- We are hiring!
-
- Thanks to your support and an unprecedented level of usage, we are looking for an experienced software developer to join our team. For more information about this position, please, click here. +
- Thanks to your support and an unprecedented level of usage, we are looking for an experienced software developer to join our team. For more information about this position, please, click here. +
+
+
+
-
Galaxy in 2010...
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+ 
+ 
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+ 
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converter
- gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v
+ gunzip -cf $input | fastq_to_fasta -Q 33 $SKIPN $RENAMESEQ -o $output -v
diff --git a/tools/fastx_toolkit/fastx_collapser.xml b/tools/fastx_toolkit/fastx_collapser.xml
index e879ad265cd..7c16e8855a9 100644
--- a/tools/fastx_toolkit/fastx_collapser.xml
+++ b/tools/fastx_toolkit/fastx_collapser.xml
@@ -1,6 +1,6 @@
sequences
- zcat -f '$input' | fastx_collapser -v -o '$output'
+ zcat -f '$input' | fastx_collapser -Q 33 -v -o '$output'
diff --git a/tools/next_gen_conversion/solid2fastq.py b/tools/next_gen_conversion/solid2fastq.py
new file mode 100644
index 00000000000..6bddab5d034
--- /dev/null
+++ b/tools/next_gen_conversion/solid2fastq.py
@@ -0,0 +1,210 @@
+#!/usr/bin/env python
+
+import sys
+import string
+import optparse
+import tempfile
+import sqlite3
+
+def stop_err( msg ):
+ sys.stderr.write( msg )
+ sys.exit()
+
+def solid2sanger( quality_string, min_qual = 0 ):
+ sanger = ""
+ quality_string = quality_string.rstrip( " " )
+ for qv in quality_string.split(" "):
+ try:
+ if int( qv ) < 0:
+ qv = '0'
+ if int( qv ) < min_qual:
+ return False
+ break
+ sanger += chr( int( qv ) + 33 )
+ except:
+ pass
+ return sanger
+
+def Translator(frm='', to='', delete='', keep=None):
+ allchars = string.maketrans('','')
+ if len(to) == 1:
+ to = to * len(frm)
+ trans = string.maketrans(frm, to)
+ if keep is not None:
+ delete = allchars.translate(allchars, keep.translate(allchars, delete))
+ def callable(s):
+ return s.translate(trans, delete)
+ return callable
+
+def 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 ):
+
+ # Reads from two files f_csfasta (reads) and f_qual (quality values) and produces output in three formats depending on out parameter,
+ # which can have three values: fastq, txt, and db
+ # fastq = fastq format
+ # txt = space delimited format with defline, reads, and qvs
+ # dp = dump data into sqlite3 db.
+ # IMPORTNAT! If out = db two optins must be provided:
+ # 1. f_out must be a db connection object initialized with sqlite3.connect()
+ # 2. table_name must be provided
+
+ if out == 'db':
+ cursor = f_out.cursor()
+ sql = "create table %s (name varchar(50) not null, read blob, qv blob)" % table_name
+ cursor.execute(sql)
+
+ lines = []
+ line = " "
+ while line:
+ for f in [ f_reads, f_qual ]:
+ line = f.readline().rstrip( '\n\r' )
+ while line.startswith( '#' ):
+ line = f.readline().rstrip( '\n\r' )
+ lines.append( line )
+
+ if lines[0].startswith( '>' ):
+ defline = lines[0][1:]
+ if trim_name and ( defline[ len( defline )-3: ] == "_F3" or defline[ len( defline )-3: ] == "_R3" ):
+ defline = defline[ : len( defline )-3 ]
+
+ else:
+
+ if trim_first_base:
+ lines[0] = lines[0][1:]
+ if double_encode:
+ de = Translator(frm="0123.", to="ACGTN")
+ lines[0] = de(lines[0])
+ qual = solid2sanger( lines[1], int( min_qual ) )
+ if qual:
+ if out == 'fastq':
+ f_out.write( "@%s%s\n%s\n+\n%s\n" % ( defline, pair_end_flag, lines[0], qual ) )
+ if out == 'txt':
+ f_out.write( '%s %s %s\n' % (defline, lines[0], qual ) )
+ if out == 'db':
+ cursor.execute('insert into %s values("%s","%s","%s")' % (table_name, defline, lines[0], qual ) )
+ lines = []
+
+def main():
+
+ usage = "%prog --fr F3.csfasta --fq R3.csfasta --fout fastq_output_file [option]"
+ parser = optparse.OptionParser(usage=usage)
+
+
+ parser.add_option(
+ '--fr','--f_reads',
+ metavar="F3_CSFASTA_FILE",
+ dest='fr',
+ help='Name of F3 file with color space reads')
+
+ parser.add_option(
+ '--fq','--f_qual',
+ metavar="F3_QUAL_FILE",
+ dest='fq',
+ help='Name of F3 file with color quality values')
+
+ parser.add_option(
+ '--fout','--f3_fastq_output',
+ metavar="F3_OUTPUT",
+ dest='fout',
+ help='Name for F3 output file')
+
+ parser.add_option(
+ '--rr','--r_reads',
+ metavar="R3_CSFASTA_FILE",
+ dest='rr',
+ default = False,
+ help='Name of R3 file with color space reads')
+
+ parser.add_option(
+ '--rq','--r_qual',
+ metavar="R3_QUAL_FILE",
+ dest='rq',
+ default = False,
+ help='Name of R3 file with color quality values')
+
+ parser.add_option(
+ '--rout',
+ metavar="R3_OUTPUT",
+ dest='rout',
+ help='Name for F3 output file')
+
+ parser.add_option(
+ '-q','--min_qual',
+ dest='min_qual',
+ default = '-1000',
+ 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')
+
+ parser.add_option(
+ '-t','--trim_name',
+ dest='trim_name',
+ action='store_true',
+ default = False,
+ help='Trim _R3 and _F3 off read names. Default is False')
+
+ parser.add_option(
+ '-f','--trim_first_base',
+ dest='trim_first_base',
+ action='store_true',
+ default = False,
+ help='Remove the first base of reads in color-space. Default is False')
+
+ parser.add_option(
+ '-d','--double_encode',
+ dest='de',
+ action='store_true',
+ default = False,
+ help='Double encode color calls as nucleotides: 0123. becomes ACGTN. Default is False')
+
+ options, args = parser.parse_args()
+
+ if not ( options.fout and options.fr and options.fq ):
+ parser.error("""
+ One or more of the three required paremetrs is missing:
+ (1) --fr F3.csfasta file
+ (2) --fq F3.qual file
+ (3) --fout name of output file
+ Use --help for more info
+ """)
+
+ fr = open ( options.fr , 'r' )
+ fq = open ( options.fq , 'r' )
+ f_out = open ( options.fout , 'w' )
+
+ if options.rr and options.rq:
+ rr = open ( options.rr , 'r' )
+ rq = open ( options.rq , 'r' )
+ if not options.rout:
+ parser.error("Provide the name for f3 output using --rout option. Use --help for more info")
+ r_out = open ( options.rout, 'w' )
+
+ db = tempfile.NamedTemporaryFile()
+ print db.name
+
+ try:
+ con = sqlite3.connect(db.name)
+ cur = con.cursor()
+ except:
+ stop_err('Cannot connect to %s\n') % db.name
+
+
+ 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" )
+ 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" )
+ cur.execute('create index f3_name on f3( name )')
+ cur.execute('create index r3_name on r3( name )')
+
+ cur.execute('select * from r3,f3 where f3.name = r3.name')
+ for item in cur:
+ f_out.write( "@%s%s\n%s\n+\n%s\n" % (item[0], "/1", item[1], item[2]) )
+ r_out.write( "@%s%s\n%s\n+\n%s\n" % (item[3], "/2", item[4], item[5]) )
+
+
+ else:
+ 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 )
+
+
+
+ f_out.close()
+
+if __name__ == "__main__":
+ main()
+
+
\ No newline at end of file
diff --git a/tools/next_gen_conversion/solid2fastq.xml b/tools/next_gen_conversion/solid2fastq.xml
new file mode 100644
index 00000000000..efe58f89715
--- /dev/null
+++ b/tools/next_gen_conversion/solid2fastq.xml
@@ -0,0 +1,159 @@
+
+ SOLiD output to fastq
+
+ #if $is_run.paired == "no" #solid2fastq.py --fr=$input1 --fq=$input2 --fout=$out_file1 -q $qual $trim_name $trim_first_base $double_encode
+ #elif $is_run.paired == "yes" #solid2fastq.py --fr=$input1 --fq=$input2 --fout=$out_file1 --rr=$input3 --rq=$input4 --rout=$out_file2 -q $qual $trim_name $trim_first_base $double_encode
+ #end if#
+
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+ is_run['paired'] == 'yes'
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+
+**What it does**
+
+Converts output of SOLiD instrument (versions 3.5 and earlier) to fastq format suitable for bowtie, bwa, and PerM mappers.
+
+--------
+
+**Input datasets**
+
+Below are examples of forward (F3) reads and quality scores:
+
+Reads::
+
+ >1831_573_1004_F3
+ T00030133312212111300011021310132222
+ >1831_573_1567_F3
+ T03330322230322112131010221102122113
+
+Quality scores::
+
+ >1831_573_1004_F3
+ 4 29 34 34 32 32 24 24 20 17 10 34 29 20 34 13 30 34 22 24 11 28 19 17 34 17 24 17 25 34 7 24 14 12 22
+ >1831_573_1567_F3
+ 8 26 31 31 16 22 30 31 28 29 22 30 30 31 32 23 30 28 28 31 19 32 30 32 19 8 32 10 13 6 32 10 6 16 11
+
+
+**Mate pairs**
+
+If your data is from a mate-paired run, you will have one additional read and quality datasets that will look similar to the ones above with one exception: the names of reads will be ending with "_R3".
+In this case choose **Yes** from the *Is this a mate-pair run?* drop down and you will be able to select R reads. When processing mate pairs this tool generated two output files: one for F3 reads and the other for R3 reads.
+The reads are guaranteed to be paired -- mated reads will be in the same position in F3 and R3 fastq file. However, because pairing is verified it may take a while to process an entire SOLiD runs (several hours).
+
+------
+
+**Explanation of parameters**
+
+**Remove reads containing color qualities below this value** - any read that contains as least one color call with quality lower than the specified value **will not** be reported.
+
+**Trim trailing "_F3" and "_R3"?** - does just that. Not necessary for bowtie. Required for BWA.
+
+**Trim first base?** - SOLiD reads contain an adapter base such as the first T in this read::
+
+ >1831_573_1004_F3
+ T00030133312212111300011021310132222
+
+this option removes this base leaving only color calls. Not necessary for bowtie. Required for BWA.
+
+**Double encode?** - converts color calls (0123.) to pseudo-nucleotides (ACGTN). Not necessary for bowtie. Required for BWA.
+
+------
+
+**Examples of output**
+
+When all parameters are left "as-is" you will get this (using reads and qualities shown above)::
+
+ @1831_573_1004
+ T00030133312212111300011021310132222
+ +
+ %>CCAA9952+C>5C.?C79,=42C292:C(9/-7
+ @1831_573_1004
+ T03330322230322112131010221102122113
+ +
+ );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1,
+
+Setting *Trim first base from reads* to **Yes** will produce this::
+
+ @1831_573_1004
+ 00030133312212111300011021310132222
+ +
+ %>CCAA9952+C>5C.?C79,=42C292:C(9/-7
+ @1831_573_1004
+ 03330322230322112131010221102122113
+ +
+ );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1,
+
+Finally, setting *Double encode* to **Yes** will yield::
+
+ @1831_573_1004
+ TAAATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
+ +
+ %>CCAA9952+C>5C.?C79,=42C292:C(9/-7
+ @1831_573_1004
+ TATTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
+ +
+ );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1,
+
+
+
+
+
+
+
Introducing Galactic Quickies
-- Galactic quickies are super-short screencasts that are always under 5 minutes. We thought it may be a good way to spread the word about Galaxy's functionality while keeping the "annoyance factor" to the minimum. The quickies will be updated weekly. -
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