Sponsored Content
Top Forums Shell Programming and Scripting Shell script for changing the accession number of DNA sequences in a FASTA file Post 302881556 by Akshay Hegde on Monday 30th of December 2013 08:56:44 AM
Old 12-30-2013
Please use CODE TAGS for data you provided in post1. Select data and press code option which is available between QUOTE and HTML, I attached screen shot of it see.

Last edited by Akshay Hegde; 05-31-2014 at 04:29 PM..
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Extracting DNA sequences from GenBank files using Perl

Hi all, Using Perl, I need to extract DNA bases from a GenBank file for a given plant species. A sample GenBank file is here... Nucleotide This is saved on my computer as NC_001666.gb. I also have a file that is saved on my computer as NC_001666.txt. This text file has a list of all... (5 Replies)
Discussion started by: akreibich07
5 Replies

2. UNIX for Dummies Questions & Answers

trying to grep -v multiple changing sequences from a file

Hello All - I am looking for help on how to solve a re-occuring problem. I have a file with certain sequences in it that need to be removed. The sequences are always different but the fix is always the same remove those sequences and leave the rest. Another team ID's the bad sequences and then I... (3 Replies)
Discussion started by: candyluv030
3 Replies

3. Shell Programming and Scripting

Tricky task with DNA sequences.

I am trying to reverse and complement my DNA sequences. The file format is FASTA, something like this: Now, to reverse the sequence, I should start reading from right to left. At the same should be complemented. Thus, "A" should be read as "T"; "C" should be read as "G"; "T" should be converted... (8 Replies)
Discussion started by: Xterra
8 Replies

4. Shell Programming and Scripting

Extract sequences from a FASTA file based on another file

I have two files. File1 is shown below. >153L:B|PDBID|CHAIN|SEQUENCE RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM DIGTTHDDYANDVVARAQYYKQHGY >16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
Discussion started by: nelsonfrans
7 Replies

5. Shell Programming and Scripting

Shorten header of protein sequences in fasta file

I have a fasta file as follows >sp|O15090|FABP4_HUMAN Fatty acid-binding protein, adipocyte OS=Homo sapiens GN=FABP4 PE=1 SV=3 MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKN TEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVM KGVTSTRVYERA >sp|L18484|AP2A2_RAT AP-2... (3 Replies)
Discussion started by: alexypaul
3 Replies

6. UNIX for Dummies Questions & Answers

Select distinct sequences from fasta file and list

Hi How can I extract sequences from a fasta file with respect a certain criteria? The beginning of my file (containing in total more than 1000 sequences) looks like this: >H8V34IS02I59VP SDACNDLTIALLQIAREVRVCNPTFSFRWHPQVKDEVMRECFDCIRQGLG YPSMRNDPILIANCMNWHGHPLEEARQWVHQACMSPCPSTKHGFQPFRMA... (6 Replies)
Discussion started by: Marion MPI
6 Replies

7. Shell Programming and Scripting

Getting unique sequences from multiple fasta file

Hi, I have a fasta file with multiple sequences. How can i get only unique sequences from the file. For example my_file.fasta >seq1 TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC >seq2... (3 Replies)
Discussion started by: Ibk
3 Replies

8. UNIX for Beginners Questions & Answers

How to count the length of fasta sequences?

I could calculate the length of entire fasta sequences by following command, awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' unique.fasta But, I need to calculate the length of a particular fasta sequence specified/listed in another txt file. The results to to be... (14 Replies)
Discussion started by: dineshkumarsrk
14 Replies

9. Shell Programming and Scripting

Shorten header of protein sequences in fasta file to only organism name

I have a fasta file as follows >sp|Q8WWQ8|STAB2_HUMAN Stabilin-2 OS=Homo sapiens OX=9606 GN=STAB2 PE=1 SV=3 MMLQHLVIFCLGLVVQNFCSPAETTGQARRCDRKSLLTIRTECRSCALNLGVKCPDGYTM ITSGSVGVRDCRYTFEVRTYSLSLPGCRHICRKDYLQPRCCPGRWGPDCIECPGGAGSPC NGRGSCAEGMEGNGTCSCQEGFGGTACETCADDNLFGPSCSSVCNCVHGVCNSGLDGDGT... (3 Replies)
Discussion started by: jerrild
3 Replies

10. UNIX for Beginners Questions & Answers

How to add specific bases at the beginning and ending of all the fasta sequences?

Hi, I have to add 7 bases of specific nucleotide at the beginning and ending of all the fasta sequences of a file. For example, I have a multi fasta file namely test.fasta as given below test.fasta >TalAA18_Xoo_CIAT_NZ_CP033194.1:_2936369-2939570:+1... (1 Reply)
Discussion started by: dineshkumarsrk
1 Replies
HTML::FormFu::Role::Element::Group(3pm) 		User Contributed Perl Documentation		   HTML::FormFu::Role::Element::Group(3pm)

NAME
HTML::FormFu::Element::_Group - grouped form field base-class DESCRIPTION
Base class for HTML::FormFu::Element::Checkboxgroup, HTML::FormFu::Element::Radiogroup, and HTML::FormFu::Element::Select fields. METHODS
options Arguments: none Arguments: @options --- elements: - type: Select name: foo options: - [ 01, January ] - [ 02, February ] - value: 03 label: March attributes: style: highlighted - [ 04, April ] If passed no arguments, it returns an arrayref of the currently set options. Use to set the list of items in the select menu / radiogroup. Its arguments must be an array-ref of items. Each item may be an array ref of the form "[ $value, $label ]" or a hash-ref of the form "{ value => $value, label => $label }". Each hash-ref may also have an "attributes" key. Passing an item containing a "group" key will, for Select fields, create an optgroup. And for Radiogroup fields or Checkboxgroup fields, create a sub-group of radiobuttons or checkboxes with a new "span" block, with the classname "subgroup". An example of Select optgroups: --- elements: - type: Select name: foo options: - label: "group 1" group: - [1a, 'item 1a'] - [1b, 'item 1b'] - label: "group 2" group: - [2a, 'item 2a'] - [2b, 'item 2b'] When using the hash-ref construct, the "label_xml" and "label_loc" variants of "label" are supported, as are the "value_xml" and "value_loc" variants of "value", the "attributes_xml" variant of "attributes" and the "label_attributes_xml" variant of "label_attributes". "container_attributes" or "container_attributes_xml" is used by HTML::FormFu::Element::Checkboxgroup and HTML::FormFu::Element::Radiogroup for the c<span> surrounding each item's input and label. It is ignored by HTML::FormFu::Element::Select elements. "label_attributes" / "label_attributes_xml" is used by HTML::FormFu::Element::Checkboxgroup and HTML::FormFu::Element::Radiogroup for the c<label> tag of each item. It is ignored by HTML::FormFu::Element::Select elements. values Arguments: @values --- elements: - type: Radiogroup name: foo values: - jan - feb - mar - apr A more concise alternative to "options". Use to set the list of values in the select menu / radiogroup. Its arguments must be an array-ref of values. The labels used are the result of "ucfirst($value)". value_range Arguments: @values --- elements: - type: Select name: foo value_range: - "" - 1 - 12 Similar to "values", but the last 2 values are expanded to a range. Any preceding values are used literally, allowing the common empty first item in select menus. empty_first If true, then a blank option will be inserted at the start of the option list (regardless of whether "options", "values" or "value_range" was used to populate the options). See also "empty_first_label". empty_first_label empty_first_label_xml empty_first_label_loc If "empty_first" is true, and "empty_first_label" is set, this value will be used as the label for the first option - so only the first option's value will be empty. SEE ALSO
Is a sub-class of, and inherits methods from HTML::FormFu::Element::_Field, HTML::FormFu::Element HTML::FormFu AUTHOR
Carl Franks, "cfranks@cpan.org" LICENSE
This library is free software, you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.14.2 2012-01-14 HTML::FormFu::Role::Element::Group(3pm)
All times are GMT -4. The time now is 10:18 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy