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1 cat_seq
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2 =======
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3
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4 A script to merge multi-sequence RichSeq files into one single-entry 'artificial' sequence file.
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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 * [Merge multi-sequence file](#merge-multi-sequence-file)
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10 * [Merge multi-sequence file and specify different output format](#merge-multi-sequence-file-and-specify-different-output-format)
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11 * [UNIX loop to concatenate each multi-sequence file in the current working directory](#unix-loop-to-concatenate-each-multi-sequence-file-in-the-current-working-directory)
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12 * [Concatenate multi-sequence fasta files faster with UNIX's `grep`](#concatenate-multi-sequence-fasta-files-faster-with-unixs-grep)
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13 * [Output](#output)
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14 * [Dependencies](#dependencies)
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15 * [Run environment](#run-environment)
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16 * [Alternative software](#alternative-software)
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17 * [Author - contact](#author---contact)
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18 * [Citation, installation, and license](#citation-installation-and-license)
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19 * [Changelog](#changelog)
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20
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21 ## Synopsis
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22
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23 perl cat_seq.pl multi-seq_file.embl
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24
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25 ## Description
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26
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27 This script concatenates multiple sequences in a RichSeq file (embl or genbank, but also fasta) to a single artificial sequence. The first sequence in the file is used as a foundation to add the subsequent sequences, along with all features and annotations.
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28
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29 Optionally, a different output file format can be specified (fasta/embl/genbank).
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30
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31 ## Usage
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32
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33 ### Merge multi-sequence file
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34
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35 perl cat_seq.pl multi-seq_file.gbk
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36
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37 ### Merge multi-sequence file and specify different output format
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38
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39 perl cat_seq.pl multi-seq_file.embl [fasta|genbank]
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40
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41 ### UNIX loop to concatenate each multi-sequence file in the current working directory
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42
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43 for i in *.[embl|fasta|gbk]; do perl cat_seq.pl $i [embl|fasta|genbank]; done
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44
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45 ### Concatenate multi-sequence fasta files faster with UNIXs *grep*
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46 If you're working only with fasta files UNIX's `grep` is a faster choice to concatenate sequences.
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47
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48 grep -v ">" seq.fasta > seq_artificial.fasta
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49
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50 Subsequently add as a first line a fasta ID (starting with '>') with an editor.
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51
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52 ## Output
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53
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54 * *\_artificial.[embl|fasta|genbank]
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55
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56 Concatenated artificial sequence in the input format, or optionally the specified output sequence format.
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57
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58 ## Dependencies
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59
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60 * BioPerl (tested with version 1.006901)
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61
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62 ## Run environment
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63
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64 The Perl script runs under Windows and UNIX flavors.
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65
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66 ## Alternative software
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67
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68 The EMBOSS (The European Molecular Biology Open Software Suite) application ***union*** can also be used for this task (http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/union.html).
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69
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70 ## Author - contact
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71
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72 Andreas Leimbach (aleimba[at]gmx[dot]de; Microbial Genome Plasticity, Institute of Hygiene, University of Muenster)
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73
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74 ## Citation, installation, and license
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75
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76 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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77
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78 ## Changelog
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79
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80 * v0.1 (08.02.2013)
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