class Bio::Fastq
Bio::Fastq is a parser for FASTQ format.
Constants
- DefaultFormatName
Default format name
- FLATFILE_SPLITTER
Splitter for
Bio::FlatFile- FormatNames
Available format names.
- Formats
Available format name symbols.
Attributes
definition; ID line (begins with @)
misc lines before the entry (String or nil)
quality as a string
raw sequence data as a String object
Public Class Methods
Creates a new Fastq object from formatted text string.
The format of quality scores should be specified later by using format= method.
Arguments:
-
str: Formatted string (String)
# File lib/bio/db/fastq.rb 383 def initialize(str = nil) 384 return unless str 385 sc = StringScanner.new(str) 386 while !sc.eos? and line = sc.scan(/.*(?:\n|\r|\r\n)?/) 387 unless add_header_line(line) then 388 sc.unscan 389 break 390 end 391 end 392 while !sc.eos? and line = sc.scan(/.*(?:\n|\r|\r\n)?/) 393 unless add_line(line) then 394 sc.unscan 395 break 396 end 397 end 398 @entry_overrun = sc.rest 399 end
Public Instance Methods
Adds a header line if the header data is not yet given and the given line is suitable for header. Returns self if adding header line is succeeded. Otherwise, returns false (the line is not added).
# File lib/bio/db/fastq.rb 324 def add_header_line(line) 325 @header ||= "" 326 if line[0,1] == "@" then 327 false 328 else 329 @header.concat line 330 self 331 end 332 end
Adds a line to the entry if the given line is regarded as a part of the current entry.
# File lib/bio/db/fastq.rb 339 def add_line(line) 340 line = line.chomp 341 if !defined? @definition then 342 if line[0, 1] == "@" then 343 @definition = line[1..-1] 344 else 345 @definition = line 346 @parse_errors ||= [] 347 @parse_errors.push Error::No_atmark.new 348 end 349 return self 350 end 351 if defined? @definition2 then 352 @quality_string ||= '' 353 if line[0, 1] == "@" and 354 @quality_string.size >= @sequence_string.size then 355 return false 356 else 357 @quality_string.concat line 358 return self 359 end 360 else 361 @sequence_string ||= '' 362 if line[0, 1] == '+' then 363 @definition2 = line[1..-1] 364 else 365 @sequence_string.concat line 366 end 367 return self 368 end 369 raise "Bug: should not reach here!" 370 end
Identifier of the entry. Normally, the first word of the ID line.
# File lib/bio/db/fastq.rb 446 def entry_id 447 unless defined? @entry_id then 448 eid = @definition.strip.split(/\s+/)[0] || @definition 449 @entry_id = eid 450 end 451 @entry_id 452 end
Estimated probability of error for each base.
- Returns
-
(Array containing Float) error probability values
# File lib/bio/db/fastq.rb 529 def error_probabilities 530 unless defined? @error_probabilities then 531 self.format ||= self.class::DefaultFormatName 532 a = @format.q2p(self.quality_scores) 533 @error_probabilities = a 534 end 535 @error_probabilities 536 end
Format name. One of “fastq-sanger”, “fastq-solexa”, “fastq-illumina”, or nil (when not specified).
- Returns
-
(String or nil) format name
# File lib/bio/db/fastq.rb 497 def format 498 ((defined? @format) && @format) ? @format.name : nil 499 end
Specify the format. If the format is not found, raises RuntimeError.
Available formats are:
"fastq-sanger" or :fastq_sanger "fastq-solexa" or :fastq_solexa "fastq-illumina" or :fastq_illumina
Arguments:
-
(required) name: format name (String or Symbol).
- Returns
-
(String) format name
# File lib/bio/db/fastq.rb 476 def format=(name) 477 if name then 478 f = FormatNames[name] || Formats[name] 479 if f then 480 reset_state 481 @format = f.instance 482 self.format 483 else 484 raise "unknown format" 485 end 486 else 487 reset_state 488 nil 489 end 490 end
Masks low quality sequence regions. For each sequence position, if the quality score is smaller than the threshold, the sequence in the position is replaced with mask_char.
Note: This method does not care quality_score_type.
Arguments:
-
(required) threshold : (Numeric) threshold
-
(optional) mask_char : (String) character used for masking
- Returns
-
Bio::Sequenceobject
# File lib/bio/db/fastq.rb 668 def mask(threshold, mask_char = 'n') 669 to_biosequence.mask_with_quality_score(threshold, mask_char) 670 end
length of naseq
# File lib/bio/db/fastq.rb 433 def nalen 434 naseq.length 435 end
returns Bio::Sequence::NA
# File lib/bio/db/fastq.rb 425 def naseq 426 unless defined? @naseq then 427 @naseq = Bio::Sequence::NA.new(@sequence_string) 428 end 429 @naseq 430 end
The meaning of the quality scores. It may be one of :phred, :solexa, or nil.
# File lib/bio/db/fastq.rb 504 def quality_score_type 505 self.format ||= self.class::DefaultFormatName 506 @format.quality_score_type 507 end
Quality score for each base. For “fastq-sanger” or “fastq-illumina”, it is PHRED score. For “fastq-solexa”, it is Solexa score.
- Returns
-
(Array containing Integer) quality score values
# File lib/bio/db/fastq.rb 515 def quality_scores 516 unless defined? @quality_scores then 517 self.format ||= self.class::DefaultFormatName 518 s = @format.str2scores(@quality_string) 519 @quality_scores = s 520 end 521 @quality_scores 522 end
returns Bio::Sequence::Generic
# File lib/bio/db/fastq.rb 438 def seq 439 unless defined? @seq then 440 @seq = Bio::Sequence::Generic.new(@sequence_string) 441 end 442 @seq 443 end
Returns sequence as a Bio::Sequence object.
Note: If you modify the returned Bio::Sequence object, the sequence or definition in this Fastq object might also be changed (but not always be changed) because of efficiency.
# File lib/bio/db/fastq.rb 653 def to_biosequence 654 Bio::Sequence.adapter(self, Bio::Sequence::Adapter::Fastq) 655 end
Returns Fastq formatted string constructed from instance variables. The string will always be consisted of four lines without wrapping of the sequence and quality string, and the third-line is always only contains “+”. This may be different from initial entry.
Note that use of the method may be inefficient and may lose performance because new string object is created every time it is called. For showing an entry as-is, consider using Bio::FlatFile#entry_raw. For output with various options, use Bio::Sequence#output(:fastq).
# File lib/bio/db/fastq.rb 420 def to_s 421 "@#{@definition}\n#{@sequence_string}\n+\n#{@quality_string}\n" 422 end
Format validation.
If an array is given as the argument, when errors are found, error objects are pushed to the array. Currently, following errors may be added to the array. (All errors are under the Bio::Fastq namespace, for example, Bio::Fastq::Error::Diff_ids).
Error::Diff_ids – the identifier in the two lines are different Error::Long_qual – length of quality is longer than the sequence Error::Short_qual – length of quality is shorter than the sequence Error::No_qual – no quality characters found Error::No_seq – no sequence found Error::Qual_char – invalid character in the quality Error::Seq_char – invalid character in the sequence Error::Qual_range – quality score value out of range Error::No_ids – sequence identifier not found Error::No_atmark – the first identifier does not begin with “@” Error::Skipped_unformatted_lines – the parser skipped unformatted lines that could not be recognized as FASTQ format
Arguments:
-
(optional) errors: (Array or nil) an array for pushing error messages. The array should be empty.
- Returns
-
true:no error, false: containing error.
# File lib/bio/db/fastq.rb 562 def validate_format(errors = nil) 563 err = [] 564 565 # if header exists, the format might be broken. 566 if defined? @header and @header and !@header.strip.empty? then 567 err.push Error::Skipped_unformatted_lines.new 568 end 569 570 # if parse errors exist, adding them 571 if defined? @parse_errors and @parse_errors then 572 err.concat @parse_errors 573 end 574 575 # check if identifier exists, and identifier matches 576 if !defined?(@definition) or !@definition then 577 err.push Error::No_ids.new 578 elsif defined?(@definition2) and 579 !@definition2.to_s.empty? and 580 @definition != @definition2 then 581 err.push Error::Diff_ids.new 582 end 583 584 # check if sequence exists 585 has_seq = true 586 if !defined?(@sequence_string) or !@sequence_string then 587 err.push Error::No_seq.new 588 has_seq = false 589 end 590 591 # check if quality exists 592 has_qual = true 593 if !defined?(@quality_string) or !@quality_string then 594 err.push Error::No_qual.new 595 has_qual = false 596 end 597 598 # sequence and quality length check 599 if has_seq and has_qual then 600 slen = @sequence_string.length 601 qlen = @quality_string.length 602 if slen > qlen then 603 err.push Error::Short_qual.new 604 elsif qlen > slen then 605 err.push Error::Long_qual.new 606 end 607 end 608 609 # sequence character check 610 if has_seq then 611 sc = StringScanner.new(@sequence_string) 612 while sc.scan_until(/[ \x00-\x1f\x7f-\xff]/n) 613 err.push Error::Seq_char.new(sc.pos - sc.matched_size) 614 end 615 end 616 617 # sequence character check 618 if has_qual then 619 fmt = if defined?(@format) and @format then 620 @format.name 621 else 622 nil 623 end 624 re = case fmt 625 when 'fastq-sanger' 626 /[^\x21-\x7e]/n 627 when 'fastq-solexa' 628 /[^\x3b-\x7e]/n 629 when 'fastq-illumina' 630 /[^\x40-\x7e]/n 631 else 632 /[ \x00-\x1f\x7f-\xff]/n 633 end 634 sc = StringScanner.new(@quality_string) 635 while sc.scan_until(re) 636 err.push Error::Qual_char.new(sc.pos - sc.matched_size) 637 end 638 end 639 640 # if "errors" is given, set errors 641 errors.concat err if errors 642 # returns true if no error; otherwise, returns false 643 err.empty? ? true : false 644 end