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1 order_fastx
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2 ===========
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3
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4 `order_fastx.pl` is a script to order sequences in FASTA or FASTQ files.
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5
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6 * [Synopsis](#synopsis)
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7 * [Description](#description)
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8 * [Usage](#usage)
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9 * [Options](#options)
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10 * [Mandatory options](#mandatory-options)
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11 * [Optional options](#optional-options)
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12 * [Output](#output)
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13 * [Run environment](#run-environment)
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14 * [Author - contact](#author---contact)
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15 * [Citation, installation, and license](#citation-installation-and-license)
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16 * [Changelog](#changelog)
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17
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18
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19 ## Synopsis
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20
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21 perl order_fastx.pl -i infile.fasta -l order_id_list.txt > ordered.fasta
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22
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23 ## Description
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24
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25 Order sequence entries in FASTA or FASTQ sequence files according to
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26 an ID list with a given order. Beware, the IDs in the order list
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27 have to be **identical** to the entire IDs in the sequence file.
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28
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29 However, the ">" or "@" ID identifiers of FASTA or FASTQ files,
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30 respectively, can be omitted in the ID list.
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31
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32 The file type is detected automatically. But, you can set the file
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33 type manually with option **-f**. FASTQ format assumes **four** lines
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34 per read, if this is not the case run the FASTQ file through
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35 [`fastx_fix.pl`](/fastx_fix) or use Heng Li's [`seqtk
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36 seq`](https://github.com/lh3/seqtk):
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37
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38 seqtk seq -l 0 infile.fq > outfile.fq
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39
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40 The script can also be used to pull a subset of sequences in the ID
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41 list from the sequence file. Probably best to set option flag **-s**
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42 in this case, see [Optional options](#optional-options) below. But, rather use
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43 [`filter_fastx.pl`](/filter_fastx).
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44
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45 ## Usage
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46
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47 perl order_fastx.pl -i infile.fq -l order_id_list.txt -s -f fastq > ordered.fq
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48
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49 perl order_fastx.pl -i infile.fasta -l order_id_list.txt -e > ordered.fasta
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50
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51 ## Options
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52
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53 ### Mandatory options
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54
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55 - -i, -input
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56
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57 Input FASTA or FASTQ file
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58
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59 - -l, -list
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60
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61 List with sequence IDs in specified order
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62
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63 ### Optional options
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64
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65 - -h, -help
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66
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67 Help (perldoc POD)
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68
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69 - -f, -file_type
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70
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71 Set the file type manually [fasta|fastq]
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72
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73 - -e, -error_files
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74
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75 Write missing IDs in the seq file or the order ID list without an equivalent in the other to error files instead of *STDERR* (see [Output](#output) below)
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76
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77 - -s, -skip_errors
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78
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79 Skip missing ID error statements, excludes option **-e**
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80
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81 - -v, -version
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82
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83 Print version number to *STDERR*
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84
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85 ## Output
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86
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87 - *STDOUT*
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88
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89 The newly ordered sequences are printed to *STDOUT*. Redirect or pipe into another tool as needed.
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90
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91 - (order_ids_missing.txt)
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92
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93 If IDs in the order list are missing in the sequence file with option **-e**
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94
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95 - (seq_ids_missing.txt)
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96
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97 If IDs in the sequence file are missing in the order ID list with option **-e**
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98
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99 ## Run environment
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100
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101 The Perl script runs under Windows and UNIX flavors.
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102
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103 ## Author - contact
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104
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105 Andreas Leimbach (aleimba[at]gmx[dot]de; Microbial Genome Plasticity, Institute of Hygiene, University of Muenster)
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106
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107 ## Citation, installation, and license
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108
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109 For [citation](https://github.com/aleimba/bac-genomics-scripts#citation), [installation](https://github.com/aleimba/bac-genomics-scripts#installation-recommendations), and [license](https://github.com/aleimba/bac-genomics-scripts#license) information please see the repository main [*README.md*](https://github.com/aleimba/bac-genomics-scripts/blob/master/README.md).
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110
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111 ## Changelog
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112
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113 - v0.1 (20.11.2014)
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