/tools/next_gen_conversion/solid2fastq.py

  1#!/usr/bin/env python
  2
  3import sys
  4import string
  5import optparse
  6import tempfile
  7import sqlite3
  8
  9def stop_err( msg ):
 10    sys.stderr.write( msg )
 11    sys.exit()
 12    
 13def solid2sanger( quality_string, min_qual = 0 ):
 14    sanger = ""
 15    quality_string = quality_string.rstrip( " " )
 16    for qv in quality_string.split(" "):
 17        try:
 18            if int( qv ) < 0:
 19                qv = '0'
 20            if int( qv ) < min_qual:
 21                return False
 22                break
 23            sanger += chr( int( qv ) + 33 )
 24        except:
 25            pass    
 26    return sanger
 27
 28def Translator(frm='', to='', delete='', keep=None):
 29    allchars = string.maketrans('','')
 30    if len(to) == 1:
 31        to = to * len(frm)
 32    trans = string.maketrans(frm, to)
 33    if keep is not None:
 34        delete = allchars.translate(allchars, keep.translate(allchars, delete))
 35    def callable(s):
 36        return s.translate(trans, delete)
 37    return callable
 38    
 39def merge_reads_qual( f_reads, f_qual, f_out, trim_name=False, out='fastq', double_encode = False, trim_first_base = False, pair_end_flag = '', min_qual = 0, table_name=None ):
 40 
 41    # Reads from two files f_csfasta (reads) and f_qual (quality values) and produces output in three formats depending on out parameter,
 42    # which can have three values: fastq, txt, and db
 43    # fastq = fastq format
 44    # txt = space delimited format with defline, reads, and qvs
 45    # dp = dump data into sqlite3 db. 
 46    # IMPORTNAT! If out = db two optins must be provided:
 47    #   1. f_out must be a db connection object initialized with sqlite3.connect()
 48    #   2. table_name must be provided
 49    
 50    if out == 'db':
 51        cursor = f_out.cursor()
 52        sql = "create table %s (name varchar(50) not null, read blob, qv blob)" % table_name
 53        cursor.execute(sql)
 54    
 55    lines = []
 56    line = " "
 57    while line:
 58        for f in [ f_reads, f_qual ]:
 59            line = f.readline().rstrip( '\n\r' )
 60            while line.startswith( '#' ):
 61                line = f.readline().rstrip( '\n\r' )
 62            lines.append( line ) 
 63            
 64        if lines[0].startswith( '>' ):
 65            defline = lines[0][1:]
 66            if trim_name and ( defline[ len( defline )-3: ] == "_F3" or defline[ len( defline )-3: ] == "_R3" ):
 67                defline = defline[ : len( defline )-3 ]
 68                
 69        else:
 70
 71            if trim_first_base:
 72                lines[0] = lines[0][1:]
 73            if double_encode:
 74                de = Translator(frm="0123.", to="ACGTN")
 75                lines[0] = de(lines[0])
 76            qual = solid2sanger( lines[1], int( min_qual ) )
 77            if qual:
 78                if out == 'fastq':
 79                    f_out.write( "@%s%s\n%s\n+\n%s\n" % ( defline, pair_end_flag, lines[0], qual ) ) 
 80                if out == 'txt':
 81                    f_out.write( '%s %s %s\n' % (defline, lines[0], qual ) )
 82                if out == 'db':
 83                    cursor.execute('insert into %s values("%s","%s","%s")' % (table_name, defline, lines[0], qual ) )     
 84        lines = []
 85
 86def main():
 87
 88    usage = "%prog --fr F3.csfasta --fq R3.csfasta --fout fastq_output_file [option]"
 89    parser = optparse.OptionParser(usage=usage)
 90    
 91        
 92    parser.add_option(
 93        '--fr','--f_reads',
 94        metavar="F3_CSFASTA_FILE",
 95        dest='fr',
 96        help='Name of F3 file with color space reads')
 97        
 98    parser.add_option(
 99        '--fq','--f_qual',
100        metavar="F3_QUAL_FILE",
101        dest='fq',
102        help='Name of F3 file with color quality values')
103        
104    parser.add_option(
105        '--fout','--f3_fastq_output',
106        metavar="F3_OUTPUT",
107        dest='fout',
108        help='Name for F3 output file')
109                
110    parser.add_option(
111        '--rr','--r_reads',
112        metavar="R3_CSFASTA_FILE",
113        dest='rr',
114        default = False,
115        help='Name of R3 file with color space reads')
116        
117    parser.add_option(
118        '--rq','--r_qual',
119        metavar="R3_QUAL_FILE",
120        dest='rq',
121        default = False,
122        help='Name of R3 file with color quality values')
123        
124    parser.add_option(
125        '--rout',
126        metavar="R3_OUTPUT",
127        dest='rout',
128        help='Name for F3 output file')
129    
130    parser.add_option(
131        '-q','--min_qual',
132        dest='min_qual',
133        default = '-1000',
134        help='Minimum quality threshold for printing reads. If a read contains a single call with QV lower than this value, it will not be reported. Default is -1000')
135        
136    parser.add_option(
137        '-t','--trim_name',
138        dest='trim_name',
139        action='store_true',
140        default = False,
141        help='Trim _R3 and _F3 off read names. Default is False')
142    
143    parser.add_option(
144        '-f','--trim_first_base',
145        dest='trim_first_base',
146        action='store_true',
147        default = False,
148        help='Remove the first base of reads in color-space. Default is False')
149        
150    parser.add_option(
151        '-d','--double_encode',
152        dest='de',
153        action='store_true',
154        default = False,
155        help='Double encode color calls as nucleotides: 0123. becomes ACGTN. Default is False')
156    
157    options, args = parser.parse_args()
158    
159    if not ( options.fout and options.fr and options.fq ):
160        parser.error("""
161        One or more of the three required paremetrs is missing:
162        (1) --fr F3.csfasta file
163        (2) --fq F3.qual file
164        (3) --fout name of output file
165        Use --help for more info
166        """)
167
168    fr =  open ( options.fr , 'r' ) 
169    fq =  open ( options.fq , 'r' ) 
170    f_out = open ( options.fout , 'w' )
171    
172    if options.rr and options.rq:
173        rr =  open ( options.rr , 'r' ) 
174        rq =  open ( options.rq , 'r' ) 
175        if not options.rout:
176            parser.error("Provide the name for f3 output using --rout option. Use --help for more info")
177        r_out = open ( options.rout, 'w' )
178    
179        db = tempfile.NamedTemporaryFile()
180        
181        try:
182            con = sqlite3.connect(db.name)
183            cur = con.cursor()
184        except:
185            stop_err('Cannot connect to %s\n') % db.name
186    
187         
188        merge_reads_qual( fr, fq, con, trim_name=options.trim_name, out='db', double_encode=options.de, trim_first_base=options.trim_first_base, min_qual=options.min_qual, table_name="f3" )
189        merge_reads_qual( rr, rq, con, trim_name=options.trim_name, out='db', double_encode=options.de, trim_first_base=options.trim_first_base, min_qual=options.min_qual, table_name="r3" )
190        cur.execute('create index f3_name on f3( name )')
191        cur.execute('create index r3_name on r3( name )')
192         
193        cur.execute('select * from r3,f3 where f3.name = r3.name')
194        for item in cur:
195            f_out.write( "@%s%s\n%s\n+\n%s\n" % (item[0], "/1", item[1], item[2]) )
196            r_out.write( "@%s%s\n%s\n+\n%s\n" % (item[3], "/2", item[4], item[5]) )
197        
198            
199    else:
200        merge_reads_qual( fr, fq, f_out, trim_name=options.trim_name, out='fastq', double_encode = options.de, trim_first_base = options.trim_first_base, min_qual=options.min_qual )
201        
202    
203      
204    f_out.close()
205
206if __name__ == "__main__":
207    main()
208    
209