Mercurial > repos > iracooke > proteomics_datatypes
changeset 16:e6a02a387448 draft
planemo upload commit 4f23896d1a519a87f189c6238a95b8f5b5933e9a-dirty
| author | iracooke |
|---|---|
| date | Sun, 17 May 2015 23:33:49 -0400 |
| parents | de34893b3834 |
| children | 29c43b953c1c |
| files | README.rst datatypes_conf.xml proteomics.py |
| diffstat | 3 files changed, 22 insertions(+), 1 deletions(-) [+] |
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--- a/README.rst Sun Mar 29 19:24:40 2015 -0400 +++ b/README.rst Sun May 17 23:33:49 2015 -0400 @@ -35,7 +35,8 @@ IdXML idxml False OpenMS_ TandemXML_ tandem False XTandem output RAW raw False Raw Mass Spec Data -Msp msp False Spectral Library +Msp_ msp True Spectral Library +SPLib splib True Spectral Library Ms2 ms2 False MS/MS Spectra XHunterAslFormat hlf False Spectral Library ================ ===================== ======= ==================================== @@ -53,6 +54,8 @@ .. _MzIdentML: http://www.psidev.info/mzidentml .. _TraML: http://www.psidev.info/traml .. _TandemXML: http://www.thegpm.org/docs/X_series_output_form.pdf +.. _Msp: http://chemdata.nist.gov/mass-spc/ftp/mass-spc/PepLib.pdf +.. _SPLib: http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST#Developer.27s_Guide Visualization -------------
--- a/datatypes_conf.xml Sun Mar 29 19:24:40 2015 -0400 +++ b/datatypes_conf.xml Sun May 17 23:33:49 2015 -0400 @@ -46,6 +46,7 @@ <datatype extension="msp" type="galaxy.datatypes.proteomics:Msp" display_in_upload="true" /> <datatype extension="ms2" type="galaxy.datatypes.proteomics:Ms2" display_in_upload="true" /> <datatype extension="hlf" type="galaxy.datatypes.proteomics:XHunterAslFormat" mimetype="application/octet-stream" display_in_upload="true" /> + <datatype extension="splib" type="galaxy.datatypes.proteomics:SPLib" display_in_upload="true" /> </registration> <sniffers> <sniffer type="galaxy.datatypes.proteomics:MzML"/> @@ -57,5 +58,7 @@ <sniffer type="galaxy.datatypes.proteomics:TraML"/> <sniffer type="galaxy.datatypes.proteomics:MzIdentML"/> <sniffer type="galaxy.datatypes.proteomics:MzQuantML"/> + <sniffer type="galaxy.datatypes.proteomics:Msp"/> + <sniffer type="galaxy.datatypes.proteomics:SPLib"/> </sniffers> </datatypes>
--- a/proteomics.py Sun Mar 29 19:24:40 2015 -0400 +++ b/proteomics.py Sun May 17 23:33:49 2015 -0400 @@ -285,6 +285,21 @@ with open(filename, 'r') as contents: return Msp.next_line_starts_with(contents, "Name:") and Msp.next_line_starts_with(contents, "MW:") + +class SPLib( Msp ): + """SpectraST Spectral Library. Closely related to msp format""" + file_ext = "splib" + + def set_peek( self, dataset, is_multi_byte=False ): + """Set the peek and blurb text""" + if not dataset.dataset.purged: + dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + dataset.blurb = 'splib Spectral Library Format' + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + class Ms2(Text): file_ext = "ms2"