allpy

changeset 99:ffc102ed0249
lib::save_fasta ugly bug fixed
author: boris <bnagaev@gmail.com>
date: Wed, 20 Oct 2010 23:38:21 +0400
parents: 3d40d7b9a123
children: a49f40ace6a8
files: lib/project.py test/test.fasta test/test.py
diffstat: 3 files changed, 7 insertions(+), 2 deletions(-) [+]
[-]

lib/project.py 2

test/test.fasta 5

test/test.py 2 lib/project.py 2 test/test.fasta 5 test/test.py 2
lib/project.py 2
test/test.fasta 5
     1.1 --- a/lib/project.py	Wed Oct 20 23:33:29 2010 +0400
     1.2 +++ b/lib/project.py	Wed Oct 20 23:38:21 2010 +0400
     1.3 @@ -158,7 +158,7 @@
     1.4          """
     1.5          for sequence in self.sequences:
     1.6              out_file.write(">%(name)s %(description)s \n" % sequence.__dict__)
     1.7 -            string = str(sequence)
     1.8 +            string = ''.join([m.monomer_type.code1 if m else '-' for m in self.alignment[sequence]])
     1.9              if long_line:
    1.10                  for i in range(0, len(string) // long_line + 1):
    1.11                      out_file.write("%s \n" % string[i*long_line : i*long_line + long_line])

     2.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     2.2 +++ b/test/test.fasta	Wed Oct 20 23:38:21 2010 +0400
     2.3 @@ -0,0 +1,5 @@
     2.4 +>seq1
     2.5 +SNAKIDQLSSDAQTANAKAQASNDANAARSDAQAAKDDAARANQRL
     2.6 +
     2.7 +>seq2
     2.8 +KIDQLSSDVQTLNAKVDQLSNDVNAARSDAQAAKDDARANQRLDNM

     3.1 --- a/test/test.py	Wed Oct 20 23:33:29 2010 +0400
     3.2 +++ b/test/test.py	Wed Oct 20 23:38:21 2010 +0400
     3.3 @@ -2,7 +2,7 @@
     3.4  
     3.5  from allpy.lib.project import Project
     3.6  
     3.7 -p = Project(open('1jcc_in.fasta'))
     3.8 +p = Project(open('test.fasta'))
     3.9  print "alignment length: %i" % len(p)
    3.10  print "sequence `: %s" % str(p.sequences[0])
    3.11