-# Copyright (C) 2007-2011 Martin A. Hansen.
+# Copyright (C) 2007-2013 Martin A. Hansen.
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
require 'pp'
require 'maasha/filesys'
require 'maasha/seq'
+require 'maasha/cigar'
REGEX_HEADER = Regexp.new(/^@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/)
REGEX_COMMENT = Regexp.new(/^@CO\t.*/)
bp = {}
bp[:REC_TYPE] = 'SAM'
- bp[:Q_ID] = sam[:QNAME]
- bp[:STRAND] = sam[:FLAG].revcomp? ? '-' : '+'
- bp[:S_ID] = sam[:RNAME]
- bp[:S_BEG] = sam[:POS]
- bp[:MAPQ] = sam[:MAPQ]
- bp[:CIGAR] = sam[:CIGAR]
+ bp[:Q_ID] = sam[:QNAME]
+ bp[:STRAND] = sam[:FLAG].revcomp? ? '-' : '+'
+ bp[:S_ID] = sam[:RNAME]
+ bp[:S_BEG] = sam[:POS]
+ bp[:S_END] = sam[:POS] + sam[:SEQ].length - 1
+ bp[:MAPQ] = sam[:MAPQ]
+ bp[:CIGAR] = sam[:CIGAR].to_s
unless sam[:RNEXT] == '*'
bp[:Q_ID2] = sam[:RNEXT]
bp[:SEQ] = sam[:SEQ].seq
unless sam[:SEQ].qual.nil?
- bp[:SCORES] = sam[:SEQ].convert_phred2illumina!.qual
+ bp[:SCORES] = sam[:SEQ].qual
end
- if sam.has_key? :NM and sam[:NM].to_i > 0
+ if sam[:NM] and sam[:NM].to_i > 0
+ bp[:NM] = sam[:NM]
+ bp[:MD] = sam[:MD]
bp[:ALIGN] = self.align_descriptors(sam)
end
bp
end
- # Create align descriptors according to the KISS format description:
+ # Class method to create a new SAM entry from a Biopiece record.
+ # FIXME
+ def self.new_bp(bp)
+ qname = bp[:Q_ID]
+ flag = 0
+ rname = bp[:S_ID]
+ pos = bp[:S_BEG]
+ mapq = bp[:MAPQ]
+ cigar = bp[:CIGAR]
+ rnext = bp[:Q_ID2] || '*'
+ pnext = bp[:S_BEG2] || 0
+ tlen = bp[:TLEN] || 0
+ seq = bp[:SEQ]
+ qual = bp[:SCORES] || '*'
+ nm = "NM:i:#{bp[:NM]}" if bp[:NM]
+ md = "MD:Z:#{bp[:MD]}" if bp[:MD]
+
+ flag |= FLAG_REVCOMP if bp[:STRAND] == '+'
+
+ if qname && flag && rname && pos && mapq && cigar && rnext && pnext && tlen && seq && qual
+ ary = [qname, flag, rname, pos, mapq, cigar, rnext, pnext, tlen, seq, qual]
+ ary << nm if nm
+ ary << md if md
+
+ ary.join("\t")
+ end
+ end
+
+ # Create alignment descriptors according to the KISS
+ # format description:
# http://code.google.com/p/biopieces/wiki/KissFormat
def self.align_descriptors(sam)
- offset = 0
- insertions = 0
- align = []
+ offset = 0
+ align = []
# Insertions
- sam[:CIGAR].scan(/([0-9]+)([MIDNSHPX=])/).each do |len, op|
- len = len.to_i
-
+ sam[:CIGAR].each do |len, op|
if op == 'I'
(0 ... len).each_with_index do |i|
nt = sam[:SEQ].seq[offset + i]
if m =~ /\d+/ # Matches
offset += m.to_i
elsif m[0] == '^' # Deletions
- m[1 .. -1].each_char do |nt|
- align << [offset, "#{nt}>-"]
-
- deletions += 1
- offset += 1
+ m.each_char do |nt|
+ unless nt == '^'
+ align << [offset, "#{nt}>-"]
+ deletions += 1
+ offset += 1
+ end
end
- else # Mismatches
+ else # Mismatches
m.each_char do |nt|
nt2 = sam[:SEQ].seq[offset - deletions]
end
end
- align.sort_by { |a| a.first }.map { |k,v| "#{k}:#{v}" }.join(",")
+ align.sort_by { |a| a.first }.map { |k, v| "#{k}:#{v}" }.join(",")
end
# Method to initialize a Sam object.
@header[:SQ][:SN] = Hash.new unless @header[:SQ][:SN].is_a? Hash
- if @header[:SQ][:SN].has_key? seq_name
+ if @header[:SQ][:SN][seq_name]
raise SamError, "Non-unique sequence name: #{seq_name}"
else
@header[:SQ][:SN][seq_name] = hash
end
end
- if hash.has_key? :FO
+ if hash[:FO]
unless hash[:FO] =~ /^\*|[ACMGRSVTWYHKDBN]+$/
raise SamError, "Bad flow order: #{hash[:FO]}"
end
end
- if hash.has_key? :PL
+ if hash[:PL]
unless hash[:PL] =~ /^(CAPILLARY|LS454|ILLUMINA|SOLID|HELICOS|IONTORRENT|PACBIO)$/
raise SamError, "Bad platform: #{hash[:PL]}"
end
@header[:RG][:ID] = Hash.new unless @header[:RG][:ID].is_a? Hash
- if @header[:RG][:ID].has_key? id
+ if @header[:RG][:ID][id]
raise SamError, "Non-unique read group identifier: #{id}"
else
@header[:RG][:ID][id] = hash
@header[:PG][:ID] = Hash.new unless @header[:PG][:ID].is_a? Hash
- if @header[:PG][:ID].has_key? id
+ if @header[:PG][:ID][id]
raise SamError, "Non-unique program record identifier: #{id}"
else
@header[:PG][:ID][id] = hash
check_rname(rname)
check_pos(pos)
check_mapq(mapq)
- check_cigar(cigar, seq)
check_rnext(rnext)
check_pnext(pnext)
check_tlen(tlen)
entry[:RNAME] = rname
entry[:POS] = pos
entry[:MAPQ] = mapq
- entry[:CIGAR] = cigar
+ entry[:CIGAR] = Cigar.new(cigar)
entry[:RNEXT] = rnext
entry[:PNEXT] = pnext
entry[:TLEN] = tlen
- entry[:SEQ] = (qual == '*') ? Seq.new(qname, seq) : Seq.new(qname, seq, qual)
+ entry[:SEQ] = (qual == '*') ? Seq.new(seq_name: qname, seq: seq) : Seq.new(seq_name: qname, seq: seq, qual: qual)
entry[:QUAL] = qual
# Optional fields - where some are really important! HATE HATE HATE SAM!!!
fields[11 .. -1].each do |field|
tag, type, val = field.split(':')
- raise SamError, "Non-unique optional tag: #{tag}" if entry.has_key? tag.to_sym
+ raise SamError, "Non-unique optional tag: #{tag}" if entry[tag.to_sym]
# A [!-~] Printable character
raise SamError, "Bad rname: #{rname}" unless rname =~ /^(\*|[!-()+-<>-~][!-~]*)$/
unless @header.empty? or rname == '*'
- unless @header[:SQ][:SN].has_key? rname.to_sym
+ unless @header[:SQ][:SN][rname.to_sym]
raise SamError, "rname not found in header hash: #{rname}"
end
end
raise SamError, "Bad mapq: #{mapq}" unless (0 .. 2**8 - 1).include? mapq
end
- # Method to check cigar string.
- def check_cigar(cigar, seq)
- raise SamError, "Bad cigar: #{cigar}" unless cigar =~ /^(\*|([0-9]+[MIDNSHPX=])+)$/
-
- unless cigar == '*'
- check_cigar_hard_clip(cigar)
- check_cigar_soft_clip(cigar)
- check_cigar_seq_len(cigar, seq) unless seq == '*'
- end
- end
-
- # Method to check cigar hard clipping only at ends.
- def check_cigar_hard_clip(cigar)
- if cigar.gsub(/^[0-9]+H|[0-9]+H$/, "").match('H')
- raise SamError, "Bad cigar with internal H: #{cigar}"
- end
- end
-
- # Method to check cigar soft clipping only at ends or H.
- def check_cigar_soft_clip(cigar)
- if cigar.gsub(/^[0-9]+H|[0-9]+H$/, "").gsub(/^[0-9]+S|[0-9]+S$/, "").match('S')
- raise SamError, "Bad cigar with internal S: #{cigar}"
- end
- end
-
- # Method to check cigar length matches sequence length.
- def check_cigar_seq_len(cigar, seq)
- cigar_len = 0
-
- cigar.scan(/([0-9]+)([MIDNSHPX=])/).each do |len, op|
- cigar_len += len.to_i if op =~ /[MISX=]/
- end
-
- if cigar_len != seq.length
- raise SamError, "cigar and sequence length mismatch: #{cigar_len} != #{seq.length}"
- end
- end
-
# Method to check if rnext, when not '*' or '='
# and @SQ header lines are present, is located
# in the header hash.
raise SamError, "Bad rnext: #{rnext}" unless rnext =~ /^(\*|=|[!-()+-<>-~][!-~]*)$/
unless @header.empty? or rnext == '*' or rnext == '='
- unless @header[:SQ][:SN].has_key? rnext.to_sym
+ unless @header[:SQ][:SN][rnext.to_sym]
raise SamError, "rnext not found in header hash: #{rnext}"
end
end
# Method to test if template have
# multiple fragments in sequencing.
def multi?
- flag & FLAG_MULTI
+ (flag & FLAG_MULTI) == 0
end
# Method to test if each fragment
# properly aligned according to the aligner.
def aligned?
- flag & FLAG_ALIGNED
+ (flag & FLAG_ALIGNED) == 0
end
# Method to test if the fragment was unmapped.
def unmapped?
- flag & FLAG_UNMAPPED
+ (flag & FLAG_UNMAPPED) == 0
end
# Method to test if the next fragment was unmapped.
def next_unmapped?
- flag & FLAG_NEXT_UNMAPPED
+ (flag & FLAG_NEXT_UNMAPPED) == 0
end
# Method to test if the fragment was reverse complemented.
def revcomp?
- flag & FLAG_REVCOMP
+ (flag & FLAG_REVCOMP) == 0
end
# Method to test if the next fragment was reverse complemented.
def next_revcomp?
- flag & FLAG_NEXT_REVCOMP
+ (flag & FLAG_NEXT_REVCOMP) == 0
end
# Method to test if the fragment was first in the template.
def first?
- flag & FLAG_FIRST
+ (flag & FLAG_FIRST) == 0
end
# Method to test if the fragment was last in the template.
def last?
- flag & FLAG_LAST
+ (flag & FLAG_LAST) == 0
end
# Method to test for secondary alignment.
def secondary_alignment?
- flag & FLAG_SECONDARY_ALIGNMENT
+ (flag & FLAG_SECONDARY_ALIGNMENT) == 0
end
# Method to test for quality fail.
def quality_fail?
- flag & FLAG_QUALITY_FAIL
+ (flag & FLAG_QUALITY_FAIL) == 0
end
# Method to test for PCR or optical duplicates.
def duplicates?
- flag & FLAG_DUPLICATES
+ (flag & FLAG_DUPLICATES) == 0
end
end
end
projects / biopieces.git / blobdiff