Mercurial > repos > iuc > vsnp_get_snps

annotate vsnp_statistics.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 9ac0b1d5560d
children
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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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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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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
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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6
1
9ac0b1d5560d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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7 class Statistics:
9ac0b1d5560d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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8
4
4535ad8b74f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
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9 def __init__(self, file_name, file_size, seq_type, num_seqs, sum_len, min_len, avg_len,
4535ad8b74f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
iuc
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10 max_len, q1, q2, q3, sum_gap, n50, pass_q20, pass_q30, read_quality_average):
4535ad8b74f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
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11 self.file_name = file_name
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12 self.file_size = file_size
4
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13 self.seq_type = seq_type
4535ad8b74f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
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14 self.num_seqs = num_seqs
4535ad8b74f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
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15 self.sum_len = sum_len
4535ad8b74f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
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16 self.min_len = min_len
4535ad8b74f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
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17 self.avg_len = avg_len
4535ad8b74f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
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18 self.max_len = max_len
4535ad8b74f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
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19 self.q1 = q1
4535ad8b74f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
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20 self.q2 = q2
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21 self.q3 = q3
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22 self.sum_gap = sum_gap
4535ad8b74f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
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23 self.n50 = n50
4535ad8b74f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
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24 self.pass_q20 = pass_q20
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25 self.pass_q30 = pass_q30
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26 self.read_quality_average = read_quality_average
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28
0
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29 def nice_size(size):
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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30 # Returns a readably formatted string with the size
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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31 words = ['bytes', 'KB', 'MB', 'GB', 'TB', 'PB', 'EB']
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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32 prefix = ''
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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33 try:
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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34 size = float(size)
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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35 if size < 0:
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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36 size = abs(size)
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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37 prefix = '-'
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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38 except Exception:
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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39 return '??? bytes'
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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40 for ind, word in enumerate(words):
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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41 step = 1024 ** (ind + 1)
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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42 if step > size:
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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43 size = size / float(1024 ** ind)
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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44 if word == 'bytes': # No decimals for bytes
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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45 return "%s%d bytes" % (prefix, size)
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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46 return "%s%.1f %s" % (prefix, size, word)
ec6e02f4eab7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
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47 return '??? bytes'
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48
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49
4
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50 def output_statistics(read1_stats, read2_stats, output_file):
1
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51 paired_reads = read2_stats is not None
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52 if paired_reads:
4
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53 columns = ['R1 FASTQ', 'R1 File Size', 'R1 Read Count', 'R1 Length Sum', 'R1 Min Length',
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54 'R1 Ave Length', 'R1 Max Length', 'R1 Q1', 'R1 Q2', 'R1 Q3', 'R1 Sum Gap',
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55 'R1 N50', 'R1 Passing Q20', 'R1 Passing Q30', 'R1 Read Quality Ave', 'R2 FASTQ',
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56 'R2 File Size', 'R2 Read Count', 'R2 Length Sum', 'R2 Min Length', 'R2 Ave Length',
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57 'R2 Max Length', 'R2 Q1', 'R2 Q2', 'R2 Q3', 'R2 Sum Gap', 'R2 N50', 'R2 Passing Q20',
4535ad8b74f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
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58 'R2 Passing Q30', 'R2 Read Quality Ave']
1
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59 else:
4
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60 columns = ['FASTQ', 'File Size', 'Read Count', 'Length Sum', 'Min Length', 'Ave Length',
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61 'Max Length', 'Q1', 'Q2', 'Q3', 'Sum Gap', 'N50', 'Passing Q20', 'Passing Q30',
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62 'Read Quality Ave']
1
9ac0b1d5560d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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63 with open(output_file, "w") as outfh:
9ac0b1d5560d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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64 # Make sure the header starts with a # so
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65 # MultiQC can properly handle the output.
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66 outfh.write("%s\n" % "\t".join(columns))
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67 line_items = []
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68 # Get the current stats and associated files.
9ac0b1d5560d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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69 # Get and output the statistics.
4
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70 line_items.append(read1_stats.file_name)
1
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71 line_items.append(read1_stats.file_size)
4
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72 line_items.append(read1_stats.num_seqs)
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73 line_items.append(read1_stats.sum_len)
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74 line_items.append(read1_stats.min_len)
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75 line_items.append(read1_stats.avg_len)
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76 line_items.append(read1_stats.max_len)
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77 line_items.append(read1_stats.q1)
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78 line_items.append(read1_stats.q2)
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79 line_items.append(read1_stats.q3)
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80 line_items.append(read1_stats.sum_gap)
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81 line_items.append(read1_stats.n50)
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82 line_items.append(read1_stats.pass_q20)
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83 line_items.append(read1_stats.pass_q30)
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84 line_items.append(read1_stats.read_quality_average)
1
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85 if paired_reads:
4
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86 line_items.append(read2_stats.file_name)
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87 line_items.append(read2_stats.file_size)
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88 line_items.append(read2_stats.num_seqs)
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89 line_items.append(read2_stats.sum_len)
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90 line_items.append(read2_stats.min_len)
4535ad8b74f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
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91 line_items.append(read2_stats.avg_len)
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92 line_items.append(read2_stats.max_len)
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93 line_items.append(read2_stats.q1)
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94 line_items.append(read2_stats.q2)
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95 line_items.append(read2_stats.q3)
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96 line_items.append(read2_stats.sum_gap)
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97 line_items.append(read2_stats.n50)
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98 line_items.append(read2_stats.pass_q20)
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99 line_items.append(read2_stats.pass_q30)
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100 line_items.append(read2_stats.read_quality_average)
1
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101 outfh.write('%s\n' % '\t'.join(str(x) for x in line_items))
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102
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103
4
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104 def get_statistics(fastq_file, seqkit_stats_file, seqkit_fx2tab_file):
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105 file_size = nice_size(os.path.getsize(fastq_file))
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106 # SeqKit statistics.
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107 with open(seqkit_stats_file, "r") as fh:
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108 # This is a 2-line file
0
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109 for i, line in enumerate(fh):
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110 if i == 0:
4
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111 # Skip header
0
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112 continue
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113 line = line.rstrip('\r\n')
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114 items = line.split("\t")
4
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115 file_name = fastq_file
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116 seq_type = items[2]
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117 num_seqs = items[3]
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118 sum_len = items[4]
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119 min_len = items[5]
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120 avg_len = items[6]
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121 max_len = items[7]
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122 q1 = items[8]
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123 q2 = items[9]
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124 q3 = items[10]
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125 sum_gap = items[11]
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126 n50 = items[12]
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127 try:
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128 pass_q20 = items[13]
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129 except IndexError:
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130 pass_q20 = 0
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131 try:
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132 pass_q30 = items[14]
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133 except IndexError:
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134 pass_q30 = 0
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135 # Average read quality is not normalized on length.
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136 avg_sum = 0
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137 with open(seqkit_fx2tab_file, "r") as fh:
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138 for i, line in enumerate(fh):
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139 if i == 0:
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140 # Skip header
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141 continue
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142 line = line.rstrip('\r\n')
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143 items = line.split("\t")
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144 avg_sum += float(items[3])
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145 read_quality_average = "{:.2f}".format(avg_sum / float(i - 1))
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146 return Statistics(file_name, file_size, seq_type, num_seqs, sum_len, min_len, avg_len,
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147 max_len, q1, q2, q3, sum_gap, n50, pass_q20, pass_q30, read_quality_average)
0
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148
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149
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150 parser = argparse.ArgumentParser()
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151
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152 parser.add_argument('--output', action='store', dest='output', help='Output Excel statistics file')
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153 parser.add_argument('--read1', action='store', dest='read1', help='Required: single read')
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154 parser.add_argument('--read2', action='store', dest='read2', required=False, default=None, help='Optional: paired read')
4
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155 parser.add_argument('--read1_seqkit_stats', action='store', dest='read1_seqkit_stats', help='Output of SeqKit statistics for forward read')
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156 parser.add_argument('--read2_seqkit_stats', action='store', dest='read2_seqkit_stats', required=False, default=None, help='Output of SeqKit statistics for reverse read')
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157 parser.add_argument('--read1_seqkit_fx2tab', action='store', dest='read1_seqkit_fx2tab', help='Output of SeqKit fx2tab for forward read')
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158 parser.add_argument('--read2_seqkit_fx2tab', action='store', dest='read2_seqkit_fx2tab', required=False, default=None, help='Output of SeqKit fx2tab for reverse read')
0
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159
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160 args = parser.parse_args()
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161
4
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162 read1_stats = get_statistics(args.read1, args.read1_seqkit_stats, args.read1_seqkit_fx2tab)
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163 if args.read2 is None:
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164 read2_stats = None
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165 else:
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166 read2_stats = get_statistics(args.read2, args.read2_seqkit_stats, args.read2_seqkit_fx2tab)
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167
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168 output_statistics(read1_stats, read2_stats, args.output)