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fastq_masker(1) [debian man page]

FASTQ_MASKER(1) 						   User Commands						   FASTQ_MASKER(1)

NAME
fastq_masker - Masks nucleotides with 'N' (or other character) based on quality DESCRIPTION
usage: fastq_masker [-h] [-v] [-q N] [-r C] [-z] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit 0.0.13.2 by A. Gordon (gordon@cshl.edu) [-h] = This helpful help screen. [-q N] = Quality threshold - nucleotides with lower quality will be masked Default is 10. [-r C] = Replace low-quality nucleotides with character C. Default is 'N' [-z] = Compress output with GZIP. [-i INFILE] = FASTQ input file. default is STDIN. [-o OUTFILE] = FASTQ output file. default is STDOUT. [-v] = Verbose - report number of sequences. If [-o] is specified, report will be printed to STDOUT. If [-o] is not specified (and output goes to STDOUT), report will be printed to STDERR. SEE ALSO
The quality of this automatically generated manpage might be insufficient. It is suggested to visit http://hannonlab.cshl.edu/fastx_toolkit/commandline.html to get a better layout as well as an overview about connected FASTX tools. fastq_masker 0.0.13.2 May 2012 FASTQ_MASKER(1)

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Bio::SeqIO::fastq(3pm)					User Contributed Perl Documentation				    Bio::SeqIO::fastq(3pm)

NAME
Bio::SeqIO::fastq - fastq sequence input/output stream SYNOPSIS
################## pertains to FASTQ parsing only ################## # grabs the FASTQ parser, specifies the Illumina variant my $in = Bio::SeqIO->new(-format => 'fastq-illumina', -file => 'mydata.fq'); # simple 'fastq' format defaults to 'sanger' variant my $out = Bio::SeqIO->new(-format => 'fastq', -file => '>mydata.fq'); # $seq is a Bio::Seq::Quality object while (my $seq = $in->next_seq) { $out->write_seq($seq); # convert Illumina 1.3 to Sanger format } # for 4x faster parsing, one can do something like this for raw data use Bio::Seq::Quality; # $data is a hash reference containing all arguments to be passed to # the Bio::Seq::Quality constructor while (my $data = $in->next_dataset) { # process $data, such as trim, etc my $seq = Bio::Seq::Quality->new(%$data); # for now, write_seq only accepts Bio::Seq::Quality, but may be modified # to allow raw hash references for speed $out->write_seq($data); } DESCRIPTION
This object can transform Bio::Seq and Bio::Seq::Quality objects to and from FASTQ flat file databases. FASTQ is a file format used frequently at the Sanger Centre and in next-gen sequencing to bundle a FASTA sequence and its quality data. A typical FASTQ entry takes the form: @HCDPQ1D0501 GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT..... +HCDPQ1D0501 !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65..... where: @ = descriptor, followed by one or more sequence lines + = optional descriptor (if present, must match first one), followed by one or more qual lines When writing FASTQ output the redundant descriptor following the '+' is by default left off to save disk space. If needed, one can set the quality_header() flag in order for this to be printed. FASTQ and Bio::Seq::Quality mapping FASTQ files have sequence and quality data on single line or multiple lines, and the quality values are single-byte encoded. Data are mapped very simply to Bio::Seq::Quality instances: Data Bio::Seq::Quality method ------------------------------------------------------------------------ first non-whitespace chars in descriptor id^ descriptor line desc^ sequence lines seq quality qual* FASTQ variant namespace ^ first nonwhitespace chars are id(), everything else after (to end of line) is in desc() * Converted to PHRED quality scores where applicable ('solexa') FASTQ variants This parser supports all variants of FASTQ, including Illumina v 1.0 and 1.3: variant note ----------------------------------------------------------- sanger original solexa Solexa, Inc.(2004), aka Illumina 1.0 illumina Illumina 1.3 The variant can be specified by passing by either passing the additional -variant parameter to the constructor: my $in = Bio::SeqIO->new(-format => 'fastq', -variant => 'solexa', -file => 'mysol.fq'); or by passing the format and variant together (Bio::SeqIO will now handle this and convert it accordingly to the proper argument): my $in = Bio::SeqIO->new(-format => 'fastq-solexa', -file => 'mysol.fq'); Variants can be converted back and forth from one another; however, due to the difference in scaling for solexa quality reads, converting from 'illumina' or 'sanger' FASTQ to solexa is not recommended. FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. 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. 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: https://redmine.open-bio.org/projects/bioperl/ AUTHORS - Chris Fields (taken over from Tony Cox) Email: cjfields at bioperl dot org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ Bio::SeqIO interface methods next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function : returns the next sequence in the stream Returns : Bio::Seq::Quality object Args : NONE Status : Stable write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function : writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq::Quality Note : This now conforms to SeqIO spec (module output is same format as next_seq) Status : Stable variant Title : variant Usage : $format = $obj->variant(); Function: Get and set method for the quality sequence variant. This is important for indicating the encoding/decoding to be used for quality data. Current values accepted are: 'sanger' (orginal FASTQ) ASCII encoding from 33-126, PHRED quality score from 0 to 93 'solexa' (aka illumina1.0) ASCII encoding from 59-104, SOLEXA quality score from -5 to 40 'illumina' (aka illumina1.3) ASCII encoding from 64-104, PHRED quality score from 0 to 40 (Derived from the MAQ website): For 'solexa', scores are converted to PHRED qual scores using: $Q = 10 * log(1 + 10 ** (ord($sq) - 64) / 10.0)) / log(10) Returns : string Args : new value, string Plugin-specific methods next_dataset Title : next_dataset Usage : $obj->next_dataset Function : returns a hash reference containing the parsed data Returns : hash reference Args : none Status : Stable write_fastq Title : write_fastq Usage : $stream->write_fastq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq::Quality object Status : Deprecated (delegates to write_seq) write_fasta Title : write_fasta Usage : $stream->write_fasta(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object Note : This method does not currently delegate to Bio::SeqIO::fasta (maybe it should?). Not sure whether we should keep this as a convenience method. Status : Unstable write_qual Title : write_qual Usage : $stream->write_qual(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq::Quality object Note : This method does not currently delegate to Bio::SeqIO::qual (maybe it should?). Not sure whether we should keep this as a convenience method. Status : Unstable validate Title : validate Usage : $obj->validate(0) Function : flag for format/qual range validation - default is 1, validate Returns : Bool (0/1) Args : Bool (0/1) Status : Stable (may be moved to interface) quality_header Title : quality_header Usage : $obj->quality_header Function : flag for printing quality header - default is 0, no header Returns : Bool (0/1) Args : Bool (0/1) Status : Unstable (name may change dep. on feedback) perl v5.14.2 2012-03-02 Bio::SeqIO::fastq(3pm)
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