cleaned up scripts

hyphaltip · Jul 9, 2010 · 5bab290 · 5bab290
1 parent 9748e62
commit 5bab290
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Showing 16 changed files with 10 additions and 501 deletions.
diff --git a/scripts/collision.py b/scripts/collision.py
diff --git a/scripts/ctb-iterative-bench-2.py b/scripts/ctb-iterative-bench-2.py
@@ -171,8 +171,7 @@
 
     print 'filtering...'
     minmax = ht.fasta_file_to_minmax(this_filename, total_reads)
-    readmask = ht.filter_fasta_file_any(this_filename, minmax,
-                                        5, readmask)
+    readmask = ht.filter_fasta_file_any(minmax, 5, readmask)
 
     n_seq_kept = readmask.n_kept()
 

diff --git a/scripts/fasta-consume.py b/scripts/fasta-consume.py
diff --git a/scripts/fasta-filter.py b/scripts/fasta-filter.py
diff --git a/scripts/filter-exact.py b/scripts/filter-exact.py
@@ -23,7 +23,7 @@
 print 'filtering...'
 
 minmax = ht.fasta_file_to_minmax(infilename, total_reads)
-readmask = ht.filter_fasta_file_any(infilename, minmax, MIN_ABUNDANCE)
+readmask = ht.filter_fasta_file_any(minmax, MIN_ABUNDANCE)
 
 print 'keeping %d reads' % readmask.n_kept()
 

diff --git a/scripts/filter-inexact-all.py b/scripts/filter-inexact-all.py
@@ -25,7 +25,7 @@
 print 'filtering...'
 
 minmax = ht.fasta_file_to_minmax(infilename, total_reads)
-readmask = ht.filter_fasta_file_all(infilename, minmax, MIN_ABUNDANCE)
+readmask = ht.filter_fasta_file_all(minmax, MIN_ABUNDANCE)
 
 print 'keeping %d reads' % readmask.n_kept()
 

diff --git a/scripts/filter-inexact-any.py b/scripts/filter-inexact-any.py
@@ -23,7 +23,7 @@
 print 'filtering...'
 
 minmax = ht.fasta_file_to_minmax(infilename, total_reads)
-readmask = ht.filter_fasta_file_any(infilename, minmax, MIN_ABUNDANCE)
+readmask = ht.filter_fasta_file_any(minmax, MIN_ABUNDANCE)
 
 print 'keeping %d reads' % readmask.n_kept()
 

diff --git a/scripts/filter-iowa.py b/scripts/filter-iowa.py
diff --git a/scripts/iowa-filter-fa.py b/scripts/iowa-filter-fa.py