Mercurial > repos > mons > genbanktofasta
changeset 3:ea16c9e1196a draft default tip
Deleted selected files
| author | mons |
|---|---|
| date | Tue, 04 Nov 2014 17:39:55 -0500 |
| parents | ddbc12fc8885 |
| children | |
| files | genbanktofasta-6b5153d02ac2/README.txt genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/.hg_archival.txt genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/README.txt genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/genbanktofasta.py genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/genbanktofasta.xml genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/image.jpg genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/repository_dependencies.xml genbanktofasta-6b5153d02ac2/genbanktofasta.py genbanktofasta-6b5153d02ac2/genbanktofasta.xml genbanktofasta-6b5153d02ac2/repository_dependencies.xml genbanktofasta-6b5153d02ac2/static/.DS_Store genbanktofasta-6b5153d02ac2/static/._.DS_Store genbanktofasta-6b5153d02ac2/static/images/.DS_Store genbanktofasta-6b5153d02ac2/static/images/._.DS_Store genbanktofasta-6b5153d02ac2/static/images/._image.jpg genbanktofasta-6b5153d02ac2/static/images/image.jpg |
| diffstat | 16 files changed, 115 insertions(+), 110 deletions(-) [+] |
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--- a/genbanktofasta-6b5153d02ac2/README.txt Tue Nov 04 17:27:17 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ - ----------------- -GenBank to FASTA ----------------- - -This package contains the GenBank to FASTA converter. - --------------------------------------------------------------------- -Instructions for integration of the "GenBank to FASTA" tool into the workflow-system -Galaxy (http://getgalaxy.org) --------------------------------------------------------------------- - -For best results, we recommand you to install it via the toolshed. - -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/.hg_archival.txt Tue Nov 04 17:39:55 2014 -0500 @@ -0,0 +1,5 @@ +repo: 6b5153d02ac202223fe4db6796a55d3fa76f258f +node: 6b5153d02ac202223fe4db6796a55d3fa76f258f +branch: default +latesttag: null +latesttagdistance: 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/README.txt Tue Nov 04 17:39:55 2014 -0500 @@ -0,0 +1,15 @@ + +---------------- +GenBank to FASTA +---------------- + +This package contains the GenBank to FASTA converter. + +-------------------------------------------------------------------- +Instructions for integration of the "GenBank to FASTA" tool into the workflow-system +Galaxy (http://getgalaxy.org) +-------------------------------------------------------------------- + +For best results, we recommand you to install it via the toolshed. + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/genbanktofasta.py Tue Nov 04 17:39:55 2014 -0500 @@ -0,0 +1,40 @@ +#!/usr/bin/env python +""" +Input: genbank file +Output: fasta nucleotide or protein sequences +This bit of code will record the full DNA nucleotide sequence for each record in the GenBank file as a fasta record. +http://www.warwick.ac.uk/go/peter_cock/python/genbank2fasta/ +""" + +import sys, os +from Bio import SeqIO + + +def __main__(): + + infile = sys.argv[1] + outfile= sys.argv[2] + input_handle = open(infile, "r") + output_handle = open(outfile, "w") + gbk_to_fna(input_handle,output_handle) + + +#Short version: +#SeqIO.write(SeqIO.parse(input_handle, "genbank"), output_handle, "fasta") +#Long version, allows full control of fasta output + +def gbk_to_fna(input_handle,output_handle): + for seq_record in SeqIO.parse(input_handle, "genbank") : + print "Dealing with GenBank record %s" % seq_record.id + output_handle.write(">%s %s\n%s\n" % ( + seq_record.id, + seq_record.description, + seq_record.seq.tostring())) + output_handle.close() + input_handle.close() + print "Done" + + + +if __name__ == "__main__" : __main__() +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/genbanktofasta.xml Tue Nov 04 17:39:55 2014 -0500 @@ -0,0 +1,51 @@ +<tool id="genbank_to_fa" name="Converting GenBank files" version="1.0.0"> + + <!-- [REQUIRED] Tool description displayed after the tool name --> + <description>to Fasta format</description> + + <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> + <requirements> + <requirement type="binary">python</requirement> + </requirements> + + <command interpreter="python"> + genbanktofasta.py $input $output + </command> + + <!-- [REQUIRED] Input files and tool parameters --> + <inputs> + <param name="input" type="data" format="genbank" label="Your Genbank input file" help="" /> + </inputs> + + <!-- [REQUIRED] Output files --> + <outputs> + <data name="output" format="fasta" label="${input.name}.fasta" /> <!-- Output file of any format --> + </outputs> + + <!-- [STRONGLY RECOMMANDED] Exit code rules --> + <stdio> + <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> + <exit_code range="1:" level="fatal" /> + </stdio> + + + <!-- [OPTIONAL] Help displayed in Galaxy --> + <help> + + +================ +GenBank to Fasta +================ + +----------- +Description +----------- + + | This tool converts a GenBank file to FASTA nucleotides format. + | Reference: http://www.warwick.ac.uk/go/peter_cock/python/genbank2fasta/ + +.. image:: image.jpg + + </help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/repository_dependencies.xml Tue Nov 04 17:39:55 2014 -0500 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="GenBank to FASTA tool requires the Galaxy applicable data format GenBank"> + <repository changeset_revision="a4a890259b82" name="genbank_complete_datatype" owner="mons" toolshed="https://testtoolshed.g2.bx.psu.edu" /> +</repositories>
--- a/genbanktofasta-6b5153d02ac2/genbanktofasta.py Tue Nov 04 17:27:17 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ -#!/usr/bin/env python -""" -Input: genbank file -Output: fasta nucleotide or protein sequences -This bit of code will record the full DNA nucleotide sequence for each record in the GenBank file as a fasta record. -http://www.warwick.ac.uk/go/peter_cock/python/genbank2fasta/ -""" - -import sys, os -from Bio import SeqIO - - -def __main__(): - - infile = sys.argv[1] - outfile= sys.argv[2] - input_handle = open(infile, "r") - output_handle = open(outfile, "w") - gbk_to_fna(input_handle,output_handle) - - -#Short version: -#SeqIO.write(SeqIO.parse(input_handle, "genbank"), output_handle, "fasta") -#Long version, allows full control of fasta output - -def gbk_to_fna(input_handle,output_handle): - for seq_record in SeqIO.parse(input_handle, "genbank") : - print "Dealing with GenBank record %s" % seq_record.id - output_handle.write(">%s %s\n%s\n" % ( - seq_record.id, - seq_record.description, - seq_record.seq.tostring())) - output_handle.close() - input_handle.close() - print "Done" - - - -if __name__ == "__main__" : __main__() -
--- a/genbanktofasta-6b5153d02ac2/genbanktofasta.xml Tue Nov 04 17:27:17 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,51 +0,0 @@ -<tool id="genbank_to_fa" name="Converting GenBank files" version="1.0.0"> - - <!-- [REQUIRED] Tool description displayed after the tool name --> - <description>to Fasta format</description> - - <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> - <requirements> - <requirement type="binary">python</requirement> - </requirements> - - <command interpreter="python"> - genbanktofasta.py $input $output - </command> - - <!-- [REQUIRED] Input files and tool parameters --> - <inputs> - <param name="input" type="data" format="genbank" label="Your Genbank input file" help="" /> - </inputs> - - <!-- [REQUIRED] Output files --> - <outputs> - <data name="output" format="fasta" label="${input.name}.fasta" /> <!-- Output file of any format --> - </outputs> - - <!-- [STRONGLY RECOMMANDED] Exit code rules --> - <stdio> - <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> - <exit_code range="1:" level="fatal" /> - </stdio> - - - <!-- [OPTIONAL] Help displayed in Galaxy --> - <help> - - -================ -GenBank to Fasta -================ - ------------ -Description ------------ - - | This tool converts a GenBank file to FASTA nucleotides format. - | Reference: http://www.warwick.ac.uk/go/peter_cock/python/genbank2fasta/ - -.. image:: image.jpg - - </help> - -</tool>
--- a/genbanktofasta-6b5153d02ac2/repository_dependencies.xml Tue Nov 04 17:27:17 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="GenBank to FASTA tool requires the Galaxy applicable data format GenBank"> - <repository changeset_revision="a4a890259b82" name="genbank_complete_datatype" owner="mons" toolshed="https://testtoolshed.g2.bx.psu.edu" /> -</repositories>