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Viewing changes to qiime/truncate_reverse_primer.py

  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2013-06-17 18:28:26 UTC
  • mfrom: (9.1.2 sid)
  • Revision ID: package-import@ubuntu.com-20130617182826-376az5ad080a0sfe
Tags: 1.7.0+dfsg-1
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qiime/truncate_reverse_primer.py
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__copyright__ = "Copyright 2011, The QIIME Project"
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__credits__ = ["William Walters"]
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__license__ = "GPL"
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__version__ = "1.5.0"
 
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__version__ = "1.7.0"
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__maintainer__ = "William Walters"
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__email__ = "William.A.Walters@colorado.edu"
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__status__ = "Release"
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    mapping_fp:  mapping filepath
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    """
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    hds, mapping_data, run_description, errors, warnings = \
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        process_id_map(mapping_fp)
 
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        process_id_map(mapping_fp, has_barcodes=False,
 
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         disable_primer_check=True)
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    if errors:
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        raise ValueError,('Errors were found with mapping file, '+\
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         'please run check_id_map.py to identify problems.')
 
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        for curr_err in errors:
 
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            if curr_err.startswith("Duplicate SampleID"):
 
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                raise ValueError,('Errors were found with mapping file, '+\
 
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                 'please run check_id_map.py to identify problems.')
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    # create dict of dicts with SampleID:{each header:mapping data}
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    for curr_id in id_map.keys():
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        try:
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            reverse_primers[curr_id] =\
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             DNA.rc(id_map[curr_id]['ReversePrimer'])
 
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             [DNA.rc(curr_rev_primer) for curr_rev_primer in\
 
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             id_map[curr_id]['ReversePrimer'].split(',')]
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        except KeyError:
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            raise KeyError,("Reverse primer not found in mapping file, "+\
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             "please include a 'ReversePrimer' column.")
 
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    # Check for valid reverse primers
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    # Will have been detected as warnings from mapping file
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    for curr_warning in warnings:
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        if curr_warning.startswith("reverse primer"):
 
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    for curr_err in errors:
 
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        if curr_err.startswith("Invalid DNA sequence detected"):
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            raise ValueError,("Problems found with reverse primers, please "+\
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             "check mapping file with check_id_map.py")
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    return reverse_primers
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def get_output_filepaths(output_dir,
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            log_data['seqs_written'] += 1
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            continue
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        rev_primer_mm, rev_primer_index =\
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         local_align_primer_seq(curr_rev_primer, seq)
 
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        mm_tests = {}
 
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        for rev_primer in curr_rev_primer: 
 
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            rev_primer_mm, rev_primer_index =\
 
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             local_align_primer_seq(rev_primer, seq)
 
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            mm_tests[rev_primer_mm] = rev_primer_index
 
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        rev_primer_mm = min(mm_tests.keys())
 
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        rev_primer_index = mm_tests[rev_primer_mm]
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        if rev_primer_mm > primer_mismatches:
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            if truncate_option == "truncate_remove":