Mercurial > repos > peterjc > seq_filter_by_id
annotate tools/seq_filter_by_id/seq_filter_by_id.py @ 5:832c1fd57852 draft
v0.2.2; New options for IDs via text parameter, ignore paired read suffix; misc changes
author | peterjc |
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date | Wed, 13 May 2015 11:03:57 -0400 |
parents | 44ab4c0f7683 |
children | 03e134cae41a |
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1 #!/usr/bin/env python |
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2 """Filter a FASTA, FASTQ or SSF file with IDs from a tabular file. |
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3 |
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4 Takes six command line options, tabular filename, ID column numbers (comma |
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5 separated list using one based counting), input filename, input type (e.g. |
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6 FASTA or SFF) and up to two output filenames (for records with and without |
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7 the given IDs, same format as input sequence file). |
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8 |
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9 When filtering an SFF file, any Roche XML manifest in the input file is |
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10 preserved in both output files. |
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11 |
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12 Note in the default NCBI BLAST+ tabular output, the query sequence ID is |
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13 in column one, and the ID of the match from the database is in column two. |
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14 Here sensible values for the column numbers would therefore be "1" or "2". |
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15 |
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16 This tool is a short Python script which requires Biopython 1.54 or later. |
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17 If you use this tool in scientific work leading to a publication, please |
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18 cite the Biopython application note: |
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19 |
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20 Cock et al 2009. Biopython: freely available Python tools for computational |
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21 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. |
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22 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. |
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23 |
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24 This script is copyright 2010-2013 by Peter Cock, The James Hutton Institute |
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25 (formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved. |
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26 See accompanying text file for licence details (MIT license). |
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27 |
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28 Use -v or --version to get the version, -h or --help for help. |
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29 """ |
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30 import os |
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31 import sys |
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32 import re |
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33 from optparse import OptionParser |
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34 |
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35 def sys_exit(msg, err=1): |
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36 sys.stderr.write(msg.rstrip() + "\n") |
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37 sys.exit(err) |
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38 |
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39 #Parse Command Line |
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40 usage = """Use as follows: |
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41 |
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42 $ python seq_filter_by_id.py [options] tab1 cols1 [, tab2 cols2, ...] |
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43 |
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44 e.g. Positive matches using column one from tabular file: |
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45 |
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46 $ seq_filter_by_id.py -i my_seqs.fastq -f fastq -p matches.fastq ids.tabular 1 |
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47 |
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48 Multiple tabular files and column numbers may be given, or replaced with |
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49 the -t or --text option. |
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50 """ |
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51 parser = OptionParser(usage=usage) |
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52 parser.add_option('-i', '--input', dest='input', |
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53 default=None, help='Input sequences filename', |
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54 metavar="FILE") |
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55 parser.add_option('-f', '--format', dest='format', |
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56 default=None, |
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57 help='Input sequence format (e.g. fasta, fastq, sff)') |
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58 parser.add_option('-t', '--text', dest='id_list', |
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59 default=None, help="Lists of white space separated IDs (instead of a tabular file)") |
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60 parser.add_option('-p', '--positive', dest='output_positive', |
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61 default=None, |
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62 help='Output filename for matches', |
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63 metavar="FILE") |
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64 parser.add_option('-n', '--negative', dest='output_negative', |
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65 default=None, |
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66 help='Output filename for non-matches', |
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67 metavar="FILE") |
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68 parser.add_option("-l", "--logic", dest="logic", |
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69 default="UNION", |
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70 help="How to combined multiple ID columns (UNION or INTERSECTION)") |
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71 parser.add_option("-s", "--suffix", dest="suffix", |
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72 action="store_true", |
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73 help="Ignore pair-read suffices for matching names") |
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74 parser.add_option("-v", "--version", dest="version", |
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75 default=False, action="store_true", |
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76 help="Show version and quit") |
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77 |
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78 options, args = parser.parse_args() |
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79 |
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80 if options.version: |
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81 print "v0.2.1" |
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82 sys.exit(0) |
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83 |
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84 in_file = options.input |
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85 seq_format = options.format |
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86 out_positive_file = options.output_positive |
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87 out_negative_file = options.output_negative |
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88 logic = options.logic |
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89 drop_suffices = bool(options.suffix) |
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90 |
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91 if in_file is None or not os.path.isfile(in_file): |
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92 sys_exit("Missing input file: %r" % in_file) |
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93 if out_positive_file is None and out_negative_file is None: |
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94 sys_exit("Neither output file requested") |
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95 if seq_format is None: |
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96 sys_exit("Missing sequence format") |
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97 if logic not in ["UNION", "INTERSECTION"]: |
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98 sys_exit("Logic agrument should be 'UNION' or 'INTERSECTION', not %r" % logic) |
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99 if options.id_list and args: |
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100 sys_exit("Cannot accepted IDs via both -t and as tabular files") |
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101 elif not options.id_list and not args: |
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102 sys_exit("Expected matched pairs of tabular files and columns (or -t given)") |
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103 if len(args) % 2: |
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104 sys_exit("Expected matched pairs of tabular files and columns, not: %r" % args) |
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105 |
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106 |
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107 #Cope with three widely used suffix naming convensions, |
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108 #Illumina: /1 or /2 |
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109 #Forward/revered: .f or .r |
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110 #Sanger, e.g. .p1k and .q1k |
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111 #See http://staden.sourceforge.net/manual/pregap4_unix_50.html |
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112 #re_f = re.compile(r"(/1|\.f|\.[sfp]\d\w*)$") |
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113 #re_r = re.compile(r"(/2|\.r|\.[rq]\d\w*)$") |
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114 re_suffix = re.compile(r"(/1|\.f|\.[sfp]\d\w*|/2|\.r|\.[rq]\d\w*)$") |
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115 assert re_suffix.search("demo.f") |
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116 assert re_suffix.search("demo.s1") |
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117 assert re_suffix.search("demo.f1k") |
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118 assert re_suffix.search("demo.p1") |
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119 assert re_suffix.search("demo.p1k") |
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120 assert re_suffix.search("demo.p1lk") |
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121 assert re_suffix.search("demo/2") |
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122 assert re_suffix.search("demo.r") |
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123 assert re_suffix.search("demo.q1") |
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124 assert re_suffix.search("demo.q1lk") |
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125 |
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126 identifiers = [] |
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127 for i in range(len(args) // 2): |
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128 tabular_file = args[2*i] |
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129 cols_arg = args[2*i + 1] |
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130 if not os.path.isfile(tabular_file): |
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131 sys_exit("Missing tabular identifier file %r" % tabular_file) |
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132 try: |
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133 columns = [int(arg)-1 for arg in cols_arg.split(",")] |
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134 except ValueError: |
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135 sys_exit("Expected list of columns (comma separated integers), got %r" % cols_arg) |
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136 if min(columns) < 0: |
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137 sys_exit("Expect one-based column numbers (not zero-based counting), got %r" % cols_arg) |
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138 identifiers.append((tabular_file, columns)) |
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139 |
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140 name_warn = False |
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141 def check_white_space(name): |
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142 parts = name.split(None, 1) |
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143 global name_warn |
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144 if not name_warn and len(parts) > 1: |
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145 name_warn = "WARNING: Some of your identifiers had white space in them, " + \ |
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146 "using first word only. e.g.:\n%s\n" % name |
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147 return parts[0] |
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148 |
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149 if drop_suffices: |
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150 def clean_name(name): |
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151 """Remove suffix.""" |
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152 name = check_white_space(name) |
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153 match = re_suffix.search(name) |
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154 if match: |
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155 # Use the fact this is a suffix, and regular expression will be |
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156 # anchored to the end of the name: |
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157 return name[:match.start()] |
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158 else: |
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159 # Nothing to do |
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160 return name |
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161 assert clean_name("foo/1") == "foo" |
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162 assert clean_name("foo/2") == "foo" |
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163 assert clean_name("bar.f") == "bar" |
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164 assert clean_name("bar.r") == "bar" |
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165 assert clean_name("baz.p1") == "baz" |
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166 assert clean_name("baz.q2") == "baz" |
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167 else: |
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168 # Just check the white space |
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169 clean_name = check_white_space |
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170 |
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171 |
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172 mapped_chars = { '>' :'__gt__', |
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173 '<' :'__lt__', |
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174 "'" :'__sq__', |
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175 '"' :'__dq__', |
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176 '[' :'__ob__', |
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177 ']' :'__cb__', |
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178 '{' :'__oc__', |
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179 '}' :'__cc__', |
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180 '@' : '__at__', |
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181 '\n' : '__cn__', |
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182 '\r' : '__cr__', |
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183 '\t' : '__tc__', |
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184 '#' : '__pd__' |
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185 } |
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186 |
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187 #Read tabular file(s) and record all specified identifiers |
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188 ids = None #Will be a set |
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189 if options.id_list: |
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190 assert not identifiers |
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191 ids = set() |
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192 id_list = options.id_list |
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193 #Galaxy turns \r into __cr__ (CR) etc |
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194 for k in mapped_chars: |
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195 id_list = id_list.replace(mapped_chars[k], k) |
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196 for x in options.id_list.split(): |
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197 ids.add(clean_name(x.strip())) |
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198 print("Have %i unique identifiers from list" % len(ids)) |
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199 for tabular_file, columns in identifiers: |
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200 file_ids = set() |
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201 handle = open(tabular_file, "rU") |
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202 if len(columns)>1: |
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203 #General case of many columns |
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204 for line in handle: |
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205 if line.startswith("#"): |
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206 #Ignore comments |
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207 continue |
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208 parts = line.rstrip("\n").split("\t") |
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209 for col in columns: |
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210 file_ids.add(clean_name(parts[col])) |
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211 else: |
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212 #Single column, special case speed up |
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213 col = columns[0] |
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214 for line in handle: |
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215 if not line.startswith("#"): |
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216 file_ids.add(clean_name(line.rstrip("\n").split("\t")[col])) |
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217 print "Using %i IDs from column %s in tabular file" % (len(file_ids), ", ".join(str(col+1) for col in columns)) |
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218 if ids is None: |
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219 ids = file_ids |
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220 if logic == "UNION": |
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221 ids.update(file_ids) |
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222 else: |
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223 ids.intersection_update(file_ids) |
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224 handle.close() |
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225 if len(identifiers) > 1: |
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226 if logic == "UNION": |
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227 print "Have %i IDs combined from %i tabular files" % (len(ids), len(identifiers)) |
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228 else: |
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229 print "Have %i IDs in common from %i tabular files" % (len(ids), len(identifiers)) |
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230 if name_warn: |
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231 sys.stderr.write(name_warn) |
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232 |
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233 def crude_fasta_iterator(handle): |
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234 """Yields tuples, record ID and the full record as a string.""" |
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235 while True: |
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236 line = handle.readline() |
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237 if line == "": |
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238 return # Premature end of file, or just empty? |
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239 if line[0] == ">": |
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240 break |
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241 |
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242 no_id_warned = False |
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243 while True: |
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244 if line[0] != ">": |
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245 raise ValueError( |
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246 "Records in Fasta files should start with '>' character") |
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247 try: |
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248 id = line[1:].split(None, 1)[0] |
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249 except IndexError: |
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250 if not no_id_warned: |
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251 sys.stderr.write("WARNING - Malformed FASTA entry with no identifier\n") |
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252 no_id_warned = True |
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253 id = None |
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254 lines = [line] |
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255 line = handle.readline() |
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256 while True: |
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257 if not line: |
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258 break |
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259 if line[0] == ">": |
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260 break |
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261 lines.append(line) |
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262 line = handle.readline() |
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263 yield id, "".join(lines) |
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264 if not line: |
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265 return # StopIteration |
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266 |
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267 |
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268 def fasta_filter(in_file, pos_file, neg_file, wanted): |
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269 """FASTA filter producing 60 character line wrapped outout.""" |
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270 pos_count = neg_count = 0 |
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271 #Galaxy now requires Python 2.5+ so can use with statements, |
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272 with open(in_file) as in_handle: |
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273 #Doing the if statement outside the loop for speed |
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274 #(with the downside of three very similar loops). |
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275 if pos_file is not None and neg_file is not None: |
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276 print "Generating two FASTA files" |
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277 with open(pos_file, "w") as pos_handle: |
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278 with open(neg_file, "w") as neg_handle: |
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279 for identifier, record in crude_fasta_iterator(in_handle): |
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280 if clean_name(identifier) in wanted: |
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281 pos_handle.write(record) |
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282 pos_count += 1 |
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283 else: |
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284 neg_handle.write(record) |
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285 neg_count += 1 |
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286 elif pos_file is not None: |
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287 print "Generating matching FASTA file" |
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288 with open(pos_file, "w") as pos_handle: |
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289 for identifier, record in crude_fasta_iterator(in_handle): |
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290 if clean_name(identifier) in wanted: |
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291 pos_handle.write(record) |
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292 pos_count += 1 |
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293 else: |
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294 neg_count += 1 |
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295 else: |
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296 print "Generating non-matching FASTA file" |
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297 assert neg_file is not None |
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298 with open(neg_file, "w") as neg_handle: |
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299 for identifier, record in crude_fasta_iterator(in_handle): |
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300 if clean_name(identifier) in wanted: |
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301 pos_count += 1 |
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302 else: |
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303 neg_handle.write(record) |
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304 neg_count += 1 |
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305 return pos_count, neg_count |
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306 |
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307 |
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308 def fastq_filter(in_file, pos_file, neg_file, wanted): |
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309 """FASTQ filter.""" |
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310 from Bio.SeqIO.QualityIO import FastqGeneralIterator |
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311 handle = open(in_file, "r") |
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312 if out_positive_file is not None and out_negative_file is not None: |
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313 print "Generating two FASTQ files" |
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314 positive_handle = open(out_positive_file, "w") |
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315 negative_handle = open(out_negative_file, "w") |
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316 print in_file |
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317 for title, seq, qual in FastqGeneralIterator(handle): |
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318 print("%s --> %s" % (title, clean_name(title.split(None, 1)[0]))) |
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319 if clean_name(title.split(None, 1)[0]) in ids: |
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320 positive_handle.write("@%s\n%s\n+\n%s\n" % (title, seq, qual)) |
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321 else: |
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322 negative_handle.write("@%s\n%s\n+\n%s\n" % (title, seq, qual)) |
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323 positive_handle.close() |
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324 negative_handle.close() |
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325 elif out_positive_file is not None: |
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326 print "Generating matching FASTQ file" |
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327 positive_handle = open(out_positive_file, "w") |
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328 for title, seq, qual in FastqGeneralIterator(handle): |
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329 if clean_name(title.split(None, 1)[0]) in ids: |
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330 positive_handle.write("@%s\n%s\n+\n%s\n" % (title, seq, qual)) |
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331 positive_handle.close() |
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332 elif out_negative_file is not None: |
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333 print "Generating non-matching FASTQ file" |
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334 negative_handle = open(out_negative_file, "w") |
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335 for title, seq, qual in FastqGeneralIterator(handle): |
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336 if clean_name(title.split(None, 1)[0]) not in ids: |
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337 negative_handle.write("@%s\n%s\n+\n%s\n" % (title, seq, qual)) |
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338 negative_handle.close() |
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339 handle.close() |
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340 # This does not currently bother to record record counts (faster) |
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341 |
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342 |
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343 def sff_filter(in_file, pos_file, neg_file, wanted): |
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344 """SFF filter.""" |
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345 try: |
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346 from Bio.SeqIO.SffIO import SffIterator, SffWriter |
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347 except ImportError: |
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348 sys_exit("SFF filtering requires Biopython 1.54 or later") |
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349 |
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350 try: |
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351 from Bio.SeqIO.SffIO import ReadRocheXmlManifest |
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352 except ImportError: |
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353 #Prior to Biopython 1.56 this was a private function |
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354 from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest |
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355 |
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356 in_handle = open(in_file, "rb") #must be binary mode! |
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357 try: |
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358 manifest = ReadRocheXmlManifest(in_handle) |
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359 except ValueError: |
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360 manifest = None |
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361 |
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362 #This makes two passes though the SFF file with isn't so efficient, |
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363 #but this makes the code simple. |
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364 pos_count = neg_count = 0 |
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365 if out_positive_file is not None: |
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366 out_handle = open(out_positive_file, "wb") |
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367 writer = SffWriter(out_handle, xml=manifest) |
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368 in_handle.seek(0) #start again after getting manifest |
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369 pos_count = writer.write_file(rec for rec in SffIterator(in_handle) if clean_name(rec.id) in ids) |
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370 out_handle.close() |
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371 if out_negative_file is not None: |
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372 out_handle = open(out_negative_file, "wb") |
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373 writer = SffWriter(out_handle, xml=manifest) |
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374 in_handle.seek(0) #start again |
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375 neg_count = writer.write_file(rec for rec in SffIterator(in_handle) if clean_name(rec.id) not in ids) |
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376 out_handle.close() |
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377 #And we're done |
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378 in_handle.close() |
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379 #At the time of writing, Galaxy doesn't show SFF file read counts, |
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380 #so it is useful to put them in stdout and thus shown in job info. |
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381 return pos_count, neg_count |
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382 |
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383 |
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384 if seq_format.lower()=="sff": |
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385 # Now write filtered SFF file based on IDs wanted |
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386 pos_count, neg_count = sff_filter(in_file, out_positive_file, out_negative_file, ids) |
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387 # At the time of writing, Galaxy doesn't show SFF file read counts, |
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388 # so it is useful to put them in stdout and thus shown in job info. |
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389 elif seq_format.lower()=="fasta": |
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390 # Write filtered FASTA file based on IDs from tabular file |
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391 pos_count, neg_count = fasta_filter(in_file, out_positive_file, out_negative_file, ids) |
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392 print "%i with and %i without specified IDs" % (pos_count, neg_count) |
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393 elif seq_format.lower().startswith("fastq"): |
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394 # Write filtered FASTQ file based on IDs from tabular file |
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395 fastq_filter(in_file, out_positive_file, out_negative_file, ids) |
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396 # This does not currently track the counts |
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397 else: |
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398 sys_exit("Unsupported file type %r" % seq_format) |