Mercurial > repos > peterjc > seq_select_by_id
annotate tools/seq_select_by_id/seq_select_by_id.py @ 6:91f55ee8fea5 draft
v0.0.11; more tests and assorting minor changes
author | peterjc |
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date | Wed, 13 May 2015 10:56:29 -0400 |
parents | 6842c0c7bc70 |
children | a5602454b0ad |
rev | line source |
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4
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1 #!/usr/bin/env python |
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2 """Select FASTA, QUAL, FASTQ or SSF sequences by IDs from a tabular file. |
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3 |
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4 Takes five command line options, tabular filename, ID column number (using |
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5 one based counting), input filename, input type (e.g. FASTA or SFF) and the |
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6 output filename (same format as input sequence file). |
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7 |
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8 When selecting from an SFF file, any Roche XML manifest in the input file is |
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9 preserved in both output files. |
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10 |
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11 This tool is a short Python script which requires Biopython 1.54 or later |
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12 for SFF file support. If you use this tool in scientific work leading to a |
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13 publication, please cite the Biopython application note: |
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14 |
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15 Cock et al 2009. Biopython: freely available Python tools for computational |
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16 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. |
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17 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. |
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18 |
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19 This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute UK. |
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20 All rights reserved. See accompanying text file for licence details (MIT |
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21 license). |
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22 """ |
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23 import sys |
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24 |
6 | 25 def sys_exit(msg, err=1): |
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26 sys.stderr.write(msg.rstrip() + "\n") |
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27 sys.exit(err) |
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28 |
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29 if "-v" in sys.argv or "--version" in sys.argv: |
6 | 30 print "v0.0.9" |
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31 sys.exit(0) |
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32 |
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33 #Parse Command Line |
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34 try: |
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35 tabular_file, col_arg, in_file, seq_format, out_file = sys.argv[1:] |
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36 except ValueError: |
6 | 37 sys_exit("Expected five arguments, got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv))) |
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38 try: |
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39 if col_arg.startswith("c"): |
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40 column = int(col_arg[1:])-1 |
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41 else: |
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42 column = int(col_arg)-1 |
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43 except ValueError: |
6 | 44 sys_exit("Expected column number, got %s" % col_arg) |
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45 |
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46 if seq_format == "fastqcssanger": |
6 | 47 sys_exit("Colorspace FASTQ not supported.") |
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48 elif seq_format.lower() in ["sff", "fastq", "qual", "fasta"]: |
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49 seq_format = seq_format.lower() |
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50 elif seq_format.lower().startswith("fastq"): |
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51 #We don't care how the qualities are encoded |
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52 seq_format = "fastq" |
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53 elif seq_format.lower().startswith("qual"): |
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54 #We don't care what the scores are |
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55 seq_format = "qual" |
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56 else: |
6 | 57 sys_exit("Unrecognised file format %r" % seq_format) |
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58 |
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59 |
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60 try: |
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61 from Bio import SeqIO |
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62 except ImportError: |
6 | 63 sys_exit("Biopython 1.54 or later is required") |
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64 |
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65 |
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66 def parse_ids(tabular_file, col): |
6 | 67 """Read tabular file and record all specified identifiers. |
68 | |
69 Will print a single warning to stderr if any of the fields have | |
70 non-trailing white space (only the first word will be used as | |
71 the identifier). | |
72 """ | |
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73 handle = open(tabular_file, "rU") |
6 | 74 warn = False |
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75 for line in handle: |
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76 if line.strip() and not line.startswith("#"): |
6 | 77 field = line.rstrip("\n").split("\t")[col].strip() |
78 parts = field.split(None, 1) | |
79 if len(parts) > 1 and not warn: | |
80 warn = "WARNING: Some of your identifiers had white space in them, " + \ | |
81 "using first word only. e.g.:\n%s\n" % field | |
82 yield parts[0] | |
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83 handle.close() |
6 | 84 if warn: |
85 sys.stderr.write(warn) | |
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86 |
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87 #Index the sequence file. |
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88 #If very big, could use SeqIO.index_db() to avoid memory bottleneck... |
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89 records = SeqIO.index(in_file, seq_format) |
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90 print "Indexed %i sequences" % len(records) |
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91 |
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92 if seq_format.lower()=="sff": |
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93 #Special case to try to preserve the XML manifest |
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94 try: |
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95 from Bio.SeqIO.SffIO import SffIterator, SffWriter |
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96 except ImportError: |
6 | 97 sys_exit("Requires Biopython 1.54 or later") |
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98 |
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99 try: |
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100 from Bio.SeqIO.SffIO import ReadRocheXmlManifest |
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101 except ImportError: |
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102 #Prior to Biopython 1.56 this was a private function |
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103 from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest |
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104 |
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105 in_handle = open(in_file, "rb") #must be binary mode! |
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106 try: |
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107 manifest = ReadRocheXmlManifest(in_handle) |
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108 except ValueError: |
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109 manifest = None |
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110 in_handle.close() |
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111 |
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112 out_handle = open(out_file, "wb") |
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113 writer = SffWriter(out_handle, xml=manifest) |
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114 count = 0 |
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115 #This does have the overhead of parsing into SeqRecord objects, |
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116 #but doing the header and index at the low level is too fidly. |
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117 iterator = (records[name] for name in parse_ids(tabular_file, column)) |
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118 try: |
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119 count = writer.write_file(iterator) |
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120 except KeyError, err: |
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121 out_handle.close() |
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122 if name not in records: |
6 | 123 sys_exit("Identifier %r not found in sequence file" % name) |
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124 else: |
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125 raise err |
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126 out_handle.close() |
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127 else: |
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128 #Avoid overhead of parsing into SeqRecord objects, |
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129 #just re-use the original formatting from the input file. |
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130 out_handle = open(out_file, "w") |
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131 count = 0 |
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132 for name in parse_ids(tabular_file, column): |
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133 try: |
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134 out_handle.write(records.get_raw(name)) |
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135 except KeyError: |
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136 out_handle.close() |
6 | 137 sys_exit("Identifier %r not found in sequence file" % name) |
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138 count += 1 |
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139 out_handle.close() |
6842c0c7bc70
Uploaded v0.0.7, depend on Biopython 1.62, tabs to spaces in XML
peterjc
parents:
diff
changeset
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140 |
6842c0c7bc70
Uploaded v0.0.7, depend on Biopython 1.62, tabs to spaces in XML
peterjc
parents:
diff
changeset
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141 print "Selected %i sequences by ID" % count |