How to read and write several DNA sequences in the format FASTA placed in one file?

vouchsafing has asked for the wisdom of the Perl Monks concerning the following question:

Hey. I'm totally new when it comes to programming in Perl. But I have to make a project and I have no idea how to do it. Maybe someone can help me. The script have to load several sequences in the format FASTA placed in one file. Example input file attached (for example 'gens.txt'):

>1

AGTATCGGACCCGAAGACATTACGCTTAGAGACTTGAAAA CCTACAGTAAAGAAGCAGCGTCTGGATAT
+CTGGAAGACAA CGGATTGAAGCTTGTAGAAAAAGAAGCATACTCAGATGAT GTTCCAGAAGGACAGG
+TTGTCAAACAAAAACCAGCAGCAG GTACGGCAGTAAAGCCGGGAAACGAAGTTGAAGTGACATT CTC
+TCTCGGACCAGAGAAAAAACCTGCGAAAACAGTGAAA GAAAAGGTCAAGATCCCCTACGAACCAGAAA
+ATGAAGGGG ACGAGCTTCAAGTGCAAATCGCGGTTGACGATGCGGATCA

>2

CCATATCGGAGACAGCAGATGCTATTTGCTTCAGGACGAT GATTTCGTTCAAGTGACAGAAGACCATTC
+GCTTGTAAATG AACTGGTTCGCACTGGAGAGATTTCCAGAGAAGACGCTGA ACATCATCCGCGAAAA
+AATGTGTTGACGAAGGCGCTTGGA ACAGACCAGTTAGTCAGTATTGACACCCGTTCCTTTGATA TAG
+AACCCGGAGACAAACTGCTTCTATGTTCTGACGGACT GACAAATAAAGTGGAAGGCACTGAGTTAAAA
+GACATCCTG TGGACAAAGCCAATCAGAATGGCGGAGAAGGCGGAGAAGC

>3

ATAAAACAACGGTATTTGCCGGTCAGTCCGGTGTTGGGAA ATCCTCGCTTCTCAACGCGATCAGTCCGG
+AGCTCGGATTA AGAACAAACGAGATTTCCGAGCATTTGGGCCGCGGGAAAC ACACAACCCGCCACGT
+GGAGCTGATTCACACGTCCGGAGG TTTGGTTGCAGATACACCGGGATTCAGCTCGCTTGAATTT ACA
+GACATTGAGGAAGAAGAGCTGGGCTATACCTTCCCTG ATATCAGAGAAAAAAGCTCTTCATGCAAATT
+TAGAGGCTG TTTACATCTGAAAGAGCCGAAATGTGCGGTGAAACAAGCT
[download]

Then the script should check how similar are the sequences and print percent identity, and then it should also generate a consensus sequence. Any help would be very precious for me!

Comment on How to read and write several DNA sequences in the format FASTA placed in one file? Download Code

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Re: How to read and write several DNA sequences in the format FASTA placed in one file?
by toolic (Bishop) on Apr 25, 2011 at 13:20 UTC

?node_id=3989;HIT=fasta%20file;re=N

2011-04-25 vouchsafing How to read and write several DNA sequences in the format FASTA placed in one file? SoPW

2011-02-08 krish28 Splitting a multi-sequence fasta file into individual sequences in individual arrays SoPW

2010-11-30 InfoSeeker Compare fasta files with different headers SoPW

2010-11-22 egorleg How do i write code for searching motifs in a FASTA file? SoPW

2010-07-30 newbie25 combine 2 fasta files into 1 SoPW

2010-07-27 Anonymous Monk Bioinformatics: Slow Parsing of a Fasta File SoPW

2010-04-08 RabidMortal simple perl script to trim a FASTA file SoPW

2009-10-29 Anonymous Monk Parse DNA fasta file SoPW

2009-06-29 statsman5 Extracting DNA sequences from FASTA files SoPW

2009-05-06 lomSpace splitting fasta file into individual fasta files SoPW

2008-09-11 ashnator While loop printing only one fasta header file SoPW

2008-07-28 nemo2 comparing two fasta files SoPW

2005-07-10 Nadiah extracting open reading frame (ORF) from a FASTA file SoPW

2003-11-18 bioinformatics Refomating a large fasta file... SoPW

2003-03-12 clairudjinn File::Wrap and Fasta format Snippet

2002-04-25 lolly Base sequence length in fasta format file SoPW

Please update your post, placing your data inside "code" tags: Writeup Formatting Tips

Re: How to read and write several DNA sequences in the format FASTA placed in one file?
by Corion (Patriarch) on Apr 25, 2011 at 13:19 UTC

Have a look at http://bioperl.org. Also, we are not biologists and thus "sequence similarity" and "consensus sequence" tell us very little. You will have to provide more technical explanations how you would measure similarity and what "consensus" would mean in your case. Also see what has to offer for FASTA.

Please note that this site is not a script writing service. While we will assist you with writing your code, we expect you to do the majority of the work and show some effort. This mostly involves you showing the code you have already written and explaining where you encounter the problem.

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