Log of /FigKernelPackages/gjoseqlib.pm
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Revision
1.18 -
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Sun Aug 15 23:51:00 2010 UTC (9 years, 4 months ago) by
golsen
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Changes since
1.17: +32 -20 lines
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previous 1.17
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selected 1.11
Minor style updates.
Add the ability of read_fasta() to interpret a reference to a sting as
a fasta format string.
use gjoseqlib; $s=join("",<>); @seq=read_fasta(\$s); print_alignment_as_fasta(\@seq);
will echo sequences from stdin.
Revision
1.13 -
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Tue Feb 12 20:08:01 2008 UTC (11 years, 10 months ago) by
golsen
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CVS Tags:
mgrast_rel_2008_0625,
mgrast_rel_2008_0806,
mgrast_rel_2008_0917,
mgrast_rel_2008_0919,
mgrast_rel_2008_0923,
mgrast_rel_2008_0924,
mgrast_rel_2008_1110,
mgrast_rel_2008_1110_v2,
rast_2008_0924,
rast_rel_2008_04_23,
rast_rel_2008_06_16,
rast_rel_2008_06_18,
rast_rel_2008_07_21,
rast_rel_2008_08_07,
rast_rel_2008_09_29,
rast_rel_2008_09_30,
rast_rel_2008_10_09,
rast_rel_2008_10_29,
rast_rel_2008_11_24,
rast_rel_2008_12_18,
rast_rel_2009_02_05,
rast_release_2008_09_29
Changes since
1.12: +1 -1 lines
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previous 1.12
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Fixed major error in read_fasta() when there is not definition.
Revision
1.12 -
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Mon Feb 11 20:37:27 2008 UTC (11 years, 10 months ago) by
golsen
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Changes since
1.11: +167 -49 lines
Diff to
previous 1.11
Fix a bug in translation with user-supplied genetic code (thank you Gordon).
Fix a bug in read_next_fasta_seq() that failed when the fasta header line
had an id, a space, and then no description.
Improve flexibility of read_next_fasta_seq() so that it will take a file
name, a file handle, or default to STDIN.
Double the speed of read_fasta by reading the whole file, then splitting
it into the structures.
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1.11 -
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Thu Jan 3 21:36:41 2008 UTC (11 years, 11 months ago) by
golsen
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Changes since
1.10: +169 -0 lines
Diff to
previous 1.10
Add routines for calculating the fractional sequence difference in a
nucleotide alignment. They sould be much faster than a loop over
pairs of positions, and allow separate weighting of gap openning and
gap extension, and of terminal versus interal gaps.
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