few updates to scripts

bin/fastaInfo

@@ -72,7 +72,7 @@ parser.add_option('-S', dest='statsSimple',
                   action='store_true')
 parser.set_defaults(graphengine="R")
 parser.add_option('-g', dest='graphengine',
-                  help='either "R" or "gnuplot" is used to generated the graphs')
+                  help='either "R", "gnuplot" or "none" is used to generated the graphs')
 parser.set_defaults(histogramsteps=50)
 parser.add_option('-b', dest='histogramsteps', type="int",
                   help='no of bins to use in the histograms')
@@ -128,7 +128,7 @@ if options.stats:
     for x in args:
         dd[x] = []
 
-funcs = ['length', 'fracn', 'id', 'scaf10', 'scaf100', 'gcfrac', 'ncount']
+funcs = ['length', 'fracn', 'id', 'scaf10', 'scaf1', 'scaf100', 'gcfrac', 'ncount']
 
 def f_id(name, seq):
     return name.split()[0]
@@ -152,8 +152,13 @@ def f_gcfrac(name, seq):
     t = seq.count('t')
     return float(g+c) / (g + c + a + t)
 
+scaf1rex = re.compile(r'n{1,}')
 scaf10rex = re.compile(r'n{10,}')
 scaf100rex = re.compile(r'n{100,}')
+
+def f_scaf1(name,seq):
+    return len(scaf10rex.split(seq))
+
 def f_scaf10(name,seq):
     return len(scaf10rex.split(seq))
 

bin/moar

@@ -2,16 +2,36 @@
 
 import os
 import sys
+import argparse
 import subprocess as sp
 
 base = os.path.abspath(os.getcwd())
+parser = argparse.ArgumentParser(description='run recursively')
+parser.add_argument('--bg', dest='background', action='store_true',
+                   default=False,
+                   help='run in the background')
+parser.add_argument('-d', dest='depth', default=0, help='depth: 1 means run only in first ' + 
+                    'level subdirs, 2 only in second level, and so on', type=int)
+parser.add_argument('command', nargs='+')
+args = parser.parse_args()
+
+cl = " ".join(args.command).strip()
+if args.background and cl[-1] != '&':
+    cl = '( ' + cl + ' )& '
+
+print 'executing:', cl
+
+if base[-1] == '/': base = base[:-1]
 
-cl = " ".join(sys.argv[1:])
-print 'executing:'
-print cl
 for path, dirs, files in os.walk(base):
     toRemove = [x for x in dirs if x[0] in ['.', '_']]
     [dirs.remove(x) for x in toRemove]
-    print 'executing in %s' % path
+    localpath =  path.replace(base, '')
+    level = len(localpath.split('/')) - 1
+
+    if args.depth and args.depth != level:
+        continue
+    print 'executing in %s' % localpath
+
     P = sp.Popen(cl, cwd=path, shell=True)
     P.wait()