Mercurial > repos > peterjc > seq_select_by_id
annotate tools/seq_select_by_id/seq_select_by_id.py @ 4:6842c0c7bc70 draft
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author | peterjc |
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date | Mon, 28 Oct 2013 05:21:45 -0400 |
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children | 91f55ee8fea5 |
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 This is version 0.0.6 of the script. |
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24 """ |
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25 import sys |
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26 |
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27 def stop_err(msg, err=1): |
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28 sys.stderr.write(msg.rstrip() + "\n") |
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29 sys.exit(err) |
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30 |
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31 if "-v" in sys.argv or "--version" in sys.argv: |
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32 print "v0.0.6" |
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33 sys.exit(0) |
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34 |
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35 #Parse Command Line |
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36 try: |
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37 tabular_file, col_arg, in_file, seq_format, out_file = sys.argv[1:] |
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38 except ValueError: |
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39 stop_err("Expected five arguments, got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv))) |
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40 try: |
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41 if col_arg.startswith("c"): |
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42 column = int(col_arg[1:])-1 |
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43 else: |
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44 column = int(col_arg)-1 |
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45 except ValueError: |
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46 stop_err("Expected column number, got %s" % col_arg) |
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47 |
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48 if seq_format == "fastqcssanger": |
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49 stop_err("Colorspace FASTQ not supported.") |
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50 elif seq_format.lower() in ["sff", "fastq", "qual", "fasta"]: |
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51 seq_format = seq_format.lower() |
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52 elif seq_format.lower().startswith("fastq"): |
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53 #We don't care how the qualities are encoded |
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54 seq_format = "fastq" |
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55 elif seq_format.lower().startswith("qual"): |
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56 #We don't care what the scores are |
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57 seq_format = "qual" |
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58 else: |
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59 stop_err("Unrecognised file format %r" % seq_format) |
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60 |
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61 |
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62 try: |
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63 from Bio import SeqIO |
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64 except ImportError: |
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65 stop_err("Biopython 1.54 or later is required") |
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66 |
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67 |
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68 def parse_ids(tabular_file, col): |
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69 """Read tabular file and record all specified identifiers.""" |
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70 handle = open(tabular_file, "rU") |
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71 for line in handle: |
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72 if line.strip() and not line.startswith("#"): |
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73 yield line.rstrip("\n").split("\t")[col].strip() |
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74 handle.close() |
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75 |
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76 #Index the sequence file. |
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77 #If very big, could use SeqIO.index_db() to avoid memory bottleneck... |
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78 records = SeqIO.index(in_file, seq_format) |
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79 print "Indexed %i sequences" % len(records) |
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80 |
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81 if seq_format.lower()=="sff": |
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82 #Special case to try to preserve the XML manifest |
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83 try: |
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84 from Bio.SeqIO.SffIO import SffIterator, SffWriter |
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85 except ImportError: |
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86 stop_err("Requires Biopython 1.54 or later") |
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87 |
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88 try: |
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89 from Bio.SeqIO.SffIO import ReadRocheXmlManifest |
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90 except ImportError: |
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91 #Prior to Biopython 1.56 this was a private function |
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92 from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest |
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93 |
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94 in_handle = open(in_file, "rb") #must be binary mode! |
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95 try: |
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96 manifest = ReadRocheXmlManifest(in_handle) |
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97 except ValueError: |
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98 manifest = None |
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99 in_handle.close() |
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100 |
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101 out_handle = open(out_file, "wb") |
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102 writer = SffWriter(out_handle, xml=manifest) |
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103 count = 0 |
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104 #This does have the overhead of parsing into SeqRecord objects, |
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105 #but doing the header and index at the low level is too fidly. |
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106 iterator = (records[name] for name in parse_ids(tabular_file, column)) |
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107 try: |
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108 count = writer.write_file(iterator) |
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109 except KeyError, err: |
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110 out_handle.close() |
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111 if name not in records: |
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112 stop_err("Identifier %r not found in sequence file" % name) |
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113 else: |
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114 raise err |
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115 out_handle.close() |
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116 else: |
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117 #Avoid overhead of parsing into SeqRecord objects, |
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118 #just re-use the original formatting from the input file. |
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119 out_handle = open(out_file, "w") |
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120 count = 0 |
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121 for name in parse_ids(tabular_file, column): |
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122 try: |
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123 out_handle.write(records.get_raw(name)) |
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124 except KeyError: |
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125 out_handle.close() |
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126 stop_err("Identifier %r not found in sequence file" % name) |
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127 count += 1 |
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128 out_handle.close() |
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129 |
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130 print "Selected %i sequences by ID" % count |