|
 |
07332ca |
diff --git a/misc/guess-ploidy.py b/misc/guess-ploidy.py
|
|
|
07332ca |
index 816a5c6..6ad3d36 100755
|
|
|
07332ca |
--- a/misc/guess-ploidy.py
|
|
|
07332ca |
+++ b/misc/guess-ploidy.py
|
|
|
07332ca |
@@ -24,6 +24,8 @@
|
|
|
07332ca |
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
|
|
|
07332ca |
# DEALINGS IN THE SOFTWARE.
|
|
|
07332ca |
|
|
|
07332ca |
+from __future__ import print_function
|
|
|
07332ca |
+
|
|
|
07332ca |
import matplotlib as mpl
|
|
|
07332ca |
mpl.use('Agg')
|
|
|
07332ca |
import matplotlib.pyplot as plt
|
|
|
07332ca |
@@ -33,8 +35,9 @@ import csv
|
|
|
07332ca |
csv.register_dialect('tab', delimiter='\t', quoting=csv.QUOTE_NONE)
|
|
|
07332ca |
|
|
|
07332ca |
if len(sys.argv) != 3:
|
|
|
07332ca |
- print >> sys.stderr, 'About: Plot output of "bcftools +guess-ploidy -v"'
|
|
|
07332ca |
- print >> sys.stderr, 'Usage: guess-ploidy.py <guess-ploidy.out> <image-prefix>'
|
|
|
07332ca |
+ print("""\
|
|
|
07332ca |
+About: Plot output of "bcftools +guess-ploidy -v"
|
|
|
07332ca |
+Usage: guess-ploidy.py <guess-ploidy.out> <image-prefix>""", file = sys.stderr)
|
|
|
07332ca |
sys.exit()
|
|
|
07332ca |
|
|
|
07332ca |
prefix = sys.argv[2]
|
|
|
07332ca |
diff --git a/misc/plot-roh.py b/misc/plot-roh.py
|
|
|
07332ca |
index 81efaaa..90dd63e 100755
|
|
|
07332ca |
--- a/misc/plot-roh.py
|
|
|
07332ca |
+++ b/misc/plot-roh.py
|
|
|
07332ca |
@@ -29,26 +29,27 @@ csv.register_dialect('tab', delimiter='\t', quoting=csv.QUOTE_NONE)
|
|
|
07332ca |
|
|
|
07332ca |
def usage(msg=None):
|
|
|
07332ca |
if msg==None:
|
|
|
07332ca |
- print 'Usage: plot.py [OPTIONS] <dir>'
|
|
|
07332ca |
- print 'Options:'
|
|
|
07332ca |
- print ' -H, --highlight +group1,-group2 Highlight calls shared within group1 but not present in group2'
|
|
|
07332ca |
- print ' -i, --interactive Run interactively'
|
|
|
07332ca |
- print ' -l, --min-length <num> Filter input regions shorter than this [0]'
|
|
|
07332ca |
- print ' -n, --min-markers <num> Filter input regions with fewer marker than this [0]'
|
|
|
07332ca |
- print ' -o, --outfile <file> Output file name [plot.png]'
|
|
|
07332ca |
- print ' -q, --min-qual <num> Filter input regions with quality smaller than this [0]'
|
|
|
07332ca |
- print ' -r, --region [^]<chr|chr:beg-end> Plot this chromosome/region only'
|
|
|
07332ca |
- print ' -s, --samples <file> List of samples to show, rename or group: "name[\\tnew_name[\\tgroup]]"'
|
|
|
07332ca |
- print ' -h, --help This usage text'
|
|
|
07332ca |
- print 'Matplotlib options:'
|
|
|
07332ca |
- print ' +adj, --adjust <str> Set plot adjust [bottom=0.18,left=0.07,right=0.98]'
|
|
|
07332ca |
- print ' +dpi, --dpi <num> Set bitmap DPI [150]'
|
|
|
07332ca |
- print ' +sxt, --show-xticks Show x-ticks (genomic coordinate)'
|
|
|
07332ca |
- print ' +twh, --track-wh <num,num> Set track width and height [20,1]'
|
|
|
07332ca |
- print ' +xlb, --xlabel <str> Set x-label'
|
|
|
07332ca |
- print ' +xli, --xlimit <num> Extend x-range by this fraction [0.05]'
|
|
|
07332ca |
+ print("""\
|
|
|
07332ca |
+Usage: plot-roh.py [OPTIONS] <dir>
|
|
|
07332ca |
+Options:
|
|
|
07332ca |
+ -H, --highlight +group1,-group2 Highlight calls shared within group1 but not present in group2
|
|
|
07332ca |
+ -i, --interactive Run interactively
|
|
|
07332ca |
+ -l, --min-length <num> Filter input regions shorter than this [0]
|
|
|
07332ca |
+ -n, --min-markers <num> Filter input regions with fewer marker than this [0]
|
|
|
07332ca |
+ -o, --outfile <file> Output file name [plot.png]
|
|
|
07332ca |
+ -q, --min-qual <num> Filter input regions with quality smaller than this [0]
|
|
|
07332ca |
+ -r, --region [^]<chr|chr:beg-end> Plot this chromosome/region only
|
|
|
07332ca |
+ -s, --samples <file> List of samples to show, rename or group: "name[\\tnew_name[\\tgroup]]"
|
|
|
07332ca |
+ -h, --help This usage text
|
|
|
07332ca |
+Matplotlib options:
|
|
|
07332ca |
+ +adj, --adjust <str> Set plot adjust [bottom=0.18,left=0.07,right=0.98]
|
|
|
07332ca |
+ +dpi, --dpi <num> Set bitmap DPI [150]
|
|
|
07332ca |
+ +sxt, --show-xticks Show x-ticks (genomic coordinate)
|
|
|
07332ca |
+ +twh, --track-wh <num,num> Set track width and height [20,1]
|
|
|
07332ca |
+ +xlb, --xlabel <str> Set x-label
|
|
|
07332ca |
+ +xli, --xlimit <num> Extend x-range by this fraction [0.05]""")
|
|
|
07332ca |
else:
|
|
|
07332ca |
- print msg
|
|
|
07332ca |
+ print(msg)
|
|
|
07332ca |
sys.exit(1)
|
|
|
07332ca |
|
|
|
07332ca |
dir = None
|