45 lines
1.3 KiB
Python
45 lines
1.3 KiB
Python
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def smdb_annot(orflist=None, input_fname='registry.genenames.tab', output_fname='yeast.annot'):
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"""Reads registry.genenames.tab from the Stanford yeast
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microarray database.
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Available from:
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ftp://genome-ftp.stanford.edu/pub/yeast/data_download/gene_registry/registry.genenames.tab
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input: orf -- list of orfs (open reading frames)
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file -- (optional) file to fetch info from
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registry.genames contains:
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0 = Locus name
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1 = Other name
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2 = Description
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3 = Gene product
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4 = Phenotype
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5 = ORF name
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6 = SGDID
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NB! Other name, Gene product and Phenotype may have more
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than one mapping. These are separated by |
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Output: writes an annotation file
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"""
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outfile = open(output_fname, 'w')
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header = "Orf\tLocus_id\tOther_name\tDescription\tGene_product\tPhenotype\tSGD_ID\n"
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outfile.write(header)
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text = open(input_fname, 'r').read().splitlines()
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for line in text:
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els = line.split('\t')
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orf_name = els.pop(5)
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if orf_name!='': # we dont care about non-named orfs
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if orflist and orf_name not in orflist:
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break
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for e in els:
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if e !='':
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outfile.write(str(e) + "\t")
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else:
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outfile.write("NA")
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f.write("\n")
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