Mercurial > repos > galaxyp > fasta_merge_files_and_filter_unique_sequences
changeset 0:7ba52c5163f6 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
| author | galaxyp |
|---|---|
| date | Fri, 16 Dec 2016 05:19:02 -0500 |
| parents | |
| children | 8593cac31de8 |
| files | COPYING README.md fasta_merge_files_and_filter_unique_sequences.py fasta_merge_files_and_filter_unique_sequences.xml test-data/1.fa test-data/2.fa test-data/res.fa |
| diffstat | 7 files changed, 294 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Fri Dec 16 05:19:02 2016 -0500 @@ -0,0 +1,121 @@ +Creative Commons Legal Code + +CC0 1.0 Universal + + CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE + LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN + ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS + INFORMATION ON AN "AS-IS" BASIS. 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Dec 16 05:19:02 2016 -0500 @@ -0,0 +1,47 @@ +GalaxyP - FASTA Merge Files and Filter Unique Sequences +======================================================= + +* Home: <https://github.com/galaxyproteomics/tools-galaxyp/> +* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/fasta_merge_files_and_filter_unique_sequences> +* Tool ID: `fasta_merge_files_and_filter_unique_sequences` + + +Description +----------- + +Merge FASTA files, keeping only unique sequences. + + +GalaxyP Community +----------------- + +Current governing community policies for [GalaxyP](https://github.com/galaxyproteomics/) and other information can be found at: + +<https://github.com/galaxyproteomics> + + +License +------- + +Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below. + +To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty. + +You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>. + +You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. + + +Contributing +------------ + +Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://github.com/galaxyproteomics/tools-galaxyp/> + + +Authors +------- + +Authors and contributors: + +* John Chilton <jmchilton@gmail.com> +* Minnesota Supercomputing Institute, Univeristy of Minnesota
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fasta_merge_files_and_filter_unique_sequences.py Fri Dec 16 05:19:02 2016 -0500 @@ -0,0 +1,66 @@ +#!/usr/bin/env python +import os +import sys + +class Sequence: + ''' Holds protein sequence information ''' + def __init__(self): + self.header = "" + self.sequence = "" + +class FASTAReader: + """ + FASTA db iterator. Returns a single FASTA sequence object. + """ + def __init__(self, fasta_name): + self.fasta_file = open(fasta_name) + + def __iter__(self): + return self + + def __next__(self): + ''' Iteration ''' + while True: + line = self.fasta_file.readline() + if not line: + raise StopIteration + if line[0] == '>': + break + + seq = Sequence() + seq.header = line.rstrip().replace('\n','').replace('\r','') + + while True: + tail = self.fasta_file.tell() + line = self.fasta_file.readline() + if not line: + break + if line[0] == '>': + self.fasta_file.seek(tail) + break + seq.sequence = seq.sequence + line.rstrip().replace('\n','').replace('\r','') + return seq + + # Python 2/3 compat + next = __next__ + + +def main(): + seen_sequences = set([]) + + out_file = open(sys.argv[1], 'w') + for fasta_file in sys.argv[2:]: + fa_reader = FASTAReader(fasta_file) + for protein in fa_reader: + if protein.sequence in seen_sequences: + pass + else: + seen_sequences.add(protein.sequence) + out_file.write(protein.header) + out_file.write(os.linesep) + out_file.write(protein.sequence) + out_file.write(os.linesep) + out_file.close() + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fasta_merge_files_and_filter_unique_sequences.xml Fri Dec 16 05:19:02 2016 -0500 @@ -0,0 +1,40 @@ +<tool id="fasta_merge_files_and_filter_unique_sequences" name="FASTA Merge Files and Filter Unique Sequences" version="1.1"> + <description>Concatenate FASTA database files together</description> + <requirements> + <requirement type="package" version="2.7.12">python</requirement> + </requirements> + <command> + python '$__tool_directory__/fasta_merge_files_and_filter_unique_sequences.py' + '$output' + #for $input in $inputs: + '$input' + #end for + </command> + <inputs> + <param name="inputs" format="fasta" multiple="True" type="data" label="Input FASTA files"/> + </inputs> + <outputs> + <data format="fasta" name="output" label="Merged and Filtered FASTA from ${on_string}"/> + </outputs> + <tests> + <test> + <param name="inputs" value="1.fa,2.fa" ftype="fasta" /> + <output name="output" file="res.fa" ftype="fasta" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +Concatenate FASTA database files together. +Only first appearence of each unique sequence will appear in output. + +------ + +**Citation** + +If you use this tool in Galaxy, please the GalaxyP developers at: https://github.com/galaxyproteomics/ + +]]> + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.fa Fri Dec 16 05:19:02 2016 -0500 @@ -0,0 +1,6 @@ +>one +ACGTACGT +>two +GGTGTGTACGT +>three +ACGTACG