g2gtools.g2g module¶
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class
g2gtools.g2g.
G2GFormatter
(fmt='[g2gtools] %(msg)s')[source]¶ Bases:
logging.Formatter
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dbg_fmt
= '[g2gtools debug] %(msg)s'¶
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err_fmt
= '[g2gtools] %(msg)s'¶
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format
(record)[source]¶ Format the specified record as text.
The record’s attribute dictionary is used as the operand to a string formatting operation which yields the returned string. Before formatting the dictionary, a couple of preparatory steps are carried out. The message attribute of the record is computed using LogRecord.getMessage(). If the formatting string uses the time (as determined by a call to usesTime(), formatTime() is called to format the event time. If there is exception information, it is formatted using formatException() and appended to the message.
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info_fmt
= '[g2gtools] %(msg)s'¶
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class
g2gtools.g2g.
Region
(seq_id, start=None, end=None, strand='+', name=None, original_base=0)[source]¶ Bases:
object
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end
¶
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start
¶
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strand
¶
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g2gtools.g2g.
exit
(message='', parser=None)[source]¶ Print message, help, and exit.
Parameters: - message – The message to print
- parser – the argument parser
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g2gtools.g2g.
get_multiplier
(factor)[source]¶ Convert the factor into a number.
Parameters: factor – the string ‘mb’, ‘m’, or ‘k’ Returns: 10000000, 1000000, 1000 or 1
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g2gtools.g2g.
parse_region
(location_str, base=0, name=None)[source]¶ Parse a string and return a location.
Format expected is seqid|start|end, where | is some sort of delimiter.
If end is None, 1 based was requested.
Parameters: - location_str – a string representing a genomic location
- base – a number 0 or 1
Returns: a Region