fast sequence extraction Post: 302665151

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Top Forums UNIX for Dummies Questions & Answers fast sequence extraction Post 302665151 by bakunin on Monday 2nd of July 2012 05:03:36 AM

07-02-2012

Registered User

While the rest of your problem description is to the point, a few points remain to be clarified:

Quote:

Originally Posted by Fahmida

I have a large text file containing DNA sequences in fasta format as follows:

Code:

>someseq
GAACTTGAGATCCGGGGAGCAGTGGATCTC
CACCAGCGGCCAGAACTGGTGCACCTCCAG
GCCAGCCTCGTCCTGCGTGTC
>another seq 
GGCATTTTTGTGTAATTTTTGGCTGGATGAGGT
GACATTTTCATTACTACCATTTTGGAGTACA
>seq3450
TTTTCCTGTTCACTGCTGCTTTTCTATAGACAGCA
GCAGCAAGCAGTAAGAGAAAGTA
etc.

Does the file really look like that (with the line breaks) or have you just broken the long lines for better readability? Because it will change a possible solution it is important how you answer this question.

Which shell are you using? What you need is, by and large, a substring-function and some shells have such a function built in, others haven't. Therefore a solution in, for instance, ksh93 (which has a substring-function) will be a lot easier and a lot faster than, say, a solution in Bourne shell or ksh88 (both of which lack such a device).

As it might happen that one of the tools used has some special feature in one OS and doesn't so in the other you might as well tell us which OS you are using.

In short: ask questions the smart way, please! How this is done you can read here in detail.

I hope this helps.

bakunin

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shells

shells(4)							   File Formats 							 shells(4)

NAME

       shells - shell database

SYNOPSIS

       /etc/shells

DESCRIPTION

       The shells file contains a list of the shells on the system. Applications use this file to determine whether a shell is valid. See getuser-
       shell(3C). For each shell a single line should be present, consisting of the shell's path, relative to root.

       A hash mark (#) indicates the beginning of a comment; subsequent characters up to the end of the line are not interpreted by  the  routines
       which search the file. Blank lines are also ignored.

       The following default shells are used by utilities: /bin/bash, /bin/csh, /bin/jsh, /bin/ksh, /bin/ksh93, /bin/pfcsh, /bin/pfksh, /bin/pfsh,
       /bin/sh, /bin/tcsh, /bin/zsh, /sbin/jsh, /sbin/sh, /usr/bin/bash, /usr/bin/csh, /usr/bin/jsh, /usr/bin/ksh, /usr/bin/ksh93, /usr/bin/pfcsh,
       /usr/bin/pfksh, /usr/bin/pfsh, and /usr/bin/sh, /usr/bin/tcsh, /usr/bin/zsh, and /usr/sfw/bin/zsh. /etc/shells overrides the default list.

       Invalid shells in /etc/shells could cause unexpected behavior, such as being unable to log in by way of ftp(1).

FILES

       /etc/shells    list of shells on system

SEE ALSO

       vipw(1B), ftpd(1M), sendmail(1M), getusershell(3C), aliases(4)

SunOS 5.11							    20 Nov 2007 							 shells(4)