details: http://www.bx.psu.edu/hg/galaxy/rev/4e7c1fe8fab8
changeset: 3247:4e7c1fe8fab8
user: Kelly Vincent <kpvincent(a)bx.psu.edu>
date: Fri Jan 15 17:12:50 2010 -0500
description:
Updated csFasta sniff method to handle sequences with dots in them (T123..32.020......23) instead of being just numbers with a leading capital letter
diffstat:
lib/galaxy/datatypes/sequence.py | 4 ++--
1 files changed, 2 insertions(+), 2 deletions(-)
diffs (21 lines):
diff -r 9cc57a489be0 -r 4e7c1fe8fab8 lib/galaxy/datatypes/sequence.py
--- a/lib/galaxy/datatypes/sequence.py Fri Jan 15 12:51:45 2010 -0500
+++ b/lib/galaxy/datatypes/sequence.py Fri Jan 15 17:12:50 2010 -0500
@@ -66,7 +66,7 @@
A sequence in FASTA format consists of a single-line description, followed by lines of sequence data.
The first character of the description line is a greater-than (">") symbol in the first column.
- All lines should be shorter than 80 charcters
+ All lines should be shorter than 80 characters
For complete details see http://www.ncbi.nlm.nih.gov/blast/fasta.shtml
@@ -139,7 +139,7 @@
break
elif line[0] not in string.ascii_uppercase:
return False
- elif len( line ) > 1 and not re.search( '^\d+$', line[1:] ):
+ elif len( line ) > 1 and not re.search( '^[\d.]+$', line[1:] ):
return False
return True
else:
details: http://www.bx.psu.edu/hg/galaxy/rev/5d5e5da2fcda
changeset: 3242:5d5e5da2fcda
user: Anton Nekrutenko <anton(a)bx.psu.edu>
date: Thu Jan 14 14:20:01 2010 -0500
description:
Small edit for the help section
diffstat:
tools/samtools/pileup_parser.xml | 6 +++---
1 files changed, 3 insertions(+), 3 deletions(-)
diffs (16 lines):
diff -r ec77ae7f9b4f -r 5d5e5da2fcda tools/samtools/pileup_parser.xml
--- a/tools/samtools/pileup_parser.xml Thu Jan 14 14:13:42 2010 -0500
+++ b/tools/samtools/pileup_parser.xml Thu Jan 14 14:20:01 2010 -0500
@@ -272,9 +272,9 @@
will report everything from the original file::
- chrM 412 A 2 ., II 0 0 0 0 2
- chrM 413 G 4 ..t, III2 0 0 0 1 3
- chrM 414 C 4 ...a III2 0 0 0 0 3
+ chrM 412 A 2 ., II 2 0 0 0 2
+ chrM 413 G 4 ..t, III2 0 0 2 1 3
+ chrM 414 C 4 ...a III2 3 0 0 0 3
chrM 415 C 4 TTTt III7 0 0 0 4 4
Here, you can see that although the total coverage at position 414 is 4 (column 4), the quality adjusted coverage is 3 (last column). This is because only three out of four reads have bases with quality above the set threshold of 20 (the actual qualities are III2 or, after conversion, 40, 40, 40, 17).