate browser tabs. e.g., when user submits form, want dynamically generate tab on browser in response submitted. e.g., might want add new tab url like: http://www.bigsurgarrapata.com/contact how in jquery? you want form target attribute action attribute. http://www.w3schools.com/tags/att_form_target.asp browsers have ultimate control on result of target attribute open new tab value of _blank. <form action="contact_submit.php" target="_blank" method="post">
Read more

node.js - Getting the socket id,user id pair of a logged in user(s) -

i have web application done using node js , in it,i have authentication system requires users log in before can access pages. have 2 pages,the homepage , updates page. from read docs,a new socket id issued when user opens tab in browser. me being admin,i know socket id of logged in user , more so,the socket id,logged in user id pair logged in users. what method can use socket id,logged in user id pair make sure broadcast realtime info users online?.
Read more

keyboard - C++ GetAsyncKeyState alternative -

i using windows.h library's getasynckeystate function define key pushed on keyboard . here program returns int value of pushed key example. #include <iostream> #include <windows.h> using namespace std; int main (){ char i; for(i=8;i<190;i++){ if(getasynckeystate(i)== -32767){ cout<<int (i)<<endl; } } return 0; } but trying make opengl simple game , function appeared slow . there function not need cycle 180 times , if statement . thanks you're trying make opengl game, you're going use glfw. if that's case can away using glfwgetkey() such: if (glfwgetkey(glfw_key_up) == glfw_press) {...} if (glfwgetkey(glfw_key_down) == glfw_press) {...} that method nicely explained in tutorial 6 opengl-tutorial.org . should start first tutorial of beginners tutorials , later intermediate tutorials . if you're going make win32 window can listen wm_keydown or wm_keyup messages , virtua
Read more