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"""Read GAF file and allow ND Evidence codes.""" |
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__copyright__ = "Copyright (C) 2016-2018, DV Klopfenstein, H Tang. All rights reserved." |
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__author__ = "DV Klopfenstein" |
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import sys |
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from goatools.associations import read_gaf |
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from goatools.base import dnld_gaf |
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def test_gaf_read(log=sys.stdout): |
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"""Return GO associations from a GAF file. Download if necessary.""" |
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# On 2017/04/10, there were 3 GO IDs with ND Evidence Codes: |
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# |
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# $ cut -f5,7 goa_human.gaf | grep ND | sort | uniq -c |
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# 739 GO:0003674 ND |
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# 484 GO:0005575 ND |
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# 639 GO:0008150 ND |
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# Example species_ids: goa_human mgi fb |
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fin_gaf = dnld_gaf('goa_human', loading_bar=None) |
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# Example 1: Read GAF |
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go2ids = read_gaf(fin_gaf, go2geneids=True) |
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num_gos_dflt = len(go2ids) |
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log.write("Read {N} GOs with all default values\n\n".format(N=num_gos_dflt)) |
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# Example 2: Read GAF using defaults (No NOT Qualifiers and no ND Evidence Codes) |
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go2ids = read_gaf(fin_gaf, go2geneids=True, keep_ND=False, keep_NOT=False) |
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log.write("Read {N} GOs; keepif is default in goatools.associations.read_gaf\n\n".format( |
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N=len(go2ids))) |
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# Example 3: Read GAF allowing GOs with ND Evidence Codes |
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go2ids = read_gaf(fin_gaf, go2geneids=True, keep_ND=True) |
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log.write("Read {N} GOs; Allow ND Evidence codes\n\n".format(N=len(go2ids))) |
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# Example 4: Read GAF allowing all GOs, even those with NOT Qualifiers or ND Evidence Codes |
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go2ids = read_gaf(fin_gaf, go2geneids=True, keep_ND=True, keep_NOT=True) |
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log.write("Read {N} GOs; Allow ND Evidence codes and NOT Qualifiers\n\n".format(N=len(go2ids))) |
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if __name__ == '__main__': |
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test_gaf_read() |
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# Copyright (C) 2016-2018, DV Klopfenstein, H Tang. All rights reserved. |
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tanghaibao /
goatools
