allpy
changeset 403:fb5b4f87d741
Replaced all calls to obsolete Alignment.to_fasta() with Alignment.to_file()
| author | Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru> |
|---|---|
| date | Mon, 07 Feb 2011 21:46:43 +0300 |
| parents | efca47965dc3 |
| children | df07f7c7ee56 |
| files | test/usecase3.py utils/flush_left.py utils/flush_left_vblock.py utils/flush_left_vblocks.py |
| diffstat | 4 files changed, 4 insertions(+), 4 deletions(-) [+] |
line diff
1.1 --- a/test/usecase3.py Mon Feb 07 21:44:38 2011 +0300 1.2 +++ b/test/usecase3.py Mon Feb 07 21:46:43 2011 +0300 1.3 @@ -31,6 +31,6 @@ 1.4 blocks = markup_to_blocks(markup) 1.5 for block in blocks["-"]: 1.6 block.flush("left") 1.7 - alignment.to_fasta(open("output.fasta", "w")) 1.8 + alignment.to_file(open("output.fasta", "w")) 1.9 1.10 main()
2.1 --- a/utils/flush_left.py Mon Feb 07 21:44:38 2011 +0300 2.2 +++ b/utils/flush_left.py Mon Feb 07 21:46:43 2011 +0300 2.3 @@ -17,7 +17,7 @@ 2.4 columns = alignment.columns[options.begin-1:options.end] 2.5 block = protein.Block.from_alignment(alignment, columns=columns) 2.6 block.flush("left") 2.7 - alignment.to_fasta(open(options.out_file, "w")) 2.8 + alignment.to_file(open(options.out_file, "w")) 2.9 if options.msf: 2.10 os.system("seqret " + options.out_file + " msf::" + options.out_file.split(".")[0] + ".msf") 2.11 os.system("rm " + options.out_file)
3.1 --- a/utils/flush_left_vblock.py Mon Feb 07 21:44:38 2011 +0300 3.2 +++ b/utils/flush_left_vblock.py Mon Feb 07 21:46:43 2011 +0300 3.3 @@ -17,7 +17,7 @@ 3.4 columns = alignment.columns[options.begin-1:options.end] 3.5 block = protein.Block.from_alignment(alignment, columns=columns) 3.6 block.flush("left") 3.7 - alignment.to_fasta(open(options.out_file, "w")) 3.8 + alignment.to_file(open(options.out_file, "w")) 3.9 if options.msf: 3.10 os.system("seqret " + options.out_file + " msf::" + options.out_file.split(".")[0] + ".msf") 3.11 os.system("rm " + options.out_file)
4.1 --- a/utils/flush_left_vblocks.py Mon Feb 07 21:44:38 2011 +0300 4.2 +++ b/utils/flush_left_vblocks.py Mon Feb 07 21:46:43 2011 +0300 4.3 @@ -24,7 +24,7 @@ 4.4 block = protein.Block.from_alignment(alignment, columns=columns) 4.5 block.flush("left") 4.6 4.7 - alignment.to_fasta(open(options.out_file, "w")) 4.8 + alignment.to_file(open(options.out_file, "w")) 4.9 if options.msf: 4.10 os.system("seqret " + options.out_file + " msf::" + options.out_file.split(".")[0] + ".msf") 4.11 os.system("rm " + options.out_file)