[med-svn] [pipasic] 01/01: More safe path names

[Andreas Tille]

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tille pushed a commit to branch master
in repository pipasic.

commit c506d95898b7db99a7f514fb9e02cc52107e6d82
Author: Andreas Tille <tille at debian.org>
Date:   Thu Oct 1 23:05:04 2015 +0200

    More safe path names
---
 debian/patches/safe_path_names.patch | 38 ++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/debian/patches/safe_path_names.patch b/debian/patches/safe_path_names.patch
index 02c17ff..72aab99 100644
--- a/debian/patches/safe_path_names.patch
+++ b/debian/patches/safe_path_names.patch
@@ -55,3 +55,41 @@ Description: Make sure directory and file are properly separated
  		succ = runTide(filepath=filepath, nSpec=nSpec, db_fasta=db_fasta, verbose=verbose)
  		if succ[0]: # database not found
  			print succ[0]
+--- a/pipasic.py
++++ b/pipasic.py
+@@ -111,7 +111,7 @@ Note: Pipasic requires two .fasta for ea
+ 				from TideProcessing import runTide_all
+ 				for spec in spectra: 
+ 					print "Started Tide for "+spec
+-					sample_counts = runTide_all(spec_mgf=options.spec_dir+spec+".mgf", db_list=db_list, db_path=options.db_dir, verbose=verbose)[0]
++					sample_counts = runTide_all(spec_mgf=os.path.join(options.spec_dir,spec+".mgf"), db_list=db_list, db_path=options.db_dir, verbose=verbose)[0]
+ 					countList.append([count for count in sample_counts])
+ 			else:
+ 				from runInspect_user_config import runInspect_config
+@@ -123,7 +123,7 @@ Note: Pipasic requires two .fasta for ea
+ 					sample_counts = []
+ 					for DB in db_list:
+ 						# compose filename of spectra and database
+-						inspectOut = options.spec_dir+spec +"_"+ DB +"_InspectOut.txt"
++						inspectOut = os.path.join(options.spec_dir,spec +"_"+ DB +"_InspectOut.txt")
+ 						try: 
+ 							count = parseInspect(inpath=inspectOut,fdr_countcut=fdr,silent=False)[1]
+ 							sample_counts.append(count)
+@@ -168,7 +168,7 @@ Note: Pipasic requires two .fasta for ea
+ 		from trypticpeptides import weightedMatrix
+ 		M_list_wtd = []
+ 		for spec in spectra:
+-			M_list_wtd.append(weightedMatrix(spectra_name=options.spec_dir+spec, dbList=dbList, fdr=fdr, init_weight=0, verbose=verbose, Tide=options.Tide, decoy_tag=decoy_tag))
++			M_list_wtd.append(weightedMatrix(spectra_name=os.path.join(options.spec_dir,spec), dbList=dbList, fdr=fdr, init_weight=0, verbose=verbose, Tide=options.Tide, decoy_tag=decoy_tag))
+ 		np.array(M_list_wtd).dump(os.path.splitext(outfile)[0]+"_mList_wtd.dat")
+ 	
+ 	# prep correction (1) - load/generate list of counts
+@@ -188,7 +188,7 @@ Note: Pipasic requires two .fasta for ea
+ 				sample_counts = []
+ 				for DB in db_list:
+ 					# compose filename of spectra and database
+-					inspectOut = options.spec_dir+spec +"_"+ DB +"_InspectOut.txt"
++					inspectOut = os.path.join(options.spec_dir,spec +"_"+ DB +"_InspectOut.txt")
+ 					try: 
+ 						count = parseInspect(inpath=inspectOut,fdr_countcut=fdr,silent=False)[1]
+ 						sample_counts.append(count)

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