Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: Command Line Perl for parsing fasta file
Top Forums Shell Programming and Scripting Command Line Perl for parsing fasta file Post 302947227 by jdilts on Tuesday 16th of June 2015 02:07:13 PM
Old 06-16-2015
Command Line Perl for parsing fasta file
I would like to take a fasta file formated like
Code:
>0001
agttcgaggtcagaatt
>0002
agttcgag
>0003
ggtaacctga

and use command line perl to move the all sample gt 8 in length to a new file. the result would be
Code:
>0001
agttcgaggtcagaatt
>0003
ggtaacctga

Code:
cat ${sample}.fasta | perl -lane 'while(<>){if /^>/}'

????? How can I achieve this?
Last edited by Scrutinizer; 06-16-2015 at 03:57 PM.. Reason: additional code tags
 

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

command line argument parsing

how to parse the command line argument to look for '@' sign and the following with '.'. In my shell script one of the argument passed is email address. I want to parse this email address to look for correct format. rmjoe123@hotmail.com has '@' sign and followed by a '.' to be more... (1 Reply)
Discussion started by: rmjoe
1 Replies

2. Shell Programming and Scripting

parsing command line switches in Perl

Hi, My perl script takes few switches which i'm parsing through GetOpt::Long module. My script looks like something : myscript.pl --file="foo" --or --file="bar" The --file switch takes 2 arguments foo and bar. The 2 values of file are separated by --or switch. I want to ensure that... (1 Reply)
Discussion started by: obelix
1 Replies

3. Shell Programming and Scripting

Perl question, parsing line by line

Hello, Im very new to PERL and as a project to work on developing my skills at PERL Im trying to parse poker hands. Ive tried many methods however I cant get the last step. $yourfile= 'FILENAME';#poker hands to parse open (FILE, "$yourfile") or die $!; @lines = <FILE>; for (@lines) ... (1 Reply)
Discussion started by: Ek0
1 Replies

4. Shell Programming and Scripting

Parsing a fasta sequence with start and end coordinates

Hi.. I have a seperate chromosome sequences and i wanted to parse some regions of chromosome based on start site and end site.. how can i achieve this? For Example Chr 1 is in following format I need regions from 2 - 10 should give me AATTCCAAA and in a similar way 15- 25 should give... (8 Replies)
Discussion started by: empyrean
8 Replies

5. UNIX for Dummies Questions & Answers

Find & Replace command - Fasta file

Hi all ! I have a fasta file that looks like that: >Sequence1 RTYIPLCASQHKLCPITFLAVK (it's just an example, obviously in reality I have several pairs of lines like that) Using UNIX command(s), would it be possible to replace all the characters except the "C" of the second line only by... (7 Replies)
Discussion started by: Cevin21
7 Replies

6. Shell Programming and Scripting

Can't Output Piped Perl In-line command to a File

Hello, I'm pretty stumped, and I don't know why I am not able to redirect the output to the 'graphme' file with the command below in Fedora 18. tcpdump -l -n -t "tcp == 18" | perl -ane '($s,$j)=split(/,/,$F,2); print "$s\n";' > graphme In case you're wondering, I was following the example... (2 Replies)
Discussion started by: ConcealedKnight
2 Replies

7. Shell Programming and Scripting

Parsing and masking regions from a single fasta file with subsequence

HI, I have a Complete genome fasta file and I have list of sub sequence regions in the format as : 4353..5633 6795..9354 1034..14456 I want a script which can mask these region in a single complete genome fasta file with the alphabet N kindly help (2 Replies)
Discussion started by: margarita
2 Replies

8. Shell Programming and Scripting

Modifying file from command line using Perl

Hi all, I am having a slight issue updating a file using perl from the command line I need some help with. The item is: DATA_FILE_TYPE=FULL When I run the below command /usr/bin/perl -p -i -e "s/DATA_FILE_TYPE=/DATA_FILE_TYPE=APPEND/g" processfile.cfg It looks to be... (2 Replies)
Discussion started by: kstevens67
2 Replies

9. Shell Programming and Scripting

Perl command line option '-n','-p' and multiple files: can it know a file name of a printed line?

I am looking for help in processing of those options: '-n' or '-p' I understand what they do and how to use them. But, I would like to use them with more than one file (and without any shell-loop; loading the 'perl' once.) I did try it and -n works on 2 files. Question is: - is it possible to... (6 Replies)
Discussion started by: alex_5161
6 Replies

10. Shell Programming and Scripting

Help with reformat single-line multi-fasta into multi-line multi-fasta

Input File: >Seq1 ASDADAFASFASFADGSDGFSDFSDFSDFSDFSDFSDFSDFSDFSDFSDFSD >Seq2 SDASDAQEQWEQeqAdfaasd >Seq3 ASDSALGHIUDFJANCAGPATHLACJHPAUTYNJKG ...... Desired Output File >Seq1 ASDADAFASF ASFADGSDGF SDFSDFSDFS DFSDFSDFSD FSDFSDFSDF SD >Seq2 (4 Replies)
Discussion started by: patrick87
4 Replies

LEARN ABOUT MOJAVE

locale::codes::langfam

Locale::Codes::LangFam(3pm)				 Perl Programmers Reference Guide			       Locale::Codes::LangFam(3pm)

NAME

       Locale::Codes::LangFam - standard codes for language extension identification

SYNOPSIS

	  use Locale::Codes::LangFam;

	  $lext = code2langfam('apa');		       # $lext gets 'Apache languages'
	  $code = langfam2code('Apache languages');    # $code gets 'apa'

	  @codes   = all_langfam_codes();
	  @names   = all_langfam_names();

DESCRIPTION

       The "Locale::Codes::LangFam" module provides access to standard codes used for identifying language families, such as those as defined in
       ISO 639-5.

       Most of the routines take an optional additional argument which specifies the code set to use. If not specified, the default ISO 639-5
       language family codes will be used.

SUPPORTED CODE SETS

       There are several different code sets you can use for identifying language families. A code set may be specified using either a name, or a
       constant that is automatically exported by this module.

       For example, the two are equivalent:

	  $lext = code2langfam('apa','alpha');
	  $lext = code2langfam('apa',LOCALE_LANGFAM_ALPHA);

       The codesets currently supported are:

       alpha
	   This is the set of three-letter (lowercase) codes from ISO 639-5 such as 'apa' for Apache languages.

	   This is the default code set.

ROUTINES

       code2langfam ( CODE [,CODESET] )
       langfam2code ( NAME [,CODESET] )
       langfam_code2code ( CODE ,CODESET ,CODESET2 )
       all_langfam_codes ( [CODESET] )
       all_langfam_names ( [CODESET] )
       Locale::Codes::LangFam::rename_langfam  ( CODE ,NEW_NAME [,CODESET] )
       Locale::Codes::LangFam::add_langfam  ( CODE ,NAME [,CODESET] )
       Locale::Codes::LangFam::delete_langfam  ( CODE [,CODESET] )
       Locale::Codes::LangFam::add_langfam_alias  ( NAME ,NEW_NAME )
       Locale::Codes::LangFam::delete_langfam_alias  ( NAME )
       Locale::Codes::LangFam::rename_langfam_code  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::LangFam::add_langfam_code_alias  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::LangFam::delete_langfam_code_alias  ( CODE [,CODESET] )
	   These routines are all documented in the Locale::Codes::API man page.

SEE ALSO

       Locale::Codes
	   The Locale-Codes distribution.

       Locale::Codes::API
	   The list of functions supported by this module.

       http://www.loc.gov/standards/iso639-5/id.php
	   ISO 639-5 .

AUTHOR

       See Locale::Codes for full author history.

       Currently maintained by Sullivan Beck (sbeck@cpan.org).

COPYRIGHT

	  Copyright (c) 2011-2013 Sullivan Beck

       This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

perl v5.18.2							    2013-11-04					       Locale::Codes::LangFam(3pm)
All times are GMT -4. The time now is 01:03 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy