Bio::T...::Sim4(3pm)

💖 Bio::T...::Sim4 💖

okay bestie, welcome to Bio::T...::Sim4, aka the Bio::Tools::Run::Alignment::Sim4 module — it's a wrapper for the Sim4 program that lets you align cdna to genomic sequences. yes it's niche. yes it's iconic. let's go ✨

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✨ NAME ✨

Bio::Tools::Run::Alignment::Sim4 — a wrapper for the Sim4 program that lets you align cdna to genomic sequences 🧬

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🌸 SYNOPSIS 🌸

bestie here's the vibe:

  use Bio::Tools::Run::Alignment::Sim4;

  my @params = (W=>15,K=>17,D=>10,N=>10,cdna_seq=>"mouse_cdna.fa",genomic_seq=>"mouse_genomic.fa");
  my $sim4 = Bio::Tools::Run::Alignment::Sim4->new(@params);

  my @exon_sets = $sim4->align;

  foreach my $set(@exon_sets){
    foreach my $exon($set->sub_SeqFeature){
        print $exon->start."\t".$exon->end."\t".$exon->strand."\n";
        print "\tMatched ".$exon->est_hit->seq_id."\t".$exon->est_hit->start."\t".$exon->est_hit->end."\n";
    }
  }

  One can also provide a est database

 $sio = Bio::SeqIO->new(-file=>"est.fa",-format=>"fasta");
 @est_seq=();
 while(my $seq = $sio->next_seq){
         push @est_seq,$seq;
 }

 my @exon_sets = $factory->align(\@est_seq,$genomic);

so like, you can also throw in an est database, no biggie 💅

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🦋 DESCRIPTION 🦋

the Sim4 program was developed by Florea et al. for aligning cdna/est sequence to genomic sequences. genuinely a slay.

Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res 1998 Sep;8(9):967-74

and the program itself is available for download here: http://globin.cse.psu.edu/ 🔥

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🫶 FEEDBACK 🫶

💌 Mailing Lists 💌

user feedback is literally an integral part of the evolution of this and other Bioperl modules. so send your comments and suggestions preferably to one of the Bioperl mailing lists, bestie. your participation is much appreciated, fr fr 🥹

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🎀 Support 🎀

please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. many experienced and reponsive experts will be able look at the problem and quickly address it. please include a thorough description of the problem with code and data examples if at all possible. give them the full picture bestie, they'll eat it up 🍓

🐛 Reporting Bugs 🐛

report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. bug reports can be submitted via the web:

  http://redmine.open-bio.org/projects/bioperl/

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👑 AUTHOR - Shawn Hoon 👑

email shawnh@fugu-sg.org

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⭐ APPENDIX ⭐

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _

🌈 program_name

• Title : program_name
• Usage : $factory->program_name()
• Function: holds the program name
• Returns: string
• Args : None

🌈 program_dir

• Title : program_dir
• Usage : $factory->program_dir(@params)
• Function: returns the program directory, obtained from ENV variable.
• Returns: string
• Args :

🌈 version

• Title : version
• Usage : not supported
• Function: Cannot determine from program
• Example :
• Returns : float or undef
• Args : none

🌈 align

• Title : align
• Usage :

             $cdna = 't/data/cdna.fa';
             $genomic = 't/data/cdna.fa';
             @exon_set = $factory->align($cdna,$genomic);
           or
             #@seq_array is array of Seq objs
             $cdna = \@seq_array;
             @exon_set = $factory->align($cdna,$genomic);
           of
             @exon_set = $factory->align($cdna->[0],$genomic)

• Function: Perform a Sim4 alignment
• Returns : An array of Bio::SeqFeature::Generic objects which has exons as sub seqfeatures.
• Args : Name of two files containing fasta sequences, or 2 Bio::SeqI objects or a combination of both — first is assumed to be cdna, second is assumed to be genomic. More than one cdna may be provided. If an object, assume that its an array ref.

🌈 _run

• Title : _run
• Usage : Internal function, not to be called directly
• Function: makes actual system call to Sim4 program
• Example :
• Returns : nothing; Sim4 output is written to a temp file
• Args : Name of a file containing a set of unaligned fasta sequences and hash of parameters to be passed to Sim4

🌈 _setinput()

• Title : _setinput
• Usage : Internal function, not to be called directly
• Function: Create input file for Sim4 program
• Example :
• Returns : name of file containing Sim4 data input
• Args : Seq or Align object reference or input file name

🌈 _setparams()

• Title : _setparams
• Usage : Internal function, not to be called directly
• Function: Create parameter inputs for Sim4 program
• Example :
• Returns : parameter string to be passed to Sim4 during align or profile_align
• Args : name of calling object

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and that's the whole page bestie, we ate and left no crumbs 💅✨ this lil doc is living its perl v5.36.0 era, dated 2023-01-22, under the manual name Bio::T...::Sim4(3pm) — no cap, that's the whole vibe 🎀🦋💖