mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 12:13:33 +08:00
Nicola Soranzo
9d74bba7fb
Upgrade syntax using `pyupgrade --py36-plus` . Manually drop several `six` imports. Also: - Remove broken pr_cache in scripts/bootstrap_history.py - Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
201 lines
6.9 KiB
Python
201 lines
6.9 KiB
Python
#!/usr/bin/env python
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import optparse
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import sqlite3
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import sys
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import tempfile
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try:
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maketrans = str.maketrans
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except AttributeError:
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from string import maketrans
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def stop_err(msg):
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sys.stderr.write(msg)
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sys.exit()
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def solid2sanger(quality_string, min_qual=0):
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sanger = ""
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quality_string = quality_string.rstrip(" ")
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for qv in quality_string.split(" "):
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try:
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if int(qv) < 0:
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qv = '0'
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if int(qv) < min_qual:
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return False
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break
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sanger += chr(int(qv) + 33)
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except Exception:
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pass
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return sanger
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def Translator(frm='', to='', delete=''):
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if len(to) == 1:
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to = to * len(frm)
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trans = maketrans(frm, to)
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def callable(s):
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return s.translate(trans, delete)
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return callable
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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):
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# Reads from two files f_csfasta (reads) and f_qual (quality values) and produces output in three formats depending on out parameter,
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# which can have three values: fastq, txt, and db
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# fastq = fastq format
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# txt = space delimited format with defline, reads, and qvs
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# dp = dump data into sqlite3 db.
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# IMPORTNAT! If out = db two optins must be provided:
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# 1. f_out must be a db connection object initialized with sqlite3.connect()
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# 2. table_name must be provided
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if out == 'db':
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cursor = f_out.cursor()
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sql = "create table %s (name varchar(50) not null, read blob, qv blob)" % table_name
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cursor.execute(sql)
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lines = []
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line = " "
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while line:
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for f in [f_reads, f_qual]:
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line = f.readline().rstrip('\n\r')
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while line.startswith('#'):
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line = f.readline().rstrip('\n\r')
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lines.append(line)
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if lines[0].startswith('>') and lines[1].startswith('>'):
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if lines[0] != lines[1]:
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stop_err('Files reads and quality score files are out of sync and likely corrupted. Please, check your input data')
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defline = lines[0][1:]
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if trim_name and (defline[len(defline) - 3:] == "_F3" or defline[len(defline) - 3:] == "_R3"):
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defline = defline[:len(defline) - 3]
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elif (not lines[0].startswith('>') and not lines[1].startswith('>') and len(lines[0]) > 0 and len(lines[1]) > 0):
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if trim_first_base:
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lines[0] = lines[0][1:]
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if double_encode:
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de = Translator(frm="0123.", to="ACGTN")
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lines[0] = de(lines[0])
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qual = solid2sanger(lines[1], int(min_qual))
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if qual:
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if out == 'fastq':
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f_out.write("@%s%s\n%s\n+\n%s\n" % (defline, pair_end_flag, lines[0], qual))
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if out == 'txt':
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f_out.write('%s %s %s\n' % (defline, lines[0], qual))
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if out == 'db':
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cursor.execute('insert into %s values("%s","%s","%s")' % (table_name, defline, lines[0], qual))
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lines = []
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def main():
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usage = "%prog --fr F3.csfasta --fq R3.csfasta --fout fastq_output_file [option]"
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parser = optparse.OptionParser(usage=usage)
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parser.add_option(
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'--fr', '--f_reads',
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metavar="F3_CSFASTA_FILE",
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dest='fr',
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help='Name of F3 file with color space reads')
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parser.add_option(
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'--fq', '--f_qual',
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metavar="F3_QUAL_FILE",
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dest='fq',
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help='Name of F3 file with color quality values')
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parser.add_option(
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'--fout', '--f3_fastq_output',
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metavar="F3_OUTPUT",
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dest='fout',
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help='Name for F3 output file')
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parser.add_option(
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'--rr', '--r_reads',
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metavar="R3_CSFASTA_FILE",
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dest='rr',
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default=False,
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help='Name of R3 file with color space reads')
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parser.add_option(
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'--rq', '--r_qual',
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metavar="R3_QUAL_FILE",
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dest='rq',
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default=False,
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help='Name of R3 file with color quality values')
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parser.add_option(
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'--rout',
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metavar="R3_OUTPUT",
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dest='rout',
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help='Name for F3 output file')
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parser.add_option(
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'-q', '--min_qual',
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dest='min_qual',
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default='-1000',
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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')
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parser.add_option(
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'-t', '--trim_name',
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dest='trim_name',
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action='store_true',
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default=False,
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help='Trim _R3 and _F3 off read names. Default is False')
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parser.add_option(
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'-f', '--trim_first_base',
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dest='trim_first_base',
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action='store_true',
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default=False,
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help='Remove the first base of reads in color-space. Default is False')
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parser.add_option(
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'-d', '--double_encode',
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dest='de',
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action='store_true',
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default=False,
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help='Double encode color calls as nucleotides: 0123. becomes ACGTN. Default is False')
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options, args = parser.parse_args()
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if not (options.fout and options.fr and options.fq):
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parser.error("""
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One or more of the three required paremetrs is missing:
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(1) --fr F3.csfasta file
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(2) --fq F3.qual file
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(3) --fout name of output file
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Use --help for more info
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""")
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fr = open(options.fr)
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fq = open(options.fq)
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f_out = open(options.fout, 'w')
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if options.rr and options.rq:
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rr = open(options.rr)
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rq = open(options.rq)
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if not options.rout:
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parser.error("Provide the name for f3 output using --rout option. Use --help for more info")
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r_out = open(options.rout, 'w')
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db = tempfile.NamedTemporaryFile()
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try:
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con = sqlite3.connect(db.name)
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cur = con.cursor()
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except Exception:
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stop_err('Cannot connect to %s\n') % db.name
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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")
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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")
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cur.execute('create index f3_name on f3( name )')
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cur.execute('create index r3_name on r3( name )')
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cur.execute('select * from f3,r3 where f3.name = r3.name')
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for item in cur:
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f_out.write("@%s%s\n%s\n+\n%s\n" % (item[0], "/1", item[1], item[2]))
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r_out.write("@%s%s\n%s\n+\n%s\n" % (item[3], "/2", item[4], item[5]))
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else:
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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)
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f_out.close()
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if __name__ == "__main__":
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main()
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