def main():
progname = get_progname()
# Get the command line options.
syntax = cmdsyntax.Syntax(syntax_description)
try:
matches = syntax.get_args(sys.argv[1:])
args = matches[0]
except IndexError:
print >>sys.stderr, "Syntax:"
print >>sys.stderr, syntax_description
sys.exit(1)
else:
if args.has_key("help"):
print >>sys.stderr, __doc__
print >>sys.stderr, "Syntax:"
print >>sys.stderr, syntax_description
sys.exit(1)
try:
fields = int(args["fields"])
except ValueError:
print >>sys.stderr, "%s: Need a number of fields/columns." % progname
sys.exit(1)
padding = args["padding"]
if args.has_key("filename"):
filename = filename_or_stream = args["filename"]
else:
filename_or_stream = reread(sys.stdin)
filename = None
reader = RawImportFileReader(filename_or_stream)
writer = RawImportFile(rewrite(sys.stdout))
try:
try:
for details in reader:
# Pad the line to have at least as many fields as indicated.
if len(details) < fields:
details += (fields - len(details)) * [padding]
writer.append(details)
except IOError, exc:
print >>sys.stderr, "%s: %s" % (progname, exc)
finally:
reader.close()
def main():
progname = get_progname()
# Get the command line options.
syntax = cmdsyntax.Syntax(syntax_description)
try:
matches = syntax.get_args(sys.argv[1:])
args = matches[0]
except IndexError:
print >> sys.stderr, "Syntax:"
print >> sys.stderr, syntax_description
sys.exit(1)
else:
if args.has_key("help"):
print >> sys.stderr, __doc__
print >> sys.stderr, "Syntax:"
print >> sys.stderr, syntax_description
sys.exit(1)
try:
fields = int(args["fields"])
except ValueError:
print >> sys.stderr, "%s: Need a number of fields/columns." % progname
sys.exit(1)
padding = args["padding"]
if args.has_key("filename"):
filename = filename_or_stream = args["filename"]
else:
filename_or_stream = reread(sys.stdin)
filename = None
reader = RawImportFileReader(filename_or_stream)
writer = RawImportFile(rewrite(sys.stdout))
try:
try:
for details in reader:
# Pad the line to have at least as many fields as indicated.
if len(details) < fields:
details += (fields - len(details)) * [padding]
writer.append(details)
except IOError, exc:
print >> sys.stderr, "%s: %s" % (progname, exc)
finally:
reader.close()
def main():
# Get the command line options.
syntax = cmdsyntax.Syntax(syntax_description)
try:
matches = syntax.get_args(sys.argv[1:])
args = matches[0]
except IndexError:
print >> sys.stderr, "Syntax:"
print >> sys.stderr, syntax_description
sys.exit(1)
else:
if args.has_key("help"):
print >> sys.stderr, __doc__
print >> sys.stderr, "Syntax:"
print >> sys.stderr, syntax_description
sys.exit(1)
fields = map(index_for_int, args["fields"].split(","))
if args.has_key("filename"):
filename = filename_or_stream = args["filename"]
else:
filename_or_stream = reread(sys.stdin)
filename = None
reader = RawImportFileReader(filename_or_stream)
writer = RawImportFile(rewrite(sys.stdout))
try:
try:
for details in reader:
# Filter the fields.
details = [
details[field] for field in fields if field is not None
]
# Cut the columns according to the field details.
writer.append(details)
except IOError, exc:
print >> sys.stderr, "%s: %s" % (get_progname(), exc)
finally:
reader.close()
def main():
# Get the command line options.
syntax = cmdsyntax.Syntax(syntax_description)
try:
matches = syntax.get_args(sys.argv[1:])
args = matches[0]
except IndexError:
print >>sys.stderr, "Syntax:"
print >>sys.stderr, syntax_description
sys.exit(1)
else:
if args.has_key("help"):
print >>sys.stderr, __doc__
print >>sys.stderr, "Syntax:"
print >>sys.stderr, syntax_description
sys.exit(1)
fields = map(index_for_int, args["fields"].split(","))
if args.has_key("filename"):
filename = filename_or_stream = args["filename"]
else:
filename_or_stream = reread(sys.stdin)
filename = None
reader = RawImportFileReader(filename_or_stream)
writer = RawImportFile(rewrite(sys.stdout))
try:
try:
for details in reader:
# Filter the fields.
details = [details[field] for field in fields if field is not None]
# Cut the columns according to the field details.
writer.append(details)
except IOError, exc:
print >>sys.stderr, "%s: %s" % (get_progname(), exc)
finally:
reader.close()
return mitab26_fields
elif file_format == "mitab27":
return mitab27_fields
elif file_format == "irefindex":
return irefindex_fields
###########
# Main
###########
if __name__ == "__main__":
from irdata.cmd import get_progname
import sys
progname = get_progname()
try:
source = sys.argv[1]
directory = sys.argv[2]
filenames = sys.argv[3:]
except IndexError:
print("Usage: %s <source> <output data directory> <filename>..." %
progname,
file=sys.stderr)
sys.exit(1)
try:
# set up based on type of file to be parsed.
file_format = detect_file_format(filenames)
if file_format == "unknown":
def main():
progname = get_progname()
# Get the command line options.
syntax = cmdsyntax.Syntax(syntax_description)
try:
matches = syntax.get_args(sys.argv[1:])
args = matches[0]
except IndexError:
print >>sys.stderr, "Syntax:"
print >>sys.stderr, syntax_description
sys.exit(1)
else:
if args.has_key("help"):
print >>sys.stderr, __doc__
print >>sys.stderr, "Syntax:"
print >>sys.stderr, syntax_description
sys.exit(1)
start_field = index_for_int(args.get("start-field", 1))
end_field = int_or_none(args.get("end-field", None)) # treat 1-index as 0-index plus one
delimiter = args.get("delimiter", "\t")
delimiter_within_fields = args.get("delimiter-within-fields", "\t")
sequence_start = int_or_none(args.get("sequence-start"))
if args.has_key("filename"):
filename_or_stream = args["filename"]
else:
filename_or_stream = reread(sys.stdin)
reader = RawImportFileReader(filename_or_stream, delimiter=delimiter)
writer = RawImportFile(rewrite(sys.stdout))
try:
try:
for details in reader:
# Process the data.
preceding, fields, following = partition(details, start_field, end_field)
if delimiter_within_fields != delimiter:
split_fields = []
for field in fields:
split_fields += field.split(delimiter_within_fields)
fields = split_fields
for i, field in enumerate(fields):
if sequence_start is not None:
values = [i + sequence_start, field]
else:
values = [field]
writer.append(preceding + values + following)
except IOError, exc:
print >>sys.stderr, "%s: %s" % (progname, exc)
finally:
writer.close()
reader.close()
"""
from irdata.data import RawImportFile, rewrite, index_for_int
from irdata.cmd import get_progname
from os.path import split, splitext
import sys, cmdsyntax, gzip
syntax_description = """
--help |
(
<interval> [ <filename> | - ] [ -f <field> ] [ -d <separator> ]
)
"""
if __name__ == "__main__":
progname = get_progname()
# Get the command line options.
syntax = cmdsyntax.Syntax(syntax_description)
try:
matches = syntax.get_args(sys.argv[1:])
args = matches[0]
except IndexError:
print >>sys.stderr, "Syntax:"
print >>sys.stderr, syntax_description
sys.exit(1)
else:
if args.has_key("help"):
print >>sys.stderr, __doc__
print >>sys.stderr, "Syntax:"
def main():
progname = get_progname()
# Get the command line options.
syntax = cmdsyntax.Syntax(syntax_description)
try:
matches = syntax.get_args(sys.argv[1:])
args = matches[0]
except IndexError:
print >>sys.stderr, "Syntax:"
print >>sys.stderr, syntax_description
sys.exit(1)
else:
if args.has_key("help"):
print >>sys.stderr, __doc__
print >>sys.stderr, "Syntax:"
print >>sys.stderr, syntax_description
sys.exit(1)
start_field = index_for_int(args.get("start-field", 1))
end_field = int_or_none(args.get("end-field", None)) # treat 1-index as 0-index plus one
delimiter = args.get("delimiter", "\t")
delimiter_within_fields = args.get("delimiter-within-fields", "\t")
sequence_start = int_or_none(args.get("sequence-start"))
if args.has_key("filename"):
filename_or_stream = args["filename"]
else:
filename_or_stream = reread(sys.stdin)
reader = RawImportFileReader(filename_or_stream, delimiter=delimiter)
writer = RawImportFile(rewrite(sys.stdout))
try:
try:
for details in reader:
# Process the data.
preceding, fields, following = partition(details, start_field, end_field)
if delimiter_within_fields != delimiter:
split_fields = []
for field in fields:
split_fields += field.split(delimiter_within_fields)
fields = split_fields
for i, field in enumerate(fields):
if sequence_start is not None:
values = [i + sequence_start, field]
else:
values = [field]
writer.append(preceding + values + following)
except IOError, exc:
print >>sys.stderr, "%s: %s" % (progname, exc)
finally:
writer.close()
reader.close()
