def fix_fasta_file(file, out_dir=None):
'''
Passes a file through biopython SeqIO to remove common
formatting issues like '\r' characters and unwrapped sequences.
The new file is saved with the suffix '_clean.fasta'.
'''
# Give up early if the file does not look like fasta
assert check_header_pattern(file), "Sorry, " + str(file) + " does not look like FASTA to me"
suffix = '_clean.fa';
(out_path,out_basename,out_ext) = general.parse_filename(file)
if out_dir is not None:
os.system("mkdir -p "+out_dir);
out_path = out_dir
fixed_file = out_path + '/' + out_basename + suffix
out_handle = general.open_write_file(fixed_file)
fasta_in = SeqIO.parse(file,'fasta');
# Iterate through the records to remove white-space
# from the ID line
new_records = []
for record in fasta_in:
header = re.sub('\s+','_',record.description)
record.id = header
record.name = header
record.description = ''
new_records.append(record)
written = SeqIO.write(new_records, out_handle,'fasta')
print str(written) + ' sequence records stored in ' + fixed_file
return(fixed_file)
def fix_headers(fasta_file_name, qc_set_func, checked_qc_set_func, out_dir=None):
'''
Remove white spaces from the headers of a FASTA file. Fixed FASTA file
is saved with the suffix '_h.fasta'.
'''
(out_path,out_basename,out_ext)=general.parse_filename(fasta_file_name)
if out_dir is not None:
out_path = out_dir # switch to user specified output directory
file_with_header = out_path + '/' + out_basename + '_h.fasta'
broken_fasta=general.open_file(fasta_file_name)
fixed_fasta=general.open_write_file(file_with_header)
header_pattern = re.compile('^>.*')
header = ''
for line in broken_fasta:
line=line.rstrip()
if header_pattern.match(line):
header = line
header = re.sub('\s+', '_', header)
line = header
fixed_fasta.write(line + '\n')
fixed_fasta.close()
broken_fasta.close()
remove_set = set(['header_whitespace']) # Remove qc step becuase it will be corrected
# in the final FASTA file
qc_set_func = qc_set_func.difference(remove_set) # skip finished repairs
checked_qc_set_func = checked_qc_set_func.difference(remove_set) # skip finished checks
return(file_with_header, qc_set_func, checked_qc_set_func)
def fix_headers(fasta_file_name,
qc_set_func,
checked_qc_set_func,
out_dir=None):
'''
Remove white spaces from the headers of a FASTA file. Fixed FASTA file
is saved with the suffix '_h.fasta'.
'''
(out_path, out_basename, out_ext) = general.parse_filename(fasta_file_name)
if out_dir is not None:
out_path = out_dir # switch to user specified output directory
file_with_header = out_path + '/' + out_basename + '_h.fasta'
broken_fasta = general.open_file(fasta_file_name)
fixed_fasta = general.open_write_file(file_with_header)
header_pattern = re.compile('^>.*')
header = ''
for line in broken_fasta:
line = line.rstrip()
if header_pattern.match(line):
header = line
header = re.sub('\s+', '_', header)
line = header
fixed_fasta.write(line + '\n')
fixed_fasta.close()
broken_fasta.close()
remove_set = set(['header_whitespace'
]) # Remove qc step becuase it will be corrected
# in the final FASTA file
qc_set_func = qc_set_func.difference(remove_set) # skip finished repairs
checked_qc_set_func = checked_qc_set_func.difference(
remove_set) # skip finished checks
return (file_with_header, qc_set_func, checked_qc_set_func)
def fix_new_line(file, header_whitespace=False, out_dir=None):
"""
Strips any new line character ('\\n' or '\\r') from each line in
file and ends each line (including the last line) with a new
line character ('\\n').
"""
suffix = "_ended.fasta"
if header_whitespace:
suffix = "_ended_h.fasta" # make suffix match QC steps taken
(out_path, out_basename, out_ext) = general.parse_filename(file)
if out_dir is not None:
out_path = out_dir # switch to user specified output directory
file_with_new_line = out_path + "/" + out_basename + suffix
broken_fasta = general.open_file(file)
fixed_fasta = general.open_write_file(file_with_new_line)
header_pattern = re.compile("^>.*")
header = ""
for line in broken_fasta:
line = line.rstrip()
if header_pattern.match(line):
header = line
header = re.sub("\s+", "_", header)
line = header
fixed_fasta.write(line + "\n")
fixed_fasta.close()
broken_fasta.close()
return file_with_new_line
def fix_wrap(fasta_file_name, qc_set_func, checked_qc_set_func, out_dir=None):
'''
Wraps text in a FASTA file so that no line of sequence has more
than 60 bases. Wrapped file is saved with the suffix '_wrap.fasta'.
'''
suffix = '_wrap.fasta'
if 'header_whitespace' in qc_set_func:
suffix = '_wrap_h.fasta'
(out_path, out_basename, out_ext) = general.parse_filename(fasta_file_name)
if out_dir is not None:
out_path = out_dir # switch to user specified output directory
file_with_wrapping = out_path + '/' + out_basename + suffix
fixed_fasta = general.open_write_file(file_with_wrapping)
header_pattern = re.compile('^>.*')
infile = general.open_file(fasta_file_name)
dna = ''
for line in infile:
line = line.rstrip()
if header_pattern.match(line): # Print headers immediately to new file
header = line
if 'header_whitespace' in qc_set_func:
header = re.sub('\s+', '_', header)
if dna:
fixed_fasta.write(dna + '\n') # print remaining sequence
# before header
fixed_fasta.write(header + '\n')
dna = '' # Reset DNA
else: # if the line is sequence data dump sequence as fast as it is
# long enough to wrap
dna = dna + line
while len(dna) > 59: # Wrap sequence lines after
# 60 bases
wrap_line = dna[0:60]
dna = dna[60:len(dna)]
fixed_fasta.write(wrap_line + '\n')
# Catch the last record
else: # For end of file
if dna:
fixed_fasta.write(dna + '\n') # print remaining sequence
# before header
fixed_fasta.close()
infile.close()
remove_set = set(['wrap', 'new_line',
'header_whitespace']) # Remove all three qc steps
# becuase all will be corrected in the final FASTA file
qc_set_func = qc_set_func.difference(remove_set) # skip finished repairs
checked_remove_set = set(['wrap'])
checked_qc_set_func = checked_qc_set_func.difference(
checked_remove_set) # skip finished checks
return (file_with_wrapping, qc_set_func, checked_qc_set_func)
def fix_wrap(fasta_file_name, qc_set_func, checked_qc_set_func, out_dir=None):
'''
Wraps text in a FASTA file so that no line of sequence has more
than 60 bases. Wrapped file is saved with the suffix '_wrap.fasta'.
'''
suffix = '_wrap.fasta'
if 'header_whitespace' in qc_set_func:
suffix = '_wrap_h.fasta'
(out_path,out_basename,out_ext)=general.parse_filename(fasta_file_name)
if out_dir is not None:
out_path = out_dir # switch to user specified output directory
file_with_wrapping = out_path + '/' + out_basename + suffix
fixed_fasta=general.open_write_file(file_with_wrapping)
header_pattern = re.compile('^>.*')
infile = general.open_file(fasta_file_name)
dna = ''
for line in infile:
line = line.rstrip()
if header_pattern.match(line): # Print headers immediately to new file
header = line
if 'header_whitespace' in qc_set_func:
header = re.sub('\s+', '_', header)
if dna:
fixed_fasta.write(dna + '\n') # print remaining sequence
# before header
fixed_fasta.write(header + '\n')
dna = '' # Reset DNA
else: # if the line is sequence data dump sequence as fast as it is
# long enough to wrap
dna = dna + line
while len(dna) > 59: # Wrap sequence lines after
# 60 bases
wrap_line = dna[0:60]
dna = dna[60:len(dna)]
fixed_fasta.write(wrap_line + '\n')
# Catch the last record
else: # For end of file
if dna:
fixed_fasta.write(dna + '\n') # print remaining sequence
# before header
fixed_fasta.close()
infile.close()
remove_set = set(['wrap','new_line','header_whitespace']) # Remove all three qc steps
# becuase all will be corrected in the final FASTA file
qc_set_func = qc_set_func.difference(remove_set) # skip finished repairs
checked_remove_set = set(['wrap'])
checked_qc_set_func = checked_qc_set_func.difference(checked_remove_set) # skip finished checks
return(file_with_wrapping, qc_set_func, checked_qc_set_func)
def fix_wrap(file, header_whitespace=False, out_dir=None):
'''
Wraps text in a FASTA file so that no line of sequence has more
than 60 bases. Wrapped file is saved with the suffix '_wrap.fasta'.
'''
suffix = '_wrap.fasta'
if header_whitespace:
suffix = '_wrap_h.fasta'
(out_path,out_basename,out_ext)=general.parse_filename(file)
if out_dir is not None:
out_path = out_dir # switch to user specified output directory
file_with_wrapping = out_path + '/' + out_basename + suffix
fixed_fasta=general.open_write_file(file_with_wrapping)
header_pattern = re.compile('^>.*')
infile = general.open_file(file)
header = '';
dna = '';
records = []
for line in infile:
line = line.rstrip()
if header_pattern.match(line):
if dna:
records.append([header,dna])
dna = ''
header = line
if header_whitespace:
header = re.sub('\s+', '_', header)
else:
dna = dna + line
# Catch the last record
if dna and header:
records.append([header,dna])
for record in records:
header, dna = record
fixed_fasta.write(header + '\n')
wrap = textwrap.fill(dna,60) # Wrap sequence lines after 60 bases
fixed_fasta.write(wrap + '\n')
fixed_fasta.close()
infile.close()
return(file_with_wrapping)
def fix_wrap(file, header_whitespace=False, out_dir=None):
"""
Wraps text in a FASTA file so that no line of sequence has more
than 60 bases. Wrapped file is saved with the suffix '_wrap.fasta'.
"""
suffix = "_wrap.fasta"
if header_whitespace:
suffix = "_wrap_h.fasta"
(out_path, out_basename, out_ext) = general.parse_filename(file)
if out_dir is not None:
out_path = out_dir # switch to user specified output directory
file_with_wrapping = out_path + "/" + out_basename + suffix
fixed_fasta = general.open_write_file(file_with_wrapping)
header_pattern = re.compile("^>.*")
infile = general.open_file(file)
dna = ""
header = ""
for line in infile:
line = line.rstrip()
if header_pattern.match(line):
if not dna == "": # skip the first (empty record)
fixed_fasta.write(header + "\n")
wrap = textwrap.fill(dna, 60) # Wrap sequence lines after
# 60 bases
fixed_fasta.write(wrap + "\n")
header = line
if header_whitespace:
header = re.sub("\s+", "_", header) # Gets rid of
# whitespace in the headers
new_dna = next(infile)
new_dna = new_dna.rstrip()
dna = new_dna
else:
dna = dna + line
else: # For end of file
fixed_fasta.write(header + "\n")
wrap = textwrap.fill(dna, 60) # Wrap sequence lines after
# 60 bases
fixed_fasta.write(wrap + "\n")
fixed_fasta.close()
infile.close()
return file_with_wrapping
def fix_new_line(fasta_file_name,
qc_set_func,
checked_qc_set_func,
out_dir=None):
'''
Strips any new line character ('\\n' or '\\r') from each line in
file and ends each line (including the last line) with a new
line character ('\\n').
'''
suffix = '_ended.fasta'
if 'header_whitespace' in qc_set_func:
suffix = '_ended_h.fasta' # make suffix match QC steps taken
(out_path, out_basename, out_ext) = general.parse_filename(fasta_file_name)
if out_dir is not None:
out_path = out_dir # switch to user specified output directory
file_with_new_line = out_path + '/' + out_basename + suffix
if sys.version_info > (3, 0):
broken_fasta = general.open_file(fasta_file_name)
else:
broken_fasta = open(fasta_file_name, 'rU')
fixed_fasta = general.open_write_file(file_with_new_line)
header_pattern = re.compile('^>.*')
header = ''
for line in broken_fasta:
line = line.rstrip()
if header_pattern.match(line):
header = line
if 'header_whitespace' in qc_set_func:
header = re.sub('\s+', '_', header)
line = header
fixed_fasta.write(line + '\n')
fixed_fasta.close()
broken_fasta.close()
remove_set = set(['new_line', 'header_whitespace']) # Remove both qc steps
# becuase they will be corrected in the final FASTA file
qc_set_func = qc_set_func.difference(remove_set) # skip finished repairs
checked_remove_set = set(['new_line'])
checked_qc_set_func = checked_qc_set_func.difference(
checked_remove_set) # skip finished checks
return (file_with_new_line, qc_set_func, checked_qc_set_func)
def fix_fasta_file(file, out_dir=None):
'''
Passes a file through biopython SeqIO to remove common
formatting issues like '\r' characters and unwrapped sequences.
The new file is saved with the suffix '_clean.fasta'.
'''
# Give up early if the file does not look like fasta
assert check_header_pattern(
file), "Sorry, " + str(file) + " does not look like FASTA to me"
suffix = '_clean.fa'
(out_path, out_basename, out_ext) = general.parse_filename(file)
if out_dir is not None:
os.system("mkdir -p " + out_dir)
out_path = out_dir
fixed_file = out_path + '/' + out_basename + suffix
out_handle = general.open_write_file(fixed_file)
fasta_in = SeqIO.parse(file, 'fasta')
# Iterate through the records to remove white-space
# from the ID line
new_records = []
for record in fasta_in:
header = re.sub('\s+', '_', record.description)
record.id = header
record.name = header
record.description = ''
new_records.append(record)
written = SeqIO.write(new_records, out_handle, 'fasta')
print str(written) + ' sequence records stored in ' + fixed_file
return (fixed_file)
def fix_headers(file, out_dir=None):
"""
Remove white spaces that break Trimmomatic and some other bioinfo tools
from the headers of a FASTA file. Fixed FASTA file is saved with the
suffix '_h.fasta'.
"""
(out_path, out_basename, out_ext) = general.parse_filename(file)
if out_dir is not None:
out_path = out_dir # switch to user specified output directory
file_with_header = out_path + "/" + out_basename + "_h.fasta"
broken_fasta = general.open_file(file)
fixed_fasta = general.open_write_file(file_with_header)
header_pattern = re.compile("^>.*")
header = ""
for line in broken_fasta:
line = line.rstrip()
if header_pattern.match(line):
header = line
header = re.sub("\s+", "_", header)
line = header
fixed_fasta.write(line + "\n")
fixed_fasta.close()
broken_fasta.close()
return file_with_header
def fix_new_line(fasta_file_name, qc_set_func, checked_qc_set_func, out_dir=None):
'''
Strips any new line character ('\\n' or '\\r') from each line in
file and ends each line (including the last line) with a new
line character ('\\n').
'''
suffix = '_ended.fasta'
if 'header_whitespace' in qc_set_func:
suffix = '_ended_h.fasta' # make suffix match QC steps taken
(out_path,out_basename,out_ext)=general.parse_filename(fasta_file_name)
if out_dir is not None:
out_path = out_dir # switch to user specified output directory
file_with_new_line = out_path + '/' + out_basename + suffix
if sys.version_info > (3, 0):
broken_fasta=general.open_file(fasta_file_name)
else:
broken_fasta = open(fasta_file_name, 'rU')
fixed_fasta=general.open_write_file(file_with_new_line)
header_pattern = re.compile('^>.*')
header = ''
for line in broken_fasta:
line=line.rstrip()
if header_pattern.match(line):
header = line
if 'header_whitespace' in qc_set_func:
header = re.sub('\s+', '_', header)
line = header
fixed_fasta.write(line + '\n')
fixed_fasta.close()
broken_fasta.close()
remove_set = set(['new_line','header_whitespace']) # Remove both qc steps
# becuase they will be corrected in the final FASTA file
qc_set_func = qc_set_func.difference(remove_set) # skip finished repairs
checked_remove_set = set(['new_line'])
checked_qc_set_func = checked_qc_set_func.difference(checked_remove_set) # skip finished checks
return(file_with_new_line, qc_set_func, checked_qc_set_func)
def fix_headers(file, out_dir=None):
'''
Remove white spaces that break Trimmomatic and some other bioinfo tools
from the headers of a FASTA file. Fixed FASTA file is saved with the
suffix '_h.fasta'.
'''
(out_path,out_basename,out_ext)=general.parse_filename(file)
if out_dir is not None:
out_path = out_dir # switch to user specified output directory
file_with_header = out_path + '/' + out_basename + '_h.fasta'
broken_fasta=general.open_file(file)
fixed_fasta=general.open_write_file(file_with_header)
header_pattern = re.compile('^>.*')
header = ''
for line in broken_fasta:
line=line.rstrip()
if header_pattern.match(line):
header = line
header = re.sub('\s+', '_', header)
line = header
fixed_fasta.write(line + '\n')
fixed_fasta.close()
broken_fasta.close()
return(file_with_header)
def main():
'''
Run full script as opposed to individual script functions.
'''
######################################################################
############ Get commandline arguments ############
######################################################################
parser = argparse.ArgumentParser(
description='DESCRIPTION: Summarize counts of all four DNA bases. \
Command-line options that may be omitted \
(i.e. are NOT required) are shown in \
square brackets.')
parser.add_argument('-v', '--verbose', action='store_true',
dest='verbose', help='Runs reporting status updates',
default=True)
parser.add_argument('-q', '--quiet', action='store_false',
dest='verbose', help='Does not report status updates')
parser.add_argument('-c', '--colorized',
help='Colorizes log reports. Use only if printing \
output to screen.',action='store_true',dest='colorized')
parser.add_argument('-r', '--read_list', dest='read_list',
help='This is the the full path (path and filename) of \
the user provided list of read files. The file should \
be tab separated with the first read file, then the \
second read file (see example_read_list_PE.tab). If a \
sample has multiple fastq files for R1 and R2 separate \
these with commas (see example_read_list_PE_multi.tab).\
For single end reads each line should be a path \
to a fastq file. For single end reads each line should \
be a path to a fastq file (see example_read_list_SE.tab\
)', required=True)
parser.add_argument('-p', '--project', dest='project',
help='The project id. This will be used to name output \
(default=project).', default='project', required=False)
parser.add_argument('-a', '--adapter', dest='adapter',
help='The adapter fasta file. This will be used to \
clean reads',default='/homes/bioinfo_software/Trimmomatic-0.33/adapters/TruSeq3-PE-2.fa', required=False)
parser.add_argument('-s', '--single_end', action='store_true', dest='single',
help='If your reads are single end use this flag. \
Without it the script assumes reads are paired end. \
Also skip the second column (the reverse fastq files) \
when making your read list', required=False,
default=False)
parser.add_argument('-x', '--convert_header', action='store_true',
dest='convert_header', help='If the illumina headers \
do not end in /1 or /2 use this parameter to indicat \
that headers need to be converted. Check your headers \
by typing "head FASTA_FULL_PATH" and read more about \
illumina headers at \
http://en.wikipedia.org/wiki/Fastq#Illumina_sequence_identifiers.',
default=False, required=False)
parser.add_argument('-m', '--min_read_length', dest='min_read_length',
help='The minimum read length in bp. (Default = 90).',
required=False, default=90)
parser.add_argument('-o', '--out', dest='out',
help='Output directory (Default=$HOME)', required=False,
default='~')
parser.add_argument('-d', '--dna', dest='sequence', help='DNA sequence to \
summarize', default='TATGAAGGGCGATGAATGCTATCTGTCCTGTAGAATTATAGAATCGACTACGTTGGGGAACTAATGGACCAGACAACTCGCTTTGACTGACGTAGACGGCGTGTTGT',
required=False)
args = parser.parse_args()
if args.colorized:
import Colorer
if args.verbose:
doc()
log.basicConfig(format='%(levelname)s: %(message)s', level=log.DEBUG)
log.info('Output is verbose. Run with -q, --quiet flag to suppress full output.')
else:
log.basicConfig(format='%(levelname)s: %(message)s')
######################################################################
############ Call custom functions with arguments ###########
######################################################################
# Get list of read FASTQ files
#######################################
print(args.read_list, args.single, args.min_read_length)
(forwards,reverses) = trimmomatic_template.parse_file(args.read_list,
args.single)
#######################################
# Sanity check read FASTQ files
#######################################
index = 0
for fastq in forwards:
f_opened_file=general.open_file(forwards[index])
f_opened_file.close()
forwards[index] = general.convert_to_full(forwards[index])
if not args.single:
r_opened_file=general.open_file(reverses[index])
r_opened_file.close()
reverses[index] = general.convert_to_full(reverses[index])
index += 1
#######################################
# Make output directory
#######################################
(out_path,out_basename,out_ext)=general.parse_filename(args.out)
out_dir=out_path + '/' + out_basename
general.path_check(out_dir) # Sanity check directory
out_dir= out_dir + '/' + args.project # final out directory is 'project_id'
general.mk_out_sub_directory(out_dir)
general.mk_out_sub_directory(out_dir + '/scripts')
general.mk_out_sub_directory(out_dir + '/qsubs')
#######################################
# Write trimmomatic script
#######################################
convert=' | awk \'{if (NR % 4 == 1) {split($1, arr, \":\"); printf \"%s_%s:%s:%s:%s:%s#0/%s\\n\", arr[1], arr[3], arr[4], arr[5], arr[6], arr[7], substr($2, 1, 1), $0} else if (NR % 4 == 3){print \"+\"} else {print $0} }\' > '
qsub_script = general.open_write_file(out_dir + '/qsubs/qsub_trimmomatic.sh')
qsub_script.write('#!/bin/bash\n')
index=0
args.adapter = fasta_o_matic.run_steps(args.adapter,['wrap', 'new_line','header_whitespace'])
for fastq in forwards:
(f_path,f_basename,f_ext)=general.parse_filename(forwards[index])
qsub_script.write('qsub -l mem=4G,h_rt=6:00:00 -pe single 16 '+ out_dir
+ '/scripts/run_trimmomatic_' + f_basename + '.sh\n' )
if not args.single:
(r_path,r_basename,r_ext)=general.parse_filename(reverses[index])
trim_script = general.open_write_file(out_dir
+ '/scripts/run_trimmomatic_'
+ f_basename + '.sh')
trim_script.write('#!/bin/bash\n')
# Convert headers
if args.convert_header:
trim_script.write('# Convert headers:\n')
new_forward_fastq = out_dir + '/' + f_basename + '_h.fastq'
trim_script.write('cat ' + forwards[index] + convert
+ new_forward_fastq + '\n')
forwards[index] = new_forward_fastq
if not args.single:
new_reverse_fastq = out_dir + '/' + r_basename + '_h.fastq'
trim_script.write('cat ' + reverses[index] + convert
+ new_reverse_fastq + '\n')
reverses[index] = new_reverse_fastq
# Trim sequences
trim_script.write('# Clean reads:\n')
if not args.single:
trim_script.write(trimmomatic_template.trim_template(
forwards[index],
reverses[index],
args.adapter,
out_dir))
else:
trim_script.write(trimmomatic_template.trim_template_single(forwards[index]))
# Section in progress... (Remember to point to a SE adapter fasta file
# by default)
trim_script.close()
index += 1
qsub_script.close()
def main():
'''
Run full script as opposed to individual script functions.
'''
######################################################################
############ Get commandline arguments ############
######################################################################
parser = argparse.ArgumentParser(
description='DESCRIPTION: Summarize counts of all four DNA bases. \
Command-line options that may be omitted \
(i.e. are NOT required) are shown in \
square brackets.')
parser.add_argument('-v',
'--verbose',
action='store_true',
dest='verbose',
help='Runs reporting status updates',
default=True)
parser.add_argument('-q',
'--quiet',
action='store_false',
dest='verbose',
help='Does not report status updates')
parser.add_argument('-c',
'--colorized',
help='Colorizes log reports. Use only if printing \
output to screen.',
action='store_true',
dest='colorized')
parser.add_argument(
'-r',
'--read_list',
dest='read_list',
help='This is the the full path (path and filename) of \
the user provided list of read files. The file should \
be tab separated with the first read file, then the \
second read file (see example_read_list_PE.tab). If a \
sample has multiple fastq files for R1 and R2 separate \
these with commas (see example_read_list_PE_multi.tab).\
For single end reads each line should be a path \
to a fastq file. For single end reads each line should \
be a path to a fastq file (see example_read_list_SE.tab\
)',
required=True)
parser.add_argument(
'-p',
'--project',
dest='project',
help='The project id. This will be used to name output \
(default=project).',
default='project',
required=False)
parser.add_argument(
'-a',
'--adapter',
dest='adapter',
help='The adapter fasta file. This will be used to \
clean reads',
default=
'/homes/bioinfo_software/Trimmomatic-0.33/adapters/TruSeq3-PE-2.fa',
required=False)
parser.add_argument('-s',
'--single_end',
action='store_true',
dest='single',
help='If your reads are single end use this flag. \
Without it the script assumes reads are paired end. \
Also skip the second column (the reverse fastq files) \
when making your read list',
required=False,
default=False)
parser.add_argument('-x',
'--convert_header',
action='store_true',
dest='convert_header',
help='If the illumina headers \
do not end in /1 or /2 use this parameter to indicat \
that headers need to be converted. Check your headers \
by typing "head FASTA_FULL_PATH" and read more about \
illumina headers at \
http://en.wikipedia.org/wiki/Fastq#Illumina_sequence_identifiers.',
default=False,
required=False)
parser.add_argument('-m',
'--min_read_length',
dest='min_read_length',
help='The minimum read length in bp. (Default = 90).',
required=False,
default=90)
parser.add_argument('-o',
'--out',
dest='out',
help='Output directory (Default=$HOME)',
required=False,
default='~')
parser.add_argument(
'-d',
'--dna',
dest='sequence',
help='DNA sequence to \
summarize',
default=
'TATGAAGGGCGATGAATGCTATCTGTCCTGTAGAATTATAGAATCGACTACGTTGGGGAACTAATGGACCAGACAACTCGCTTTGACTGACGTAGACGGCGTGTTGT',
required=False)
args = parser.parse_args()
if args.colorized:
import Colorer
if args.verbose:
doc()
log.basicConfig(format='%(levelname)s: %(message)s', level=log.DEBUG)
log.info(
'Output is verbose. Run with -q, --quiet flag to suppress full output.'
)
else:
log.basicConfig(format='%(levelname)s: %(message)s')
######################################################################
############ Call custom functions with arguments ###########
######################################################################
# Get list of read FASTQ files
#######################################
print(args.read_list, args.single, args.min_read_length)
(forwards,
reverses) = trimmomatic_template.parse_file(args.read_list, args.single)
#######################################
# Sanity check read FASTQ files
#######################################
index = 0
for fastq in forwards:
f_opened_file = general.open_file(forwards[index])
f_opened_file.close()
forwards[index] = general.convert_to_full(forwards[index])
if not args.single:
r_opened_file = general.open_file(reverses[index])
r_opened_file.close()
reverses[index] = general.convert_to_full(reverses[index])
index += 1
#######################################
# Make output directory
#######################################
(out_path, out_basename, out_ext) = general.parse_filename(args.out)
out_dir = out_path + '/' + out_basename
general.path_check(out_dir) # Sanity check directory
out_dir = out_dir + '/' + args.project # final out directory is 'project_id'
general.mk_out_sub_directory(out_dir)
general.mk_out_sub_directory(out_dir + '/scripts')
general.mk_out_sub_directory(out_dir + '/qsubs')
#######################################
# Write trimmomatic script
#######################################
convert = ' | awk \'{if (NR % 4 == 1) {split($1, arr, \":\"); printf \"%s_%s:%s:%s:%s:%s#0/%s\\n\", arr[1], arr[3], arr[4], arr[5], arr[6], arr[7], substr($2, 1, 1), $0} else if (NR % 4 == 3){print \"+\"} else {print $0} }\' > '
qsub_script = general.open_write_file(out_dir +
'/qsubs/qsub_trimmomatic.sh')
qsub_script.write('#!/bin/bash\n')
index = 0
args.adapter = fasta_o_matic.run_steps(
args.adapter, ['wrap', 'new_line', 'header_whitespace'])
for fastq in forwards:
(f_path, f_basename, f_ext) = general.parse_filename(forwards[index])
qsub_script.write('qsub -l mem=4G,h_rt=6:00:00 -pe single 16 ' +
out_dir + '/scripts/run_trimmomatic_' + f_basename +
'.sh\n')
if not args.single:
(r_path, r_basename,
r_ext) = general.parse_filename(reverses[index])
trim_script = general.open_write_file(out_dir +
'/scripts/run_trimmomatic_' +
f_basename + '.sh')
trim_script.write('#!/bin/bash\n')
# Convert headers
if args.convert_header:
trim_script.write('# Convert headers:\n')
new_forward_fastq = out_dir + '/' + f_basename + '_h.fastq'
trim_script.write('cat ' + forwards[index] + convert +
new_forward_fastq + '\n')
forwards[index] = new_forward_fastq
if not args.single:
new_reverse_fastq = out_dir + '/' + r_basename + '_h.fastq'
trim_script.write('cat ' + reverses[index] + convert +
new_reverse_fastq + '\n')
reverses[index] = new_reverse_fastq
# Trim sequences
trim_script.write('# Clean reads:\n')
if not args.single:
trim_script.write(
trimmomatic_template.trim_template(forwards[index],
reverses[index],
args.adapter, out_dir))
else:
trim_script.write(
trimmomatic_template.trim_template_single(forwards[index]))
# Section in progress... (Remember to point to a SE adapter fasta file
# by default)
trim_script.close()
index += 1
qsub_script.close()
