trunc_seq v0.2 with README

merged functionality of 'trunc_seq' and 'run_trunc_seq' in one script,
output for single file input via STDOUT, results dir for fof input '-r',
POD and pod2usage, autodie, Getopt::Long, '-o' output format,
version switch, remove filepaths and skip empty/comment lines from fof input,
check and warn if multi-seq file as input

Author: aleimba

trunc_seq/README.md

@@ -0,0 +1,138 @@
+trunc_seq
+=========
+
+`trunc_seq.pl` is a script to truncate sequence files.
+
+* [Synopsis](#synopsis)
+* [Description](#description)
+* [Usage](#usage)
+* [Options](#options)
+* [Output](#output)
+* [Run environment](#run-environment)
+* [Dependencies](#dependencies)
+* [Author - contact](#author---contact)
+* [Citation, installation, and license](#citation-installation-and-license)
+* [Changelog](#changelog)
+
+## Synopsis
+
+    perl trunc_seq.pl 20 3500 seq-file.embl > seq-file_trunc_20_3500.embl
+
+**or**
+
+    perl trunc_seq.pl file_of_filenames_and_coords.tsv
+
+## Description
+
+This script truncates sequence files according to the given
+coordinates. The features/annotations in RichSeq files (e.g. EMBL or
+GENBANK format) will also be adapted accordingly. Use option **-o** to
+specify a different output sequence format. Input can be given directly
+as a file and truncation coordinates to the script, with the start
+position as the first argument, stop as the second and (the path to)
+the sequence file as the third. In this case the truncated sequence
+entry is printed to *STDOUT*. Input sequence files should contain only
+one sequence entry, if a multi-sequence file is used as input only the
+**first** sequence entry is truncated.
+
+Alternatively, a file of filenames (fof) with respective coordinates
+and sequence files in the following **tab-separated** format can be
+given to the script (the header is optional):
+
+    #start stop seq-file
+    300 9000 (path/to/)seq-file
+    50 1300 (path/to/)seq-file2
+
+With a fof the resulting truncated sequence files are printed into a
+results directory. Use option **-r** to specify a different results
+directory than the default.
+
+It is also possible to truncate a RichSeq sequence file loaded into the
+[Artemis](http://www.sanger.ac.uk/science/tools/artemis) genome browser
+from the Sanger Institute: Select a subsequence and then go to Edit ->
+Subsequence (and Features)
+
+## Usage
+
+    perl trunc_seq.pl -o gbk 120 30000 seq-file.embl > seq-file_trunc_120_3000.gbk
+
+**or**
+
+    perl trunc_seq.pl -o fasta 5300 18500 seq-file.gbk | perl revcom_seq.pl -i fasta > seq-file_trunc_revcom.fasta
+
+**or**
+
+    perl trunc_seq.pl -r path/to/trunc_embl_dir -o embl file_of_filenames_and_coords.tsv
+
+## Options
+
+- **-h**, **-help**
+
+    Help (perldoc POD)
+
+- **-o**=*str*, **-outformat**=*str*
+
+    Specify different sequence format for the output (files) [fasta, embl, or gbk]
+
+- **-r**=*str*, **-result\_dir**=*str*
+
+    Path to result folder for fof input \[default = './trunc\_seq\_results'\]
+
+- **-v**, **-version**
+
+    Print version number to *STDOUT*
+
+## Output
+
+- *STDOUT*
+
+    If a single sequence file is given to the script the truncated sequence
+    file is printed to *STDOUT*. Redirect or pipe into another tool as
+    needed.
+
+**or**
+
+- ./trunc_seq_results
+
+    If a fof is given to the script, all output files are stored in a
+    results folder
+
+- ./trunc_seq_results/seq-file_trunc_start_stop.format
+
+    Truncated output sequence files are named appended with 'trunc' and the
+    corresponding start and stop positions
+
+## Run environment
+
+The Perl script runs under Windows and UNIX flavors.
+
+## Dependencies
+
+- [**BioPerl**](http://www.bioperl.org) (tested version 1.007001)
+
+## Author - contact
+
+Andreas Leimbach (aleimba[at]gmx[dot]de; Microbial Genome Plasticity, Institute of Hygiene, University of Muenster)
+
+## Citation, installation, and license
+
+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).
+
+## Changelog
+
+* v0.2 (2015-12-07)
+    * Merged funtionality of `trunc_seq.pl` and `run_trunc_seq.pl` in one single script
+        * Allows now single file and file of filenames (fof) with coordinates input
+        * output for single file input printed to *STDOUT* now
+        * output for fof input printed into files in a result directory, new option **-r** to specify result directory
+    * included a POD instead of a simple usage text
+    * included `pod2usage` with Pod::Usage
+    * included 'use autodie' pragma
+    * options with Getopt::Long
+    * output format now specified with option **-o**
+    * included version switch, **-v**
+    * fixed bug to remove input filepaths from fof input for output files
+    * skip empty or comment lines (/^#/) in fof input
+    * check and warn if input seq file has more than one seq entries
+* v0.1 (2013-02-08)
+    * In v0.1 `trunc_seq.pl` only for single sequence input, but included additional wrapper script `run_trunc_seq.pl` for a fof input