Mercurial > repos > sanbi-uwc > plink_datatypes
changeset 0:57bd7c6a72cd draft
planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit 2bf82b5426ec792b408104250a875585cbf7347f
| author | sanbi-uwc |
|---|---|
| date | Wed, 29 Aug 2018 08:26:08 -0400 |
| parents | |
| children | 0e9c114c748f |
| files | bim/bim.py bim/datatypes_conf.xml bim/test-data/test1.bim datatypes_conf.xml fam/datatypes_conf.xml fam/fam.py fam/test-data/test1.fam readme.rst |
| diffstat | 7 files changed, 48251 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bim/bim.py Wed Aug 29 08:26:08 2018 -0400 @@ -0,0 +1,61 @@ +# -*- coding: utf-8 -*- +from galaxy import eggs + + +import pkg_resources +pkg_resources.require( "bx-python" ) + + +import logging, os, sys, time, sets, tempfile, shutil +import data +from galaxy import util +from galaxy.datatypes.sniff import * +from cgi import escape +import urllib +from bx.intervals.io import * +from galaxy.datatypes import metadata +from galaxy.datatypes.metadata import MetadataElement +from galaxy.datatypes.tabular import Tabular + + +class Bim( Tabular ): + """Tab delimited data in bim format""" + file_ext = "bim" + + MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True ) + + + def __init__ (self, **kwd): + """Initialize bim datatype""" + Tabular. __init__ (self, **kwd) + self.do_something_else() + + + def init_meta( self, dataset, copy_from=None ): + Tabular.init_meta( self, dataset, copy_from=copy_from ) + if elems_len == 8: + try: + map( int, [hdr[6], hdr[7]] ) + proceed = True + except: + pass + + + def sniff( self, filename ): + headers = get_headers( filename, '\t' ) + try: + if len(headers) < 2: + return False + for hdr in headers: + if len( hdr ) > 1 and hdr[0] and not hdr[0].startswith( '#' ): + if len(hdr) != 8: + return False + try: + map( int, [hdr[6], hdr[7]] ) + except: + return False + # Do other necessary checking here... + except: + return False + # If we haven't yet returned False, then... + return True \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bim/datatypes_conf.xml Wed Aug 29 08:26:08 2018 -0400 @@ -0,0 +1,10 @@ +<?xml version="1.0"?> + <datatypes> + <datatype_files> + <datatype_file name="plink.py"/> + </datatype_files> + <registration> + <datatype extension="bim" type="galaxy.datatypes.tabular:Bim" subclass="True"/> + <sniffers> + </sniffers> +</datatypes>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bim/test-data/test1.bim Wed Aug 29 08:26:08 2018 -0400 @@ -0,0 +1,47613 @@ +6 rs4959515 0 165391 A G +6 rs719065 0 165632 A G +6 rs6909153 0 174769 G A +6 rs1535051 0 180959 A C +6 rs12660307 0 181348 C T +6 rs17564634 0 184775 0 C +6 rs9502887 0 184903 0 C +6 rs736296 0 185616 A G +6 rs736864 0 186221 C A +6 rs2281351 0 187344 A G +6 rs17133610 0 187837 T C +6 rs17133609 0 187876 0 C +6 rs12191783 0 192106 A G +6 rs9501719 0 194920 A G +6 rs9502915 0 196357 0 A +6 rs17329846 0 201054 C T +6 rs1002064 0 203249 G A +6 rs9392298 0 203878 T C +6 rs7762550 0 204909 G T +6 rs1418706 0 205878 G A +6 rs5000996 0 205920 T G +6 rs4282439 0 205947 A C +6 rs17744451 0 209117 G A +6 rs17133789 0 209462 G T +6 rs7771527 0 213782 T C +6 rs11970426 0 215423 A G +6 rs4959585 0 217201 A G +6 rs7741853 0 217334 T C +6 rs9501753 0 221146 A G +6 rs12195328 0 221515 T C +6 rs2143738 0 223039 C T +6 rs17133761 0 223418 A G +6 rs11964365 0 223584 A C +6 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Wed Aug 29 08:26:08 2018 -0400 @@ -0,0 +1,14 @@ +<?xml version="1.0"?> + <datatypes> + <datatype_files> + <!--<datatype_file name="plink.py"/> --> + </datatype_files> + <registration> + <datatype extension="bim" type="galaxy.datatypes.tabular:Bim" subclass="True" /> + <datatype extension="fam" type="galaxy.datatypes.tabular:Fam" subclass="True"/> + </registration> + <sniffers> + <sniffer type="galaxy.datatypes.tabular:Bim"/> + <sniffer type="galaxy.datatypes.tabular:Fam"/> + </sniffers> +</datatypes>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fam/datatypes_conf.xml Wed Aug 29 08:26:08 2018 -0400 @@ -0,0 +1,10 @@ +<?xml version="1.0"?> + <datatypes> + <datatype_files> + <datatype_file name="plink.py"/> + </datatype_files> + <registration> + <datatype extension="fam" type="galaxy.datatypes.tabular:Fam" subclass="True"/> + <sniffers> + </sniffers> +</datatypes>
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Wed Aug 29 08:26:08 2018 -0400 @@ -0,0 +1,54 @@ +======================================================== +Collection of Galaxy Datatypes for Population Genetics +======================================================== + +That repository should be a starting point to collect all Population Genetics (PG) +file formats. + +Development will happen in https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes. Feel free to contribute. + +Copyright 2018 by: + +* Ziphozakhe Mashologu + +============ +Installation +============ + +Please install these datatypes with the Galaxy Tool Shed: + +================== +Included Datatypes +================== + +- Bim +- Fam + +(*) + +======= +History +======= + +=============================== +Wrapper Licence (MIT/BSD style) +=============================== + +Permission to use, copy, modify, and distribute this software and its +documentation with or without modifications and for any purpose and +without fee is hereby granted, provided that any copyright notices +appear in all copies and that both those copyright notices and this +permission notice appear in supporting documentation, and that the +names of the contributors or copyright holders not be used in +advertising or publicity pertaining to distribution of the software +without specific prior permission. + +THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +OR PERFORMANCE OF THIS SOFTWARE. +