Merge branch 'master' of github.com:brantp/rtd

Conflicts:
	mcl_id_triples_by_blat.py

101013_lane7_sample_data.csv

@@ -0,0 +1,48 @@
+,BC110,3,A1,rad48,101013,7
+,BC538,3,A2,rad48,101013,7
+,BC621,2,A3,rad48,101013,7
+,BC777,2,A4,rad48,101013,7
+,BC846,4,A5,rad48,101013,7
+,BC1006,4,A6,rad48,101013,7
+,BC244,2,B1,rad48,101013,7
+,BC540,1,B2,rad48,101013,7
+,BC673,2,B3,rad48,101013,7
+,BC779,1,B4,rad48,101013,7
+,BC885,1,B5,rad48,101013,7
+,BC1010,4,B6,rad48,101013,7
+,BC254,3,C1,rad48,101013,7
+,BC567,3,C2,rad48,101013,7
+,BC675,3,C3,rad48,101013,7
+,BC790,3,C4,rad48,101013,7
+,BC954,3,C5,rad48,101013,7
+,BC1029,4,C6,rad48,101013,7
+,BC301,1,D1,rad48,101013,7
+,BC606,2,D2,rad48,101013,7
+,BC689,2,D3,rad48,101013,7
+,BC793,3,D4,rad48,101013,7
+,BC958,4,D5,rad48,101013,7
+,BC1032,4,D6,rad48,101013,7
+,BC306,2,E1,rad48,101013,7
+,BC608,1,E2,rad48,101013,7
+,BC709,3,E3,rad48,101013,7
+,BC796,4,E4,rad48,101013,7
+,BC973,3,E5,rad48,101013,7
+,BC1054,4,E6,rad48,101013,7
+,BC442,3,F1,rad48,101013,7
+,BC613,2,F2,rad48,101013,7
+,BC744,1,F3,rad48,101013,7
+,BC826,4,F4,rad48,101013,7
+,BC974,1,F5,rad48,101013,7
+,BC1058,2,F6,rad48,101013,7
+,BC497,1,G1,rad48,101013,7
+,BC616,2,G2,rad48,101013,7
+,BC749,1,G3,rad48,101013,7
+,BC828,4,G4,rad48,101013,7
+,BC980,1,G5,rad48,101013,7
+,BC1059,1,G6,rad48,101013,7
+,BC527,2,H1,rad48,101013,7
+,BC620,1,H2,rad48,101013,7
+,BC750,2,H3,rad48,101013,7
+,BC834,4,H4,rad48,101013,7
+,BC985,4,H5,rad48,101013,7
+,BC1023B,3,H6,rad48,101013,7

USAGE_NOTES

@@ -64,6 +64,9 @@ Finally, note that the first sample had no index; this is fine, this
 just means we didn't do illumina-style "third read" multiplexing for
 that sample, whereas for the second example we did (using index #11)
 
+Example data for DB_library_data can be found at:
+https://docs.google.com/spreadsheet/ccc?key=0AnHEwF1NpAxDdFlXRXliTElXQzF6dkswZk5HenlTclE
+
 - RUN preprocess_radtag_lane.py
 
 we start with the s_X_[1|2]_sequence[_indexZ].txt[.gz]
@@ -78,4 +81,4 @@ $ preprocess_radtag_lane.py -h
 - RUN rtd_run.py
 
 using the .uniqued.gz files generated for each lane/index, invoke rtd_run.py per help:
-$ rtd_run.py -h
+$ rtd_run.py -h

mcl_id_triples_by_blat.py

@@ -7,7 +7,11 @@
 
 '''
 
+<<<<<<< HEAD
 import os, sys, re, gzip
+=======
+import os, sys, re, numpy
+>>>>>>> 9746a9d04d8803a838c0229517a1dacbdb12cb1b
 from config import SCRATCH as scratch
 
 fail_to_local = False #must set to "True" to allow use of working directory for blat output
@@ -35,7 +39,11 @@ def space_free_on_volume(vol,unit='M',verbose=False):
     from subprocess import Popen,PIPE
     if verbose:
         print >> sys.stderr, 'checking free space on volume %s ...' % vol,
-    free = int(Popen('df -P --sync -B %s %s' % (unit,vol), shell=True, stdout=PIPE).stdout.readlines()[-1].strip().split()[3].rstrip(unit))
+    try:
+        free = int(Popen('df -P --sync -B %s %s' % (unit,vol), shell=True, stdout=PIPE).stdout.readlines()[-1].strip().split()[3].rstrip(unit))
+    except:
+        print >> sys.stderr, 'free space check failed; proceeding.  MONITOR AVAILABLE SPACE ON %s' % vol
+        free = numpy.inf
     if verbose:
         print >> sys.stderr, '%s %sB' % (free,unit)
     return free