allpy
changeset 402:efca47965dc3
Replaced all calls to obsolete Block.flush_left() with Block.flush("left")
| author | Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru> |
|---|---|
| date | Mon, 07 Feb 2011 21:44:38 +0300 |
| parents | 387f692e2356 |
| children | fb5b4f87d741 |
| 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 21:40:14 2011 +0300 1.2 +++ b/test/usecase3.py Mon Feb 07 21:44:38 2011 +0300 1.3 @@ -30,7 +30,7 @@ 1.4 markup = ranges_to_markup(conservative) 1.5 blocks = markup_to_blocks(markup) 1.6 for block in blocks["-"]: 1.7 - block.flush_left() 1.8 + block.flush("left") 1.9 alignment.to_fasta(open("output.fasta", "w")) 1.10 1.11 main()
2.1 --- a/utils/flush_left.py Mon Feb 07 21:40:14 2011 +0300 2.2 +++ b/utils/flush_left.py Mon Feb 07 21:44:38 2011 +0300 2.3 @@ -16,7 +16,7 @@ 2.4 options.end = len(alignment.columns) 2.5 columns = alignment.columns[options.begin-1:options.end] 2.6 block = protein.Block.from_alignment(alignment, columns=columns) 2.7 - block.flush_left() 2.8 + block.flush("left") 2.9 alignment.to_fasta(open(options.out_file, "w")) 2.10 if options.msf: 2.11 os.system("seqret " + options.out_file + " msf::" + options.out_file.split(".")[0] + ".msf")
3.1 --- a/utils/flush_left_vblock.py Mon Feb 07 21:40:14 2011 +0300 3.2 +++ b/utils/flush_left_vblock.py Mon Feb 07 21:44:38 2011 +0300 3.3 @@ -16,7 +16,7 @@ 3.4 options.end = len(alignment.columns) 3.5 columns = alignment.columns[options.begin-1:options.end] 3.6 block = protein.Block.from_alignment(alignment, columns=columns) 3.7 - block.flush_left() 3.8 + block.flush("left") 3.9 alignment.to_fasta(open(options.out_file, "w")) 3.10 if options.msf: 3.11 os.system("seqret " + options.out_file + " msf::" + options.out_file.split(".")[0] + ".msf")
4.1 --- a/utils/flush_left_vblocks.py Mon Feb 07 21:40:14 2011 +0300 4.2 +++ b/utils/flush_left_vblocks.py Mon Feb 07 21:44:38 2011 +0300 4.3 @@ -22,7 +22,7 @@ 4.4 for begin, end in ranges: 4.5 columns = alignment.columns[begin-1:end] 4.6 block = protein.Block.from_alignment(alignment, columns=columns) 4.7 - block.flush_left() 4.8 + block.flush("left") 4.9 4.10 alignment.to_fasta(open(options.out_file, "w")) 4.11 if options.msf: