def __main__():
options, args = doc_optparse.parse(__doc__)
try:
range_file = file(args[0])
nib_file = file(args[1])
except:
doc_optparse.exit()
nib = bx.seq.nib.NibFile(nib_file)
for line in range_file:
fields = line.split()
start, end = int(fields[0]), int(fields[1])
print ">", start, end
print_wrapped(nib.get(start, end - start))
def __main__():
options, args = doc_optparse.parse( __doc__ )
try:
range_file = file( args[0] )
nib_file = file( args[1] )
except:
doc_optparse.exit()
nib = bx.seq.nib.NibFile( nib_file )
for line in range_file:
fields = line.split()
start, end = int( fields[0] ), int( fields[1] )
print ">", start, end
print_wrapped( nib.get( start, end - start ) )
def __main__():
options, args = doc_optparse.parse( __doc__ )
try:
nib_dir = args[0]
except:
doc_optparse.exit()
nibs = {}
for line in sys.stdin:
fields = line.split()
chrom, start, end = fields[0], int( fields[1] ), int( fields[2] )
print ">", chrom, start, end
if chrom in nibs:
nib = nibs[chrom]
else:
nibs[chrom] = nib = bx.seq.nib.NibFile( file( "%s/%s.nib" % ( nib_dir, chrom ) ) )
print_wrapped( nib.get( start, end - start ) )
def __main__():
options, args = doc_optparse.parse( __doc__ )
try:
nib_dir = args[0]
except:
doc_optparse.exit()
nibs = {}
for line in sys.stdin:
fields = line.split()
chrom, start, end = fields[0], int( fields[1] ), int( fields[2] )
print ">", chrom, start, end
if chrom in nibs:
nib = nibs[chrom]
else:
nibs[chrom] = nib = bx.seq.nib.NibFile( file( "%s/%s.nib" % ( nib_dir, chrom ) ) )
print_wrapped( nib.get( start, end - start ) )
def __main__():
options, args = cookbook.doc_optparse.parse( __doc__ )
try:
nib_dir = args[0]
except:
cookbook.doc_optparse.exit()
nibs = {}
for line in sys.stdin:
fields = line.split()
chrom, start, end = fields[0], int( fields[1] ), int( fields[2] )
if chrom in nibs:
nib = nibs[chrom]
else:
nibs[chrom] = nib = bx.seq.nib.NibFile( file( "%s/%s.nib" % ( nib_dir, chrom ) ) )
seq = nib.get( start, end - start ).upper()
n = 0
for i in range( 0, len( seq ) - 1 ):
if seq[i] == 'C' and seq[i+1] == 'G':
n += 1
print n / len( seq )
if strand not in ['+', '-']:
strand = '+'
sequence = ''
else:
continue
# Open sequence file and get sequence for feature/interval.
if seq_path and os.path.exists("%s/%s.nib" % (seq_path, chrom)):
# TODO: improve support for GFF-nib interaction.
if chrom in nibs:
nib = nibs[chrom]
else:
nibs[chrom] = nib = bx.seq.nib.NibFile(
file("%s/%s.nib" % (seq_path, chrom)))
try:
sequence = nib.get(start, end - start)
except Exception, e:
warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " % (
start, end - start, dbkey)
warnings.append(warning)
if not invalid_lines:
invalid_lines = get_lines(feature)
first_invalid_line = line_count
skipped_lines += len(invalid_lines)
continue
elif seq_path and os.path.isfile(seq_path):
if not (twobitfile):
twobitfile = bx.seq.twobit.TwoBitFile(file(seq_path))
try:
if options.gff and interpret_features:
# Create sequence from intervals within a feature.
def __main__():
#
# Parse options, args.
#
options, args = doc_optparse.parse(__doc__)
try:
if len(options.cols.split(',')) == 5:
# BED file
chrom_col, start_col, end_col, strand_col, name_col = parse_cols_arg(
options.cols)
else:
# gff file
chrom_col, start_col, end_col, strand_col = parse_cols_arg(
options.cols)
name_col = False
dbkey = options.dbkey
output_format = options.output_format
gff_format = options.gff
interpret_features = options.interpret_features
GALAXY_DATA_INDEX_DIR = options.GALAXY_DATA_INDEX_DIR
fasta_file = options.fasta
input_filename, output_filename = args
except:
doc_optparse.exception()
includes_strand_col = strand_col >= 0
strand = None
nibs = {}
#
# Set path to sequence data.
#
if fasta_file:
# Need to create 2bit file from fasta file.
try:
seq_path = tempfile.NamedTemporaryFile(dir=".").name
cmd = "faToTwoBit %s %s" % (fasta_file, seq_path)
tmp_name = tempfile.NamedTemporaryFile(dir=".").name
tmp_stderr = open(tmp_name, 'wb')
proc = subprocess.Popen(args=cmd,
shell=True,
stderr=tmp_stderr.fileno())
returncode = proc.wait()
tmp_stderr.close()
# Get stderr, allowing for case where it's very large.
tmp_stderr = open(tmp_name, 'rb')
stderr = ''
buffsize = 1048576
try:
while True:
stderr += tmp_stderr.read(buffsize)
if not stderr or len(stderr) % buffsize != 0:
break
except OverflowError:
pass
tmp_stderr.close()
# Error checking.
if returncode != 0:
raise Exception(stderr)
except Exception as e:
stop_err('Error running faToTwoBit. ' + str(e))
else:
seq_path = check_seq_file(dbkey, GALAXY_DATA_INDEX_DIR)
if not os.path.exists(seq_path):
# If this occurs, we need to fix the metadata validator.
stop_err(
"No sequences are available for '%s', request them by reporting this error."
% dbkey)
#
# Fetch sequences.
#
# Get feature's line(s).
def get_lines(feature):
if isinstance(feature, gff_util.GFFFeature):
return feature.lines()
else:
return [feature.rstrip('\r\n')]
skipped_lines = 0
first_invalid_line = 0
invalid_lines = []
fout = open(output_filename, "w")
warnings = []
warning = ''
twobitfile = None
file_iterator = open(input_filename)
if gff_format and interpret_features:
file_iterator = gff_util.GFFReaderWrapper(file_iterator,
fix_strand=False)
line_count = 1
for feature in file_iterator:
# Ignore comments, headers.
if isinstance(feature, (Header, Comment)):
line_count += 1
continue
name = ""
if gff_format and interpret_features:
# Processing features.
gff_util.convert_gff_coords_to_bed(feature)
chrom = feature.chrom
start = feature.start
end = feature.end
strand = feature.strand
else:
# Processing lines, either interval or GFF format.
line = feature.rstrip('\r\n')
if line and not line.startswith("#"):
fields = line.split('\t')
try:
chrom = fields[chrom_col]
start = int(fields[start_col])
end = int(fields[end_col])
if name_col:
name = fields[name_col]
if gff_format:
start, end = gff_util.convert_gff_coords_to_bed(
[start, end])
if includes_strand_col:
strand = fields[strand_col]
except:
warning = "Invalid chrom, start or end column values. "
warnings.append(warning)
if not invalid_lines:
invalid_lines = get_lines(feature)
first_invalid_line = line_count
skipped_lines += len(invalid_lines)
continue
if start > end:
warning = "Invalid interval, start '%d' > end '%d'. " % (
start, end)
warnings.append(warning)
if not invalid_lines:
invalid_lines = get_lines(feature)
first_invalid_line = line_count
skipped_lines += len(invalid_lines)
continue
if strand not in ['+', '-']:
strand = '+'
sequence = ''
else:
continue
# Open sequence file and get sequence for feature/interval.
if seq_path and os.path.exists("%s/%s.nib" % (seq_path, chrom)):
# TODO: improve support for GFF-nib interaction.
if chrom in nibs:
nib = nibs[chrom]
else:
nibs[chrom] = nib = bx.seq.nib.NibFile(
open("%s/%s.nib" % (seq_path, chrom)))
try:
sequence = nib.get(start, end - start)
except Exception as e:
warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " % (
start, end - start, dbkey)
warnings.append(warning)
if not invalid_lines:
invalid_lines = get_lines(feature)
first_invalid_line = line_count
skipped_lines += len(invalid_lines)
continue
elif seq_path and os.path.isfile(seq_path):
if not (twobitfile):
twobitfile = bx.seq.twobit.TwoBitFile(open(seq_path))
try:
if options.gff and interpret_features:
# Create sequence from intervals within a feature.
sequence = ''
for interval in feature.intervals:
sequence += twobitfile[
interval.chrom][interval.start:interval.end]
else:
sequence = twobitfile[chrom][start:end]
except:
warning = "Unable to fetch the sequence from '%d' to '%d' for chrom '%s'. " % (
start, end - start, chrom)
warnings.append(warning)
if not invalid_lines:
invalid_lines = get_lines(feature)
first_invalid_line = line_count
skipped_lines += len(invalid_lines)
continue
else:
warning = "Chromosome by name '%s' was not found for build '%s'. " % (
chrom, dbkey)
warnings.append(warning)
if not invalid_lines:
invalid_lines = get_lines(feature)
first_invalid_line = line_count
skipped_lines += len(invalid_lines)
continue
if sequence == '':
warning = "Chrom: '%s', start: '%s', end: '%s' is either invalid or not present in build '%s'. " % \
( chrom, start, end, dbkey )
warnings.append(warning)
if not invalid_lines:
invalid_lines = get_lines(feature)
first_invalid_line = line_count
skipped_lines += len(invalid_lines)
continue
if includes_strand_col and strand == "-":
sequence = reverse_complement(sequence)
if output_format == "fasta":
l = len(sequence)
c = 0
if gff_format:
start, end = gff_util.convert_bed_coords_to_gff([start, end])
fields = [dbkey, str(chrom), str(start), str(end), strand]
meta_data = "_".join(fields)
if name.strip():
fout.write(">%s %s\n" % (meta_data, name))
else:
fout.write(">%s\n" % meta_data)
while c < l:
b = min(c + 50, l)
fout.write("%s\n" % str(sequence[c:b]))
c = b
else: # output_format == "interval"
if gff_format and interpret_features:
# TODO: need better GFF Reader to capture all information needed
# to produce this line.
meta_data = "\t".join([
feature.chrom, "galaxy_extract_genomic_dna", "interval",
str(feature.start),
str(feature.end), feature.score, feature.strand, ".",
gff_util.gff_attributes_to_str(feature.attributes, "GTF")
])
else:
meta_data = "\t".join(fields)
if gff_format:
format_str = "%s seq \"%s\";\n"
else:
format_str = "%s\t%s\n"
fout.write(format_str % (meta_data, str(sequence)))
# Update line count.
if isinstance(feature, gff_util.GFFFeature):
line_count += len(feature.intervals)
else:
line_count += 1
fout.close()
if warnings:
warn_msg = "%d warnings, 1st is: " % len(warnings)
warn_msg += warnings[0]
print warn_msg
if skipped_lines:
# Error message includes up to the first 10 skipped lines.
print 'Skipped %d invalid lines, 1st is #%d, "%s"' % (
skipped_lines, first_invalid_line, '\n'.join(invalid_lines[:10]))
# Clean up temp file.
if fasta_file:
os.remove(seq_path)
os.remove(tmp_name)
def __main__():
options, args = doc_optparse.parse( __doc__ )
try:
chrom_col, start_col, end_col, strand_col = parse_cols_arg( options.cols )
dbkey = options.dbkey
output_format = options.output_format
GALAXY_DATA_INDEX_DIR = options.GALAXY_DATA_INDEX_DIR
input_filename, output_filename = args
except:
doc_optparse.exception()
includes_strand_col = strand_col >= 0
strand = None
nibs = {}
twobits = {}
seq_path = check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR )
if not os.path.exists( seq_path ):
# If this occurs, we need to fix the metadata validator.
stop_err( "No sequences are available for '%s', request them by reporting this error." % dbkey )
skipped_lines = 0
first_invalid_line = 0
invalid_line = ''
fout = open( output_filename, "w" )
warnings = []
warning = ''
twobitfile = None
for i, line in enumerate( open( input_filename ) ):
line = line.rstrip( '\r\n' )
if line and not line.startswith( "#" ):
fields = line.split( '\t' )
try:
chrom = fields[chrom_col]
start = int( fields[start_col] )
end = int( fields[end_col] )
if includes_strand_col:
strand = fields[strand_col]
except:
warning = "Invalid chrom, start or end column values. "
warnings.append( warning )
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
continue
if start > end:
warning = "Invalid interval, start '%d' > end '%d'. " % ( start, end )
warnings.append( warning )
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
continue
if strand not in ['+', '-']:
strand = '+'
sequence = ''
if seq_path and os.path.exists( "%s/%s.nib" % ( seq_path, chrom ) ):
if chrom in nibs:
nib = nibs[chrom]
else:
nibs[chrom] = nib = bx.seq.nib.NibFile( file( "%s/%s.nib" % ( seq_path, chrom ) ) )
try:
sequence = nib.get( start, end-start )
except:
warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey )
warnings.append( warning )
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
continue
elif seq_path and os.path.isfile( seq_path ):
if not(twobitfile):
twobitfile = bx.seq.twobit.TwoBitFile( file( seq_path ) )
try:
sequence = twobitfile[chrom][start:end]
except:
warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey )
warnings.append( warning )
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
continue
else:
warning = "Chromosome by name '%s' was not found for build '%s'. " % ( chrom, dbkey )
warnings.append( warning )
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
continue
if sequence == '':
warning = "Chrom: '%s', start: '%s', end: '%s' is either invalid or not present in build '%s'. " %( chrom, start, end, dbkey )
warnings.append( warning )
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
continue
if includes_strand_col and strand == "-":
sequence = reverse_complement( sequence )
if output_format == "fasta" :
l = len( sequence )
c = 0
fields = [dbkey, str( chrom ), str( start ), str( end ), strand]
meta_data = "_".join( fields )
fout.write( ">%s\n" % meta_data )
while c < l:
b = min( c + 50, l )
fout.write( "%s\n" % str( sequence[c:b] ) )
c = b
else: # output_format == "interval"
meta_data = "\t".join( fields )
fout.write( "%s\t%s\n" % ( meta_data, str( sequence ) ) )
fout.close()
if warnings:
warn_msg = "%d warnings, 1st is: " % len( warnings )
warn_msg += warnings[0]
print warn_msg
if skipped_lines:
print 'Skipped %d invalid lines, 1st is #%d, "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
def __main__():
#
# Parse options, args.
#
options, args = doc_optparse.parse( __doc__ )
try:
if len(options.cols.split(',')) == 5:
# BED file
chrom_col, start_col, end_col, strand_col, name_col = parse_cols_arg( options.cols )
else:
# gff file
chrom_col, start_col, end_col, strand_col = parse_cols_arg( options.cols )
name_col = False
dbkey = options.dbkey
output_format = options.output_format
gff_format = options.gff
interpret_features = options.interpret_features
GALAXY_DATA_INDEX_DIR = options.GALAXY_DATA_INDEX_DIR
fasta_file = options.fasta
input_filename, output_filename = args
except:
doc_optparse.exception()
includes_strand_col = strand_col >= 0
strand = None
nibs = {}
#
# Set path to sequence data.
#
if fasta_file:
# Need to create 2bit file from fasta file.
try:
seq_path = tempfile.NamedTemporaryFile( dir="." ).name
cmd = "faToTwoBit %s %s" % ( fasta_file, seq_path )
tmp_name = tempfile.NamedTemporaryFile( dir="." ).name
tmp_stderr = open( tmp_name, 'wb' )
proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() )
returncode = proc.wait()
tmp_stderr.close()
# Get stderr, allowing for case where it's very large.
tmp_stderr = open( tmp_name, 'rb' )
stderr = ''
buffsize = 1048576
try:
while True:
stderr += tmp_stderr.read( buffsize )
if not stderr or len( stderr ) % buffsize != 0:
break
except OverflowError:
pass
tmp_stderr.close()
# Error checking.
if returncode != 0:
raise Exception(stderr)
except Exception as e:
stop_err( 'Error running faToTwoBit. ' + str( e ) )
else:
seq_path = check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR )
if not os.path.exists( seq_path ):
# If this occurs, we need to fix the metadata validator.
stop_err( "No sequences are available for '%s', request them by reporting this error." % dbkey )
#
# Fetch sequences.
#
# Get feature's line(s).
def get_lines( feature ):
if isinstance( feature, gff_util.GFFFeature ):
return feature.lines()
else:
return [ feature.rstrip( '\r\n' ) ]
skipped_lines = 0
first_invalid_line = 0
invalid_lines = []
fout = open( output_filename, "w" )
warnings = []
warning = ''
twobitfile = None
file_iterator = open( input_filename )
if gff_format and interpret_features:
file_iterator = gff_util.GFFReaderWrapper( file_iterator, fix_strand=False )
line_count = 1
for feature in file_iterator:
# Ignore comments, headers.
if isinstance( feature, ( Header, Comment ) ):
line_count += 1
continue
name = ""
if gff_format and interpret_features:
# Processing features.
gff_util.convert_gff_coords_to_bed( feature )
chrom = feature.chrom
start = feature.start
end = feature.end
strand = feature.strand
else:
# Processing lines, either interval or GFF format.
line = feature.rstrip( '\r\n' )
if line and not line.startswith( "#" ):
fields = line.split( '\t' )
try:
chrom = fields[chrom_col]
start = int( fields[start_col] )
end = int( fields[end_col] )
if name_col:
name = fields[name_col]
if gff_format:
start, end = gff_util.convert_gff_coords_to_bed( [start, end] )
if includes_strand_col:
strand = fields[strand_col]
except:
warning = "Invalid chrom, start or end column values. "
warnings.append( warning )
if not invalid_lines:
invalid_lines = get_lines( feature )
first_invalid_line = line_count
skipped_lines += len( invalid_lines )
continue
if start > end:
warning = "Invalid interval, start '%d' > end '%d'. " % ( start, end )
warnings.append( warning )
if not invalid_lines:
invalid_lines = get_lines( feature )
first_invalid_line = line_count
skipped_lines += len( invalid_lines )
continue
if strand not in ['+', '-']:
strand = '+'
sequence = ''
else:
continue
# Open sequence file and get sequence for feature/interval.
if seq_path and os.path.exists( "%s/%s.nib" % ( seq_path, chrom ) ):
# TODO: improve support for GFF-nib interaction.
if chrom in nibs:
nib = nibs[chrom]
else:
nibs[chrom] = nib = bx.seq.nib.NibFile( open( "%s/%s.nib" % ( seq_path, chrom ) ) )
try:
sequence = nib.get( start, end - start )
except Exception as e:
warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " % ( start, end - start, dbkey )
warnings.append( warning )
if not invalid_lines:
invalid_lines = get_lines( feature )
first_invalid_line = line_count
skipped_lines += len( invalid_lines )
continue
elif seq_path and os.path.isfile( seq_path ):
if not(twobitfile):
twobitfile = bx.seq.twobit.TwoBitFile( open( seq_path ) )
try:
if options.gff and interpret_features:
# Create sequence from intervals within a feature.
sequence = ''
for interval in feature.intervals:
sequence += twobitfile[interval.chrom][interval.start:interval.end]
else:
sequence = twobitfile[chrom][start:end]
except:
warning = "Unable to fetch the sequence from '%d' to '%d' for chrom '%s'. " % ( start, end - start, chrom )
warnings.append( warning )
if not invalid_lines:
invalid_lines = get_lines( feature )
first_invalid_line = line_count
skipped_lines += len( invalid_lines )
continue
else:
warning = "Chromosome by name '%s' was not found for build '%s'. " % ( chrom, dbkey )
warnings.append( warning )
if not invalid_lines:
invalid_lines = get_lines( feature )
first_invalid_line = line_count
skipped_lines += len( invalid_lines )
continue
if sequence == '':
warning = "Chrom: '%s', start: '%s', end: '%s' is either invalid or not present in build '%s'. " % \
( chrom, start, end, dbkey )
warnings.append( warning )
if not invalid_lines:
invalid_lines = get_lines( feature )
first_invalid_line = line_count
skipped_lines += len( invalid_lines )
continue
if includes_strand_col and strand == "-":
sequence = reverse_complement( sequence )
if output_format == "fasta":
l = len( sequence )
c = 0
if gff_format:
start, end = gff_util.convert_bed_coords_to_gff( [ start, end ] )
fields = [dbkey, str( chrom ), str( start ), str( end ), strand]
meta_data = "_".join( fields )
if name.strip():
fout.write( ">%s %s\n" % (meta_data, name) )
else:
fout.write( ">%s\n" % meta_data )
while c < l:
b = min( c + 50, l )
fout.write( "%s\n" % str( sequence[c:b] ) )
c = b
else: # output_format == "interval"
if gff_format and interpret_features:
# TODO: need better GFF Reader to capture all information needed
# to produce this line.
meta_data = "\t".join(
[feature.chrom, "galaxy_extract_genomic_dna", "interval",
str( feature.start ), str( feature.end ), feature.score, feature.strand,
".", gff_util.gff_attributes_to_str( feature.attributes, "GTF" ) ] )
else:
meta_data = "\t".join( fields )
if gff_format:
format_str = "%s seq \"%s\";\n"
else:
format_str = "%s\t%s\n"
fout.write( format_str % ( meta_data, str( sequence ) ) )
# Update line count.
if isinstance( feature, gff_util.GFFFeature ):
line_count += len( feature.intervals )
else:
line_count += 1
fout.close()
if warnings:
warn_msg = "%d warnings, 1st is: " % len( warnings )
warn_msg += warnings[0]
print(warn_msg)
if skipped_lines:
# Error message includes up to the first 10 skipped lines.
print('Skipped %d invalid lines, 1st is #%d, "%s"' % ( skipped_lines, first_invalid_line, '\n'.join( invalid_lines[:10] ) ))
# Clean up temp file.
if fasta_file:
os.remove( seq_path )
os.remove( tmp_name )
if strand not in ['+', '-']:
strand = '+'
sequence = ''
else:
continue
# Open sequence file and get sequence for feature/interval.
if seq_path and os.path.exists( "%s/%s.nib" % ( seq_path, chrom ) ):
# TODO: improve support for GFF-nib interaction.
if chrom in nibs:
nib = nibs[chrom]
else:
nibs[chrom] = nib = bx.seq.nib.NibFile( file( "%s/%s.nib" % ( seq_path, chrom ) ) )
try:
sequence = nib.get( start, end-start )
except Exception, e:
warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey )
warnings.append( warning )
if not invalid_lines:
invalid_lines = get_lines( feature )
first_invalid_line = line_count
skipped_lines += len( invalid_lines )
continue
elif seq_path and os.path.isfile( seq_path ):
if not(twobitfile):
twobitfile = bx.seq.twobit.TwoBitFile( file( seq_path ) )
try:
if options.gff and interpret_features:
# Create sequence from intervals within a feature.
sequence = ''
def __main__():
lflank = 0
rflank = 0
options, args = doc_optparse.parse(__doc__)
try:
chrom_col, start_col, end_col, strand_col = parse_cols_arg(
options.cols)
output_format = options.output_format
seq_path = options.seq_path
if (options.left_flank): lflank = int(options.left_flank)
if (options.right_flank): rflank = int(options.right_flank)
input_filename, output_filename = args
except:
doc_optparse.exception()
includes_strand_col = strand_col >= 0
strand = None
nibs = {}
twobits = {}
if not os.path.exists(seq_path):
# If this occurs, we need to fix the metadata validator.
print "No sequences are available for '%s', request them by reporting this error."
skipped_lines = 0
first_invalid_line = 0
invalid_line = ''
fout = open(output_filename, "w")
warnings = []
warning = ''
twobitfile = None
dbkey = seq_path
for i, line in enumerate(open(input_filename)):
line = line.rstrip('\r\n')
if line and not line.startswith("#"):
fields = line.split('\t')
try:
chrom = fields[chrom_col]
ostart = int(fields[start_col])
oend = int(fields[end_col])
start = ostart - lflank
end = oend + rflank
if includes_strand_col:
strand = fields[strand_col]
except:
warning = "Invalid chrom, start or end column values. "
warnings.append(warning)
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
continue
if start > end:
warning = "Invalid interval, start '%d' > end '%d'. " % (
start, end)
warnings.append(warning)
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
continue
if strand not in ['+', '-']:
strand = '+'
sequence = ''
if seq_path and os.path.exists("%s/%s.nib" % (seq_path, chrom)):
if chrom in nibs:
nib = nibs[chrom]
else:
nibs[chrom] = nib = bx.seq.nib.NibFile(
file("%s/%s.nib" % (seq_path, chrom)))
try:
sequence = nib.get(start, end - start)
except:
warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " % (
start, end - start, dbkey)
warnings.append(warning)
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
continue
elif seq_path and os.path.isfile(seq_path):
if not (twobitfile):
twobitfile = bx.seq.twobit.TwoBitFile(file(seq_path))
try:
sequence = twobitfile[chrom][start:end]
except:
warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " % (
start, end - start, dbkey)
warnings.append(warning)
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
continue
else:
warning = "Chromosome by name '%s' was not found for build '%s'. " % (
chrom, dbkey)
warnings.append(warning)
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
continue
if sequence == '':
warning = "Chrom: '%s', start: '%s', end: '%s' is either invalid or not present in build '%s'. " % (
chrom, start, end, dbkey)
warnings.append(warning)
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
continue
if includes_strand_col and strand == "-":
sequence = reverse_complement(sequence)
sequence = sequence[0:lflank].lower(
) + sequence[lflank:len(sequence) - rflank +
1].upper() + sequence[len(sequence) - rflank +
1:len(sequence)].lower()
if output_format == "fasta":
l = len(sequence)
c = 0
fields = [dbkey, str(chrom), str(ostart), str(oend), strand]
meta_data = "_".join(fields)
fout.write(">%s\n" % meta_data)
while c < l:
b = min(c + 50, l)
fout.write("%s\n" % str(sequence[c:b]))
c = b
else: # output_format == "interval"
meta_data = "\t".join(fields)
fout.write("%s\t%s\n" % (meta_data, str(sequence)))
fout.close()
if warnings:
warn_msg = "%d warnings, 1st is: " % len(warnings)
warn_msg += warnings[0]
print warn_msg
if skipped_lines:
print 'Skipped %d invalid lines, 1st is #%d, "%s"' % (
skipped_lines, first_invalid_line, invalid_line)