bowtie build #12
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bowtie build #12
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Merge branch 'master' of https://github.com/jkanbar/tcga-1
wasade
reviewed
Nov 8, 2016
| taxa_levels, | ||
| read_per_taxa): | ||
| """Absolute abundance of number of reads matching a defined taxa level. | ||
| Parameters |
| taxonomic_abundances= [] | ||
| for report_fp in kraken_mpa_report_fp: | ||
| with open(report_fp) as report_fp: | ||
| for line in report_fp: |
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would it be possible to break this parser out? seems like a logical point for decomposition. i'm not seeing a paired unit test or set of tests either...?
| taxonomic_abundances.append(taxonomy_parse) | ||
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| taxonomies = set([k for k, v in | ||
| collections.Counter(taxonomic_abundances).iteritems() |
| output_filename): | ||
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| """Return sets for sample IDs and taxonomy strings. | ||
| Parameters |
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| @click.command() | ||
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| with open(scores_repophlan_fp) as scores_repophlan_f: | ||
| # header | ||
| line = scores_repophlan_f.readline() | ||
| line = line.strip().split('\t') |
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yea... i think pandas would be so nice here
| # only want tax_ids for genomes passing quality filter | ||
| if genome_id in genomes: | ||
| tax_id = line[tax_id_idx] | ||
| # tax_id must be an integer, if not check the field |
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that sucks. has this bug been reported to the repophlan maintainers?
| taxid = info[1] | ||
| genome_fp_name = basename(splitext(genome_fp)[0]) | ||
| # check FNA file exists for genome | ||
| if genome_fp_name != "": |
| output_fp = join(repophlan_scores_filtered_genomes_dp, | ||
| genome_fp_name) | ||
| # skip files already modified (e.g. from previous run) | ||
| if not isfile(output_fp): |
| """Edit qualified genomes' labels to Kraken format. | ||
| """ | ||
| # .fna.bz2 genomes folder | ||
| all_genomes_bz2_dp = sys.argv[1] |
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Continuing from #10