def __init__(self, fnames, keepExons=False, labels=None, verbose=False):
"""
Driver function to actually parse files. The steps are as follows:
1) skip to the first non-comment line
2) Infer the type from that
3) Call a type-specific processing function accordingly
* These call the underlying C code for storage
* These handle chromsome name conversions (python-level)
Required inputs are as follows:
fnames: A list of (possibly compressed with gzip or bzip2) GTF or BED files.
Optional input is:
keepExons: For BED12 files, exons are ignored by default.
labels: Override the feature labels supplied in the file(s).
Note that this might instead be replaced later in the .features attribute.
verbose: Whether to print warnings (default: False)
"""
self.fname = []
self.filename = ""
self.chroms = []
self.features = []
self.tree = tree.initTree()
self.keepExons = keepExons
self.verbose = verbose
if not isinstance(fnames, list):
fnames = [fnames]
# Load the files
for labelIdx, fname in enumerate(fnames):
self.filename = fname
fp = openPossiblyCompressed(fname)
line, labelColumn = self.firstNonComment(fp)
if line is None:
# This will only ever happen if a file is empty or just has a header/comment
continue
line = line.strip()
ftype = self.inferType(fp, line, labelColumn)
if ftype != 'GTF' and labels is not None:
assert(len(labels) > labelIdx)
bname = labels[labelIdx]
else:
bname = basename(fname)
if ftype == 'GTF':
self.parseGTF(fp, line)
elif ftype == 'BED3':
self.parseBED(fp, line, 3, feature=bname, labelColumn=labelColumn)
elif ftype == 'BED6':
self.parseBED(fp, line, 6, feature=bname, labelColumn=labelColumn)
else:
self.parseBED(fp, line, 12, feature=bname, labelColumn=labelColumn)
fp.close()
# Sanity check
if self.tree.countEntries() == 0:
raise RuntimeError("None of the input BED/GTF files had valid regions")
if len(self.features) == 0:
raise RuntimeError("There were no valid feature labels!")
# vine -> tree
self.tree.finish()
def __init__(self, fnames, keepExons=False, labels=None, verbose=False):
"""
Driver function to actually parse files. The steps are as follows:
1) skip to the first non-comment line
2) Infer the type from that
3) Call a type-specific processing function accordingly
* These call the underlying C code for storage
* These handle chromsome name conversions (python-level)
Required inputs are as follows:
fnames: A list of (possibly compressed with gzip or bzip2) GTF or BED files.
Optional input is:
keepExons: For BED12 files, exons are ignored by default.
labels: Override the feature labels supplied in the file(s).
Note that this might instead be replaced later in the .features attribute.
verbose: Whether to print warnings (default: False)
"""
self.fname = []
self.filename = ""
self.chroms = []
self.features = []
self.tree = tree.initTree()
self.keepExons = keepExons
self.verbose = verbose
if not isinstance(fnames, list):
fnames = [fnames]
# Load the files
for labelIdx, fname in enumerate(fnames):
self.filename = fname
fp = openPossiblyCompressed(fname)
line, labelColumn = self.firstNonComment(fp)
if line is None:
# This will only ever happen if a file is empty or just has a header/comment
continue
line = line.strip()
ftype = self.inferType(fp, line, labelColumn)
if ftype != 'GTF' and labels is not None:
assert(len(labels) > labelIdx)
bname = labels[labelIdx]
else:
bname = basename(fname)
if ftype == 'GTF':
self.parseGTF(fp, line)
elif ftype == 'BED3':
self.parseBED(fp, line, 3, feature=bname, labelColumn=labelColumn)
elif ftype == 'BED6':
self.parseBED(fp, line, 6, feature=bname, labelColumn=labelColumn)
else:
self.parseBED(fp, line, 12, feature=bname, labelColumn=labelColumn)
fp.close()
# Sanity check
if self.tree.countEntries() == 0:
raise RuntimeError("None of the input BED/GTF files had valid regions")
if len(self.features) == 0:
raise RuntimeError("There were no valid feature labels!")
# vine -> tree
self.tree.finish()
def __init__(self, fnames, exonID="exon", transcriptID="transcript", keepExons=False, labels=[], transcript_id_designator="transcript_id", defaultGroup=None, verbose=False):
"""
Driver function to actually parse files. The steps are as follows:
1) skip to the first non-comment line
2) Infer the type from that
3) Call a type-specific processing function accordingly
* These call the underlying C code for storage
* These handle chromsome name conversions (python-level)
* These handle labels (python-level, with a C-level numeric attribute)
4) Sanity checking (do the number of labels make sense?)
Required inputs are as follows:
fnames: A list of (possibly compressed with gzip or bzip2) GTF or BED files.
Optional input is:
exonID: For GTF files, the feature column (column 3) label for
exons, or whatever else should be stored as exons. The
default is 'exon', though one could use 'CDS' instead.
transcriptID: As above, but for transcripts. The default is
'transcript_id'.
keepExons: For BED12 and GTF files, exons are ignored by default.
labels: A list of group labels.
transcript_id_designator: For gtf files, this is the key used in a searching for the transcript ID.
If one sets transcriptID to 'gene', then
transcript_id_designator would need to be changed to
'gene_id' or 'gene_name' to extract the gene ID/name from
the attributes.
defaultGroup: The default group name. If None, the file name is used.
verbose: Whether to produce warning messages (default: False)
"""
self.fname = []
self.filename = ""
self.chroms = []
self.exons = []
self.labels = []
self.transcriptIDduplicated = []
self.tree = tree.initTree()
self.labelIdx = 0
self.transcript_id_designator = transcript_id_designator
self.exonID = exonID
self.transcriptID = transcriptID
self.keepExons = keepExons
self.defaultGroup = defaultGroup
self.verbose = verbose
if labels != []:
self.already_input_labels = True
if not isinstance(fnames, list):
fnames = [fnames]
# Load the files
for fname in fnames:
self.filename = fname
fp = openPossiblyCompressed(fname)
line, labelColumn = self.firstNonComment(fp)
if line is None:
# This will only ever happen if a file is empty or just has a header/comment
continue
line = line.strip()
ftype = self.inferType(fp, line, labelColumn)
if ftype == 'GTF':
self.parseGTF(fp, line)
elif ftype == 'BED3':
self.parseBED(fp, line, 3, labelColumn)
elif ftype == 'BED6':
self.parseBED(fp, line, 6, labelColumn)
else:
self.parseBED(fp, line, 12, labelColumn)
fp.close()
# Sanity check
if self.tree.countEntries() == 0:
raise RuntimeError("None of the input BED/GTF files had valid regions")
# Replace labels
if len(labels) > 0:
if len(labels) != len(self.labels):
raise RuntimeError("The number of labels found ({0}) does not match the number input ({1})!".format(self.labels, labels))
else:
self.labels = labels
# vine -> tree
self.tree.finish()
def __init__(self,
fnames,
exonID="exon",
transcriptID="transcript",
keepExons=False,
labels=[],
transcript_id_designator="transcript_id",
defaultGroup=None,
verbose=False):
"""
Driver function to actually parse files. The steps are as follows:
1) skip to the first non-comment line
2) Infer the type from that
3) Call a type-specific processing function accordingly
* These call the underlying C code for storage
* These handle chromsome name conversions (python-level)
* These handle labels (python-level, with a C-level numeric attribute)
4) Sanity checking (do the number of labels make sense?)
Required inputs are as follows:
fnames: A list of (possibly compressed with gzip or bzip2) GTF or BED files.
Optional input is:
exonID: For GTF files, the feature column (column 3) label for
exons, or whatever else should be stored as exons. The
default is 'exon', though one could use 'CDS' instead.
transcriptID: As above, but for transcripts. The default is
'transcript_id'.
keepExons: For BED12 and GTF files, exons are ignored by default.
labels: A list of group labels.
transcript_id_designator: For gtf files, this is the key used in a searching for the transcript ID.
If one sets transcriptID to 'gene', then
transcript_id_designator would need to be changed to
'gene_id' or 'gene_name' to extract the gene ID/name from
the attributes.
defaultGroup: The default group name. If None, the file name is used.
verbose: Whether to produce warning messages (default: False)
"""
self.fname = []
self.filename = ""
self.chroms = []
self.exons = []
self.labels = []
self.transcriptIDduplicated = []
self.tree = tree.initTree()
self.labelIdx = 0
self.transcript_id_designator = transcript_id_designator
self.exonID = exonID
self.transcriptID = transcriptID
self.keepExons = keepExons
self.defaultGroup = defaultGroup
self.verbose = verbose
if labels != []:
self.already_input_labels = True
if not isinstance(fnames, list):
fnames = [fnames]
# Load the files
for fname in fnames:
self.filename = fname
fp = openPossiblyCompressed(fname)
line, labelColumn = self.firstNonComment(fp)
if line is None:
# This will only ever happen if a file is empty or just has a header/comment
continue
line = line.strip()
ftype = self.inferType(fp, line, labelColumn)
if ftype == 'GTF':
self.parseGTF(fp, line)
elif ftype == 'BED3':
self.parseBED(fp, line, 3, labelColumn)
elif ftype == 'BED6':
self.parseBED(fp, line, 6, labelColumn)
else:
self.parseBED(fp, line, 12, labelColumn)
fp.close()
# Sanity check
if self.tree.countEntries() == 0:
raise RuntimeError(
"None of the input BED/GTF files had valid regions")
# Replace labels
if len(labels) > 0:
if len(labels) != len(self.labels):
raise RuntimeError(
"The number of labels found ({0}) does not match the number input ({1})!"
.format(self.labels, labels))
else:
self.labels = labels
# vine -> tree
self.tree.finish()