[FIX] several small fixes

- return list instead of numpy array
- small fix: remove old option in analyze_multipeptides
- remove unnecessary check
- [FIX] ammend to r245: option not present

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@246 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE] also read gzipped files

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@247 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE] print out single/multiple protein hits

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@248 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE] add linear alignment option

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@249 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE] ProteinFDR estimation

add two scripts that can generate input to the MAYU program for Protein
FDR estimation of OpenSWATH output

- ProtFDRTraML2Fasta converts a TraML CSV to a .fasta file
- ProtFDRmProphet2Mayu converts an mProphet or feature_alignment.py
  output to MAYU input (csv)

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@250 db641661-14cc-1e01-c2f8-e77ac6f8a696
compute full matrix from output file

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@251 db641661-14cc-1e01-c2f8-e77ac6f8a696
mzXML to SWATH: using TMPDIR

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@252 db641661-14cc-1e01-c2f8-e77ac6f8a696
finish mProphet2Mayu

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@253 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FIX] catch error in transformation and display better error message

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@254 db641661-14cc-1e01-c2f8-e77ac6f8a696
mzXML to SWATH using TMPDIR

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@255 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FIX] also read pyProphet decoy classification

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@256 db641661-14cc-1e01-c2f8-e77ac6f8a696
[DOC] Small improvements in error messages and doc

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@257 db641661-14cc-1e01-c2f8-e77ac6f8a696
mzXML to SWATH: using TMPDIR

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@258 db641661-14cc-1e01-c2f8-e77ac6f8a696
raise exception if file could not be read

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@259 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FIX] remove transition_group_record for now (pyProphet does not write it)

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@260 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FIX] move logic of set_decoy to parent class

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@261 db641661-14cc-1e01-c2f8-e77ac6f8a696