Mercurial > repos > dereeper > pangenome_explorer
comparison COG/bac-genomics-scripts/order_fastx/README.md @ 3:e42d30da7a74 draft
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1 order_fastx | |
2 =========== | |
3 | |
4 `order_fastx.pl` is a script to order sequences in FASTA or FASTQ files. | |
5 | |
6 * [Synopsis](#synopsis) | |
7 * [Description](#description) | |
8 * [Usage](#usage) | |
9 * [Options](#options) | |
10 * [Mandatory options](#mandatory-options) | |
11 * [Optional options](#optional-options) | |
12 * [Output](#output) | |
13 * [Run environment](#run-environment) | |
14 * [Author - contact](#author---contact) | |
15 * [Citation, installation, and license](#citation-installation-and-license) | |
16 * [Changelog](#changelog) | |
17 | |
18 | |
19 ## Synopsis | |
20 | |
21 perl order_fastx.pl -i infile.fasta -l order_id_list.txt > ordered.fasta | |
22 | |
23 ## Description | |
24 | |
25 Order sequence entries in FASTA or FASTQ sequence files according to | |
26 an ID list with a given order. Beware, the IDs in the order list | |
27 have to be **identical** to the entire IDs in the sequence file. | |
28 | |
29 However, the ">" or "@" ID identifiers of FASTA or FASTQ files, | |
30 respectively, can be omitted in the ID list. | |
31 | |
32 The file type is detected automatically. But, you can set the file | |
33 type manually with option **-f**. FASTQ format assumes **four** lines | |
34 per read, if this is not the case run the FASTQ file through | |
35 [`fastx_fix.pl`](/fastx_fix) or use Heng Li's [`seqtk | |
36 seq`](https://github.com/lh3/seqtk): | |
37 | |
38 seqtk seq -l 0 infile.fq > outfile.fq | |
39 | |
40 The script can also be used to pull a subset of sequences in the ID | |
41 list from the sequence file. Probably best to set option flag **-s** | |
42 in this case, see [Optional options](#optional-options) below. But, rather use | |
43 [`filter_fastx.pl`](/filter_fastx). | |
44 | |
45 ## Usage | |
46 | |
47 perl order_fastx.pl -i infile.fq -l order_id_list.txt -s -f fastq > ordered.fq | |
48 | |
49 perl order_fastx.pl -i infile.fasta -l order_id_list.txt -e > ordered.fasta | |
50 | |
51 ## Options | |
52 | |
53 ### Mandatory options | |
54 | |
55 - -i, -input | |
56 | |
57 Input FASTA or FASTQ file | |
58 | |
59 - -l, -list | |
60 | |
61 List with sequence IDs in specified order | |
62 | |
63 ### Optional options | |
64 | |
65 - -h, -help | |
66 | |
67 Help (perldoc POD) | |
68 | |
69 - -f, -file_type | |
70 | |
71 Set the file type manually [fasta|fastq] | |
72 | |
73 - -e, -error_files | |
74 | |
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) | |
76 | |
77 - -s, -skip_errors | |
78 | |
79 Skip missing ID error statements, excludes option **-e** | |
80 | |
81 - -v, -version | |
82 | |
83 Print version number to *STDERR* | |
84 | |
85 ## Output | |
86 | |
87 - *STDOUT* | |
88 | |
89 The newly ordered sequences are printed to *STDOUT*. Redirect or pipe into another tool as needed. | |
90 | |
91 - (order_ids_missing.txt) | |
92 | |
93 If IDs in the order list are missing in the sequence file with option **-e** | |
94 | |
95 - (seq_ids_missing.txt) | |
96 | |
97 If IDs in the sequence file are missing in the order ID list with option **-e** | |
98 | |
99 ## Run environment | |
100 | |
101 The Perl script runs under Windows and UNIX flavors. | |
102 | |
103 ## Author - contact | |
104 | |
105 Andreas Leimbach (aleimba[at]gmx[dot]de; Microbial Genome Plasticity, Institute of Hygiene, University of Muenster) | |
106 | |
107 ## Citation, installation, and license | |
108 | |
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). | |
110 | |
111 ## Changelog | |
112 | |
113 - v0.1 (20.11.2014) |