fastQ_brew - a module for preprocessing of fastQ formatted files
use fastQ_brew; use List::Util qw(min max sum); use fastQ_brew_Utilities; use Cwd; my $lib = "sanger"; my $file_path = cwd(); my $in_file = "sample_sanger.fastq"; my $tmp = fastQ_brew->new(); $tmp->load_fastQ_brew( library_type => $lib || "illumina", file_path => $file_path, in_file => $in_file, summary => "Y", de_duplex => "Y", qual_filter => 30, length_filter => 25, adapter_left => "GTACGTGTGGTGGGGAT", mismatches_l => 1, adapter_right => "TAGCGCGCGATGATT", mismatches_r => 1, left_trim => 5, right_trim => 8, fasta_convert => "Y", dna_rna => "Y", rev_comp => "Y", remove_n => "Y", cleanup => "Y" ); $tmp->run_fastQ_brew();
Returns summary statistics for all reads from fastQ formatted files and provides methods for filtering and trimming reads by lenght and quality.
damienoh@gwu.edu
User feedback is an integral part of the evolution of this module. Send your comments and suggestions preferably to one of the mailing lists. Your participation is much appreciated.
Please direct usage questions or support issues to: <damienoh@gwu.edu> Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the GitHub bug tracking system to help keep track of the bugs and their resolution. Bug reports can be submitted via the GitHub page:
https://github.com/dohalloran/fastQ_brew/issues
Email: damienoh@gwu.edu
The rest of the documentation details each of the object methods.
Title : new() Usage : my $tmp = fastQ_brew->new(); Function: constructor routine Returns : a blessed object Args : none
Title : load_fastQ_brew() Usage : $tmp->load_fastQ_brew( library_type => $lib || "illumina", file_path => $file_path, in_file => $in_file, summary => "Y", de_duplex => "Y", qual_filter => 30, length_filter => 25, adapter_left => "GTACGTGTGGTGGGGAT", mismatches_l => 1, adapter_right => "GTACGTGTGGTGGGGAT", mismatches_r => 1, left_trim => 5, right_trim => 8, fasta_convert => "Y", dna_rna => "Y", rev_comp => "Y", remove_n => "Y", cleanup => "Y" ); Function: Populates the user data into $self hash Returns : nothing returned Args : -library_type, either sanger or illumina -file_path, path to sequences -in_file, the name of the files containing the fastQ reads -summary, return summary statistics for the unfiltered and filtered fastq data -de_duplex, remove duplicate entries -qual_filter, fiter reads by Q score: N=no, 200=remove reads with Quality (Q) scores below 200 -adapter_left, remove adapter from left side -mismatches_l, remove adapter from left side that include a number of mismatches -adapter_right, remove adapter from right side -mismatches_r, remove adapter from right side that include a number of mismatches -left_trim, remove x number of bases from left end -right_trim, remove x nnumber of bases from right end -length_filter, fiter reads by length: N=no, 40=remove reads shorter than 40 bases -fasta_convert, option to convert to fastA file: Y=yes, N=no -dna_rna, transcribe reads in fastQ file: N=no, Y=yes -rev_comp, reverse complement reads in fastQ file: N=no, Y=yes -remove_n, remove reads with non-designated bases (i.e. N's) in fastQ file: N=no, Y=yes -cleanup, option to delete tmp file: Y=yes, N=no
Title : run_fastQ_brew() Usage : $self->run_fastQ_brew(%arg) Function: processes the input file and start cycle Returns : tmp file with only phred score and sequence for each read Args : fastQ file
Title : _summary_stats() Usage : _summary_stats(); Function: runs the summary stats Returns : the stats Args : $self, %arg
Title : _de_duplex Usage : _de_duplex(); Function: remove duplicate reads Returns : fastQ file with only singletons Args : Y=yes, N=no
Title : _remove_n() Usage : $self->_remove_n(%arg) Function: option to remove reads with N's Returns : fastQ file Args : Y=yes, N=no
Title : _remove_adapter_left Usage : _remove_adapter_left(); Function: option to remove specific adapters from left side Returns : fastQ file Args : string="GTCGAGT" and mismatches=integer
Title : _remove_adapter_right Usage : _remove_adapter_right(); Function: option to remove specific adapters from right side Returns : fastQ file Args : string="GTCGAGT" and mismatches=integer
Title : _right_trim() Usage : $self->_right_trim(%arg) Function: option to remove right side bases from reads Returns : right trimmed fastQ file Args : integer=yes, N=no
Title : _left_trim() Usage : $self->_left_trim(%arg) Function: option to remove left side bases from reads Returns : left trimmed fastQ file Args : integer=yes, N=no
Title : _prune_fastq() Usage : _prune_fastq(); Function: option to remove reads below phred score Returns : pruned fastQ file Args : integer=yes, N=no
Title : _trim_length() Usage : $self->_trim_length(%arg) Function: option to remove reads below specified length Returns : trimmed fastQ file Args : integer=yes, N=no
Title : _convert_fasta() Usage : _convert_fasta(); Function: option to convert fastQ file to fastA Returns : fastA file Args : Y=yes, N=no
Title : _reverse_comp() Usage : $self->_reverse_comp(%arg) Function: option to rev comp fastQ reads Returns : reverse complemented fastQ file Args : Y=yes, N=no
Title : _dna_rna() Usage : $self->_dna_rna(%arg) Function: option to convert dna to rna for fastQ reads Returns : RNA fastQ file Args : Y=yes, N=no
Title : _post_fastQ_brew Usage : _post_fastQ_brew(); Function: runs the summary stats after filtering Returns : the stats Args : $self, %arg
Title : _cleanup() Usage : _cleanup(); Function: option to delete tmp files Returns : nothing Args : Y=yes, N=no
Title : DESTROY Usage : DESTROY(); Function: garbage collection Returns : nothing Args : automatically called
Title : get_lib_type() Usage : my $get_lib_type= $tmp->get_lib_type(); Function: Retrieves the library type used Returns : A string of the type e.g. Sanger Args : none
Title : set_lib_type() Usage : my $set_lib_type = $tmp->set_lib_type("sanger"); Function: Populates the $self->{lib_type} property Returns : $self->{lib_type} Args : the lib as a string
Title : get_in_file() Usage : my $get_in_file = $tmp->get_in_file(); Function: Retrieves the input filename Returns : A string containing filename Args : none
Title : set_in_file() Usage : my $set_in_file= $tmp->set_in_file("myOutPutFile.txt"); Function: Populates the $self->{in_file} property Returns : $self->{in_file} Args : name of the user provided input file
Title : get_de_duplex() Usage : my $get_de_duplex= $tmp->get_de_duplex(); Function: Retrieves the de_duplex choice Returns : Y or N Args : none
Title : set_de_duplex() Usage : my $set_de_duplex= $tmp->set_de_duplex(); Function: Sets the de_duplex choice Returns : Populates the $self->{de_duplex} property Args : Y or N
Title : get_qual_filter() Usage : my $get_qual_filter= $tmp->get_qual_filter(); Function: Retrieves the qual filter used Returns : integer Args : none
Title : set_qual_filter() Usage : my $set_qual_filter= $tmp->set_qual_filter(); Function: Sets the qual filter used Returns : Populates the $self->{qual_filter} property Args : integer
Title : get_len_filte() Usage : my $get_len_filte= $tmp->get_len_filte(); Function: Retrieves the length filter Returns : integer Args : none
Title : set_len_filter() Usage : my $set_len_filter= $tmp->set_len_filter(); Function: Sets the len filter used Returns : Populates the $self->{length_filter} property Args : integer
Title : get_adapter_l() Usage : my $get_adapter_l= $tmp->get_adapter_l(); Function: Retrieves the left adapter specified Returns : A string of the left adapater Args : none
Title : set_adapter_l() Usage : my $set_adapter_l= $tmp->set_adapter_l(); Function: Sets the $self->{adapter_left} property Returns : Populates the $self->{adapter_left} property Args : string
Title : get_adapter_r() Usage : my $get_adapter_r= $tmp->get_adapter_r(); Function: Retrieves the right adapter specified Returns : A string of the right adapater Args : none
Title : set_adapter_r() Usage : my $set_adapter_r= $tmp->set_adapter_r(); Function: Sets the $self->{adapter_right} property Returns : Populates the $self->{adapter_right} property Args : string
Title : get_left_trim() Usage : my $get_left_trim= $tmp->get_left_trim(); Function: Retrieves the left trim number Returns : integer Args : none
Title : set_left_trim() Usage : my $set_left_trim = $tmp->set_left_trim(); Function: Populates the $self->{left_trim} property Returns : $self->{left_trim} Args : integer
Title : get_right_trim() Usage : my $get_right_trim= $tmp->get_right_trim(); Function: gets the right trim number Returns : integer Args : none
Title : set_right_trim() Usage : my $set_right_trim = $tmp->set_right_trim(); Function: Populates the $self->{right_trim} property Returns : $self->{right_trim} Args : integer
Title : get_fasta() Usage : my $get_fasta= $tmp->get_fasta(); Function: Retrieves the get_fasta option Returns : Y or N Args : none
Title : set_fasta() Usage : my $set_fasta = $tmp->set_fasta(); Function: Populates the $self->{fasta_convert} property Returns : $self->{fasta_convert} Args : a command to execute fastA convert or not: Y=yes, N=no
Title : get_rev_com() Usage : my $get_rev_com= $tmp->get_rev_com(); Function: Retrieves the rev_comp option Returns : Y or N Args : none
Title : set_rev_com() Usage : my $set_rev_com = $tmp->set_rev_com(); Function: Populates the $self->{rev_comp} property Returns : $self->{rev_comp} Args : a command to execute rev_comp or not: Y=yes, N=no
Title : get_remove_n() Usage : my $get_remove_n= $tmp->get_remove_n(); Function: Retrieves the command for N removal reads Returns : Y or N Args : none
Title : set_remove_n() Usage : my $set_remove_n = $tmp->set_remove_n(); Function: Populates the $self->{remove_n} property Returns : $self->{remove_n} Args : a command to remove reads with N or not: Y=yes, N=no
Title : get_cleanup() Usage : my $get_cleanup = $tmp->get_cleanup(); Function: returns the value option for cleanup Returns : Y or N Args : none
Title : set_cleanup() Usage : my $set_cleanup = $tmp->set_cleanup("Y"); Function: Populates the $self->{cleanup} property Returns : $self->{cleanup} Args : a command to execute cleanup or not: Y=yes, N=no
Copyright (C) 2017 Damien M. O'Halloran GNU GENERAL PUBLIC LICENSE
To install fastQ_brew, copy and paste the appropriate command in to your terminal.
cpanm
cpanm fastQ_brew
CPAN shell
perl -MCPAN -e shell install fastQ_brew
For more information on module installation, please visit the detailed CPAN module installation guide.