allpy
changeset 753:2fe9695e3e46
realtive paths in sbbs_2009 are made relative to programs, not to working directory
| author | Boris Burkov <BurkovBA@gmail.com> |
|---|---|
| date | Mon, 11 Jul 2011 22:12:50 +0400 |
| parents | 15633bca9c90 |
| children | e460ca5a071f |
| files | sbbs_2009/blocks_finder.py sbbs_2009/modules/alignment.py sbbs_2009/modules/block.py sbbs_2009/test_homology.py sequence_based_blocks_search/test_homology.py |
| diffstat | 5 files changed, 21 insertions(+), 16 deletions(-) [+] |
line diff
1.1 --- a/sbbs_2009/blocks_finder.py Mon Jul 11 14:36:57 2011 +0400 1.2 +++ b/sbbs_2009/blocks_finder.py Mon Jul 11 22:12:50 2011 +0400 1.3 @@ -2,8 +2,9 @@ 1.4 1.5 import sys 1.6 import traceback 1.7 +import os 1.8 1.9 -sys.path.append("./modules") 1.10 +sys.path.append(str(os.path.dirname(__file__))+"/modules") 1.11 import block 1.12 import blocks 1.13 import alignment 1.14 @@ -78,7 +79,7 @@ 1.15 1.16 1.17 def blocks2homology_file(blocks, homology_file): 1.18 - sys.path.append("../allpy/") 1.19 + sys.path.append(os.path.dirname(__file__)+"/../allpy/") 1.20 from homology import MonomerHomology 1.21 class_counter = 0 1.22 for b in blocks:
2.1 --- a/sbbs_2009/modules/alignment.py Mon Jul 11 14:36:57 2011 +0400 2.2 +++ b/sbbs_2009/modules/alignment.py Mon Jul 11 22:12:50 2011 +0400 2.3 @@ -133,9 +133,9 @@ 2.4 None 2.5 """ 2.6 import sys 2.7 - os.system("seqret " + file_name + " ../jobs/temp_alignment.fasta") 2.8 + os.system("seqret " + file_name + str(os.path.dirname(__file__))+"/../jobs/temp_alignment.fasta") 2.9 try: 2.10 - f=open("../jobs/temp_alignment.fasta") 2.11 + f=open(str(os.path.dirname(__file__))+"/../jobs/temp_alignment.fasta") 2.12 self.get_from_fasta(f) 2.13 f.close() 2.14 except IOError, errmessage:
3.1 --- a/sbbs_2009/modules/block.py Mon Jul 11 14:36:57 2011 +0400 3.2 +++ b/sbbs_2009/modules/block.py Mon Jul 11 22:12:50 2011 +0400 3.3 @@ -362,13 +362,13 @@ 3.4 parenthetic_structure to tree 3.5 """ 3.6 if mode == "external": 3.7 - f=open("./jobs/temptree.fasta","w") 3.8 + f=open(os.path.dirname(__file__)+"/../jobs/temptree.fasta","w") 3.9 self.to_fasta(f) 3.10 f.close() 3.11 3.12 - os.system("fprotdist ./jobs/temptree.fasta -out ./jobs/temptree.dist -method d 2>>./jobs/temptree.log >>./jobs/temptree.log ") 3.13 - os.system("fneighbor ./jobs/temptree.dist -outfile ./jobs/temptree.nj -outtreefile ./jobs/temptree.tre -treetype u 2>>./jobs/temptree.log >>./jobs/temptree.log") 3.14 - f=open("./jobs/temptree.tre", "r") 3.15 + os.system("fprotdist "+os.path.dirname(__file__)+"/../jobs/temptree.fasta -out "+os.path.dirname(__file__)+"/../jobs/temptree.dist -method d 2>>"+os.path.dirname(__file__)+"/../jobs/temptree.log >>"+os.path.dirname(__file__)+"/../jobs/temptree.log ") 3.16 + os.system("fneighbor "+os.path.dirname(__file__)+"/../jobs/temptree.dist -outfile "+os.path.dirname(__file__)+"/../jobs/temptree.nj -outtreefile "+os.path.dirname(__file__)+"/../jobs/temptree.tre -treetype u 2>>"+os.path.dirname(__file__)+"/../jobs/temptree.log >>"+os.path.dirname(__file__)+"/../jobs/temptree.log") 3.17 + f=open(os.path.dirname(__file__)+"/../jobs/temptree.tre", "r") 3.18 tree=f.readlines() 3.19 f.close() 3.20 line="" 3.21 @@ -376,11 +376,11 @@ 3.22 elif mode == "semiexternal": 3.23 mat = self.create_distance_matrix() 3.24 #if mat.max() == 0: return False 3.25 - f=open("./jobs/temptree.dist","w") 3.26 + f=open(os.path.dirname(__file__)+"/../jobs/temptree.dist","w") 3.27 f.write(str(mat)) 3.28 f.close() 3.29 - os.system("fneighbor ./jobs/temptree.dist -outfile ./jobs/temptree.nj -outtreefile ./jobs/temptree.tre -treetype u 2>>./jobs/temptree.log >>./jobs/temptree.log") 3.30 - f=open("./jobs/temptree.tre", "r") 3.31 + os.system("fneighbor "+os.path.dirname(__file__)+"/../jobs/temptree.dist -outfile "+os.path.dirname(__file__)+"/../jobs/temptree.nj -outtreefile "+os.path.dirname(__file__)+"/../jobs/temptree.tre -treetype u 2>>"+os.path.dirname(__file__)+"/../jobs/temptree.log >>"+os.path.dirname(__file__)+"/../jobs/temptree.log") 3.32 + f=open(""+os.path.dirname(__file__)+"/../jobs/temptree.tre", "r") 3.33 tree=f.readlines() 3.34 f.close() 3.35 line="" 3.36 @@ -390,7 +390,7 @@ 3.37 # end if - elif 3.38 self.rooted_tree=Rooted_tree() 3.39 self.rooted_tree.parenthetic_structure_to_tree(parenthetic_structure) 3.40 - os.system("rm ./jobs/temptree.*") 3.41 + os.system("rm "+os.path.dirname(__file__)+"/../jobs/temptree.*") 3.42 return True 3.43 #sys.exit() 3.44
4.1 --- a/sbbs_2009/test_homology.py Mon Jul 11 14:36:57 2011 +0400 4.2 +++ b/sbbs_2009/test_homology.py Mon Jul 11 22:12:50 2011 +0400 4.3 @@ -1,5 +1,7 @@ 4.4 -import sys 4.5 -from blocks_finder import * 4.6 +if __name__ == "__main__": 4.7 + import sys 4.8 + from blocks_finder import * 4.9 4.10 -blocks = main(sys.argv[1]) 4.11 -blocks2homology_file(blocks, open(sys.argv[2], 'w')) 4.12 + blocks = main(sys.argv[1]) 4.13 + blocks2homology_file(blocks, open(sys.argv[2], 'w')) 4.14 +
5.1 --- a/sequence_based_blocks_search/test_homology.py Mon Jul 11 14:36:57 2011 +0400 5.2 +++ b/sequence_based_blocks_search/test_homology.py Mon Jul 11 22:12:50 2011 +0400 5.3 @@ -17,3 +17,5 @@ 5.4 find_links(groups_content, alignment) 5.5 create_file_with_monomer_homology(alignment, output_file_name) 5.6 5.7 +if __name__ == "__main__": 5.8 + alignment_file2homology_file(sys.argv[1], sys.argv[2])