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Merge pull request #68 from artic-network/1.3.0-dev
patch 1.2.0 > 1.2.1
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| #!/usr/bin/env python | ||
| import json | ||
| import re | ||
| import sys | ||
| from collections import OrderedDict | ||
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| from .vcftagprimersites import read_bed_file | ||
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| # Alignment_Length_Threshold drops binned reads that are <X% of amplicon length) | ||
| Alignment_Length_Threshold = 0.95 | ||
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| # Amplicon_Dropout_Val will report amplicon dropout in any amplicon which has fewer than X reads | ||
| Amplicon_Dropout_Val = 50 | ||
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| # Template for the amplicon plot data | ||
| amplicon_plot_template = { | ||
| "id": "custom_data_lineplot", | ||
| "section_name": "ARTIC: Amplicon Coverage", | ||
| "description": "This plot summarises the number of reads that were assigned to each amplicon in the primer scheme.\nWe use the align_trim report file from the ARTIC pipeline and group each read by its assigned amplicon.\nIf the length of alignment between read and reference is <{}% of the amplicon length, the read discarded from the coverage plot.\nIf the total number of reads assigned to an amplicon is below {} (red dashed line),\nthe amplicon is marked as dropped out." .format(Alignment_Length_Threshold, Amplicon_Dropout_Val), | ||
| "plot_type": "linegraph", | ||
| "pconfig": { | ||
| "id": "custom_data_linegraph", | ||
| "title": "", | ||
| "categories": "True", | ||
| "yDecimals": "False", | ||
| "xDecimals": "False", | ||
| "ylab": "# reads", | ||
| "xlab": "amplicon", | ||
| "yPlotLines": [{ | ||
| "color": "#FF0000", | ||
| "width": 2, | ||
| "dashStyle": "LongDash", | ||
| "label": "Amplicon dropout", | ||
| "value": Amplicon_Dropout_Val | ||
| }] | ||
| }, | ||
| "data": {} | ||
| } | ||
|
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| # Template for the stats table data | ||
| amplicon_stats_template = { | ||
| "id": "custom_data_json_table", | ||
| "section_name": "ARTIC: General Stats", | ||
| "description": "A summary of stats from the consensus genome pipeline.", | ||
| "plot_type": "table", | ||
| "pconfig": { | ||
| "id": "custom_data_json_table_table", | ||
| "title": "", | ||
| "min": 0, | ||
| "scale": "RdYlGn-rev", | ||
| "format": "{:,.0f}" | ||
| }, | ||
| "data": {} | ||
| } | ||
|
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| def getSchemeAmplicons(schemeFile): | ||
| """Get the expected amplicon names from the provided scheme. | ||
| Parameters | ||
| ---------- | ||
| schemeFile : string | ||
| The filename of the primer scheme | ||
| Returns | ||
| ------- | ||
| dict | ||
| A dict of amplicon names -> zeroed counter | ||
| """ | ||
| amplicons = {} | ||
| primer_scheme = read_bed_file(schemeFile) | ||
| for primer in primer_scheme: | ||
| amplicon = "" | ||
| if primer["direction"] == "+": | ||
| amplicon = primer["Primer_ID"].split("_LEFT")[0] | ||
| else: | ||
| amplicon = primer["Primer_ID"].split("_RIGHT")[0] | ||
| if amplicon not in amplicons: | ||
| amplicons[amplicon] = 0 | ||
| amplicons[amplicon] += 1 | ||
| named_amplicons = {} | ||
| for amplicon in amplicons: | ||
| if amplicons[amplicon] != 2: | ||
| print("in correct numbers of primer for {}" .format(amplicon), file=sys.stderr) | ||
| raise SystemExit(1) | ||
| named_amplicons[("{}_LEFT_{}_RIGHT" .format(amplicon, amplicon))] = 0 | ||
| return named_amplicons | ||
|
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| def getAmpliconCounts(amplicons, align_trim_report): | ||
| """Get the read counts per amplicon. | ||
| Parameters | ||
| ---------- | ||
| amplicons : list | ||
| Dict of amplicon names found in scheme, linked to a zeroed counter | ||
| align_trim_report: string | ||
| File path to the align_trim report | ||
| Returns | ||
| ------- | ||
| dict | ||
| Dict of amplicon names -> populated read counts | ||
| """ | ||
| # process the align_trim report | ||
| with open(align_trim_report, "r") as fh: | ||
|
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| # skip the first line (header) | ||
| fh.readline() | ||
|
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| # process each line and add to counts | ||
| for l in fh: | ||
| fields = l.rstrip().split('\t') | ||
|
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| # check read is from a properly paired amplicon | ||
| if int(fields[12]) != 1: | ||
| continue | ||
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| # check the read alignment length covers enough of the amplicon | ||
| aLen = int(fields[11]) - int(fields[10]) | ||
| rLen = int(fields[2]) - int(fields[1]) | ||
| if aLen < (Alignment_Length_Threshold * rLen): | ||
| continue | ||
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| # increment the read count for this amplicon | ||
| if fields[3] not in amplicons: | ||
| print("amplicon in align_trim report but not in primer scheme {}" .format(fields[3]), file=sys.stderr) | ||
| raise SystemExit(1) | ||
| amplicons[fields[3]] += 1 | ||
| return amplicons | ||
|
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| def getVCFreportInfo(vcf_report): | ||
| """Get the read counts per amplicon. | ||
| Parameters | ||
| ---------- | ||
| vcf_report: string | ||
| File path to the vcf_report | ||
| Returns | ||
| ------- | ||
| dict | ||
| Dict of vcf stats -> values | ||
| """ | ||
| # Read vcfcheck report and get important stuff out (NOTE: more to be added in next release) | ||
| stats = dict() | ||
| total_vars = 0 | ||
| passed_vars = 0 | ||
| with open(vcf_report, "r") as fh: | ||
| for l in fh: | ||
| match = re.search(r'.*\t(\d+)\svariant\srecords\sprocessed', l) | ||
| if match: | ||
| total_vars = int(match.group(1)) | ||
| match = re.search(r'.*\t(\d+)\svariant\srecords\spassed\schecks', l) | ||
| if match: | ||
| passed_vars = int(match.group(1)) | ||
| stats["# overlap var. fails"] = total_vars - passed_vars | ||
| return stats | ||
|
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| def run(args): | ||
| """Collect stats from ARTIC pipeline output and generate files for use by MultiQC. | ||
| """ | ||
| # get a list of expected amplicon names | ||
| amplicons = getSchemeAmplicons(args.scheme) | ||
|
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| # open align trim output and count reads per amplicon in scheme | ||
| amplicon_counts = getAmpliconCounts(amplicons, args.align_report) | ||
|
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| # replace amplicon names with ints and count number of dropouts | ||
| dropouts = 0 | ||
| amplicon_renamed_counts = dict() | ||
| for amplicon, count in amplicon_counts.items(): | ||
| amplicon_renamed_counts[int(amplicon.split('_')[1])] = count | ||
| if count < Amplicon_Dropout_Val: | ||
| dropouts += 1 | ||
|
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| # add counts to multiqc amplicon plot template | ||
| amplicon_plot_template["data"][args.sample] = amplicon_renamed_counts | ||
|
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| # write the amplicon plot output | ||
| with open("{}.amplicon_plot_data_mqc.json" .format(args.sample), "w") as amplicon_plot_mqc_file: | ||
| json.dump(amplicon_plot_template, amplicon_plot_mqc_file, indent=4, sort_keys=False) | ||
| amplicon_plot_mqc_file.close() | ||
|
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| # add counts to multiqc stats template | ||
| amplicon_stats_template["data"][args.sample] = dict() | ||
| amplicon_stats_template["data"][args.sample]["# low cov. amplicons"] = dropouts | ||
|
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| # parse VCF report if provided and add to the stats template | ||
| if args.vcf_report: | ||
| for stat, value in getVCFreportInfo(args.vcf_report).items(): | ||
| amplicon_stats_template["data"][args.sample][stat] = value | ||
|
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| # write the stats output | ||
| with open("{}.amplicon_stats_data_mqc.json" .format(args.sample), "w") as amplicon_stats_mqc_file: | ||
| json.dump(amplicon_stats_template, amplicon_stats_mqc_file, indent=4, sort_keys=False) | ||
| amplicon_stats_mqc_file.close() | ||
|
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| def main(): | ||
| import argparse | ||
| parser = argparse.ArgumentParser(description='Collect stats from ARTIC pipeline output and generate files for use by MultiQC') | ||
| parser.add_argument('--scheme', required=True, type=str, help='the amplicon scheme used') | ||
| parser.add_argument('--align-report', required=True, type=str, help='the report file from align_trim (*.alignreport.txt') | ||
| parser.add_argument('--vcf-report', required=False, type=str, help='the report file from vcf_check (*.vcfreport.txt') | ||
| parser.add_argument('sample', type=str, help='the sample name') | ||
| args = parser.parse_args() | ||
| run(args) | ||
|
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| if __name__ == "__main__": | ||
| main() | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| __version__ = "1.2.0" | ||
| __version__ = "1.2.1" |
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