76 lines
2.7 KiB
Python
Executable File
76 lines
2.7 KiB
Python
Executable File
#!/usr/bin/env python
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import operator, FlatFileTable
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class db_file:
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filename = ""
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def __init__(self, filenm):
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self.filename = filenm
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def count_fields(self, fixed_field, fixed_field_values, count_field):
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record_gen = FlatFileTable.record_generator(self.filename)
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counts = dict()
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#fixed_field_num = self.field_names[fixed_field]
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print count_field+" for "+fixed_field+" = "+" or ".join(fixed_field_values)
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for record in record_gen:
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if record[fixed_field] in fixed_field_values:
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#fixed_field_value = fields[fixed_field_num]
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count_field_num = record[count_field]
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if counts.has_key(count_field_num):
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counts[count_field_num] += 1
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else:
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counts[count_field_num] = 0
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for k,v in sorted(counts.items(), key=operator.itemgetter(1), cmp=lambda x,y: y-x ):
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print str(k)+"\t"+str(v)
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def count_bases(self, fixed_field_values): #, fixed_field_values):
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record_gen = FlatFileTable.record_generator(self.filename)
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base_count = 0
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#fixed_field_num = self.field_names[fixed_field]
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#print "For "+fixed_field+" = "+" or ".join(fixed_field_values)+":",
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print "For "+ " AND ".join( [one_ffv[0]+" = "+" OR ".join(one_ffv[1]) for one_ffv in fixed_field_values] )
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for record in record_gen:
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#if record[fixed_field] in fixed_field_values:
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if FlatFileTable.record_matches_values(record, fixed_field_values):
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try:
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base_count += int(record["BASE_COUNT"])
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except ValueError:
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pass
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print "%e bases" % base_count
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if __name__ == "__main__":
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db = db_file("sequence.index")
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platforms = (("ILLUMINA",), ("AB SOLiD","SOLID","ABI_SOLID","AB SOLiD System 2.0"), ("LS454",))
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studies = (("1000Genomes Project Pilot 1",), ("1000Genomes Project Pilot 2",), ("1000Genomes Project Pilot 3",))
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for select_field, select_field_values in (): #(("INSTRUMENT_PLATFORM", platforms), ("STUDY_NAME", studies)):
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for count_field in ("CENTER_NAME", "STUDY_NAME", "INSTRUMENT_PLATFORM"):
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for select_field_value in select_field_values:
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db.count_fields(select_field, select_field_value, count_field)
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for select_field_value in select_field_values:
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db.count_bases(((select_field, select_field_value),))
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print
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for field1, value1 in zip(["INSTRUMENT_PLATFORM"]*len(platforms), platforms):
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for field2, value2 in zip(["STUDY_NAME"]*len(studies), studies):
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db.count_bases(((field1, value1), (field2, value2)))
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