Mercurial > repos > iuc > vsnp_get_snps

annotate vsnp_add_zero_coverage.py @ 4:4535ad8b74f3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
author iuc
date Fri, 10 Jun 2022 06:08:49 +0000
parents ec6e02f4eab7
children
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ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
iuc
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diff changeset
1 #!/usr/bin/env python
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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2
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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3 import argparse
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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4 import os
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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5 import re
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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6 import shutil
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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8 import pandas
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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9 import pysam
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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10 from Bio import SeqIO
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ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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13 def get_sample_name(file_path):
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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14 base_file_name = os.path.basename(file_path)
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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15 if base_file_name.find(".") > 0:
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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16 # Eliminate the extension.
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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17 return os.path.splitext(base_file_name)[0]
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18 return base_file_name
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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21 def get_coverage_df(bam_file):
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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22 # Create a coverage dictionary.
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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23 coverage_dict = {}
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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24 coverage_list = pysam.depth(bam_file, split_lines=True)
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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25 for line in coverage_list:
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26 chrom, position, depth = line.split('\t')
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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27 coverage_dict["%s-%s" % (chrom, position)] = depth
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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28 # Convert it to a data frame.
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29 coverage_df = pandas.DataFrame.from_dict(coverage_dict, orient='index', columns=["depth"])
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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30 return coverage_df
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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31
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32
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33 def get_zero_df(reference):
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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34 # Create a zero coverage dictionary.
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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35 zero_dict = {}
4
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36 reference_length = 0
0
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37 for record in SeqIO.parse(reference, "fasta"):
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38 chrom = record.id
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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39 total_len = len(record.seq)
4
4535ad8b74f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
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40 reference_length = reference_length + len(record.seq)
0
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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41 for pos in list(range(1, total_len + 1)):
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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42 zero_dict["%s-%s" % (str(chrom), str(pos))] = 0
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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43 # Convert it to a data frame with depth_x
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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44 # and depth_y columns - index is NaN.
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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45 zero_df = pandas.DataFrame.from_dict(zero_dict, orient='index', columns=["depth"])
4
4535ad8b74f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
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46 return zero_df, reference_length
0
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47
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48
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49 def output_zc_vcf_file(base_file_name, vcf_file, zero_df, total_zero_coverage, output_vcf):
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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50 column_names = ["CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO", "FORMAT", "Sample"]
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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51 vcf_df = pandas.read_csv(vcf_file, sep='\t', header=None, names=column_names, comment='#')
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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52 good_snp_count = len(vcf_df[(vcf_df['ALT'].str.len() == 1) & (vcf_df['REF'].str.len() == 1) & (vcf_df['QUAL'] > 150)])
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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53 if total_zero_coverage > 0:
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54 header_file = "%s_header.csv" % base_file_name
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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55 with open(header_file, 'w') as outfile:
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56 with open(vcf_file) as infile:
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57 for line in infile:
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58 if re.search('^#', line):
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59 outfile.write("%s" % line)
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60 vcf_df_snp = vcf_df[vcf_df['REF'].str.len() == 1]
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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61 vcf_df_snp = vcf_df_snp[vcf_df_snp['ALT'].str.len() == 1]
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62 vcf_df_snp['ABS_VALUE'] = vcf_df_snp['CHROM'].map(str) + "-" + vcf_df_snp['POS'].map(str)
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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63 vcf_df_snp = vcf_df_snp.set_index('ABS_VALUE')
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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64 cat_df = pandas.concat([vcf_df_snp, zero_df], axis=1, sort=False)
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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65 cat_df = cat_df.drop(columns=['CHROM', 'POS', 'depth'])
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66 cat_df[['ID', 'ALT', 'QUAL', 'FILTER', 'INFO']] = cat_df[['ID', 'ALT', 'QUAL', 'FILTER', 'INFO']].fillna('.')
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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67 cat_df['REF'] = cat_df['REF'].fillna('N')
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68 cat_df['FORMAT'] = cat_df['FORMAT'].fillna('GT')
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69 cat_df['Sample'] = cat_df['Sample'].fillna('./.')
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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70 cat_df['temp'] = cat_df.index.str.rsplit('-', n=1)
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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71 cat_df[['CHROM', 'POS']] = pandas.DataFrame(cat_df.temp.values.tolist(), index=cat_df.index)
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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72 cat_df = cat_df[['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT', 'Sample']]
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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73 cat_df['POS'] = cat_df['POS'].astype(int)
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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74 cat_df = cat_df.sort_values(['CHROM', 'POS'])
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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75 body_file = "%s_body.csv" % base_file_name
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76 cat_df.to_csv(body_file, sep='\t', header=False, index=False)
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77 with open(output_vcf, "w") as outfile:
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78 for cf in [header_file, body_file]:
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79 with open(cf, "r") as infile:
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80 for line in infile:
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81 outfile.write("%s" % line)
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82 else:
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83 shutil.move(vcf_file, output_vcf)
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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84 return good_snp_count
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85
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86
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87 def output_metrics_file(base_file_name, average_coverage, genome_coverage, good_snp_count, dbkey, reference,
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88 reference_length, total_zero_coverage, percent_ref_with_zero_coverage, output_metrics):
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89 columns = ["BAM File", "Reference", "reference Length", "Genome with Coverage", "Average Depth",
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90 "No Coverage Bases", "Percent Ref with Zero Coverage", "Quality SNPs"]
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91 values = [base_file_name, dbkey, str(reference_length), genome_coverage, average_coverage,
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92 str(total_zero_coverage), percent_ref_with_zero_coverage, str(good_snp_count)]
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93 with open(output_metrics, "w") as fh:
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94 fh.write("# %s\n" % "\t".join(columns))
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95 fh.write("%s\n" % "\t".join(values))
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96
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97
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98 def output_files(vcf_file, total_zero_coverage, percent_ref_with_zero_coverage, zero_df, output_vcf,
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99 average_coverage, genome_coverage, output_metrics, reference, reference_length, dbkey):
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100 base_file_name = get_sample_name(vcf_file)
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101 good_snp_count = output_zc_vcf_file(base_file_name, vcf_file, zero_df, total_zero_coverage, output_vcf)
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102 output_metrics_file(base_file_name, average_coverage, genome_coverage, good_snp_count, dbkey, reference,
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103 reference_length, total_zero_coverage, percent_ref_with_zero_coverage, output_metrics)
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104
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105
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106 def get_coverage_and_snp_count(bam_file, vcf_file, dbkey, reference, output_metrics, output_vcf):
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107 coverage_df = get_coverage_df(bam_file)
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108 zero_df, reference_length = get_zero_df(reference)
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109 coverage_df = zero_df.merge(coverage_df, left_index=True, right_index=True, how='outer')
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110 # depth_x "0" column no longer needed.
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111 coverage_df = coverage_df.drop(columns=['depth_x'])
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112 coverage_df = coverage_df.rename(columns={'depth_y': 'depth'})
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113 # Covert the NaN to 0 coverage and get some metrics.
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114 coverage_df = coverage_df.fillna(0)
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115 coverage_df['depth'] = coverage_df['depth'].apply(int)
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116 total_length = len(coverage_df)
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117 average_coverage = "{:.2f}".format(coverage_df['depth'].mean())
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118 zero_df = coverage_df[coverage_df['depth'] == 0]
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119 total_zero_coverage = len(zero_df)
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120 percent_ref_with_zero_coverage = "{:.6%}".format(total_zero_coverage / reference_length * 100)
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121 total_coverage = total_length - total_zero_coverage
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122 genome_coverage = "{:.2%}".format(total_coverage / total_length)
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123 # Output a zero-coverage vcf fil and the metrics file.
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124 output_files(vcf_file, total_zero_coverage, percent_ref_with_zero_coverage, zero_df, output_vcf,
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125 average_coverage, genome_coverage, output_metrics, reference, reference_length, dbkey)
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126
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127
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128 if __name__ == '__main__':
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129 parser = argparse.ArgumentParser()
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130
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131 parser.add_argument('--bam_input', action='store', dest='bam_input', help='bam input file')
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132 parser.add_argument('--dbkey', action='store', dest='dbkey', help='bam input dbkey')
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133 parser.add_argument('--output_metrics', action='store', dest='output_metrics', required=False, default=None, help='Output metrics text file')
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134 parser.add_argument('--output_vcf', action='store', dest='output_vcf', required=False, default=None, help='Output VCF file')
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135 parser.add_argument('--reference', action='store', dest='reference', help='Reference dataset')
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136 parser.add_argument('--vcf_input', action='store', dest='vcf_input', help='vcf input file')
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137
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138 args = parser.parse_args()
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139
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140 get_coverage_and_snp_count(args.bam_input, args.vcf_input, args.dbkey, args.reference, args.output_metrics, args.output_vcf)