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fixed for short read build distribution tool. remove unused arrays. also update test data output.

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This commit is contained in:
Wen-Yu Chung
2008-12-19 12:25:52 -05:00
parent 4dc6d12546
commit 170f9d2d77
2 changed files with 13 additions and 22 deletions
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test-data/454Score.png
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tools/metag_tools/short_reads_figure_score.py
+13 -22
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@@ -62,6 +62,9 @@ def merge_to_20_datapoints( score ):
return score_points
def __main__():
invalid_lines = 0
infile_score_name = sys.argv[1].strip()
outfile_R_name = sys.argv[2].strip()
@@ -150,7 +153,7 @@ def __main__():
number_of_points = 20
else:
number_of_points = read_length
quality_score = {} # quantile dictionary
read_length_threshold = 100 # minimal read length for 454 file
score_points = []
score_matrix = []
@@ -177,12 +180,7 @@ def __main__():
big = 0
tmp_array.append( big )
score_points.append( tmp_array )
# quartile
for j, k in enumerate( tmp_array ):
if quality_score.has_key( ( j, k ) ):
quality_score[ ( j, k ) ] += 1
else:
quality_score[ ( j, k ) ] = 1
elif seq_method == '454':
# skip the last fasta sequence
score = ''
@@ -203,12 +201,6 @@ def __main__():
score_points_tmp = merge_to_20_datapoints( score )
score_points.append( score_points_tmp )
tmp_array = score_points_tmp
# quartile
for j, k in enumerate( tmp_array ):
if quality_score.has_key( ( j, k ) ):
quality_score[ ( j, k ) ] += 1
else:
quality_score[ ( j ,k ) ] = 1
score = ''
else:
score = "%s %s" % ( score, line )
@@ -222,19 +214,16 @@ def __main__():
score_points_tmp = merge_to_20_datapoints( score )
score_points.append( score_points_tmp )
tmp_array = score_points_tmp
for j, k in enumerate( tmp_array ):
if quality_score.has_key( ( j, k ) ):
quality_score[ ( j, k ) ] += 1
else:
quality_score[ ( j, k ) ] = 1
# reverse the matrix, for R
tmp_array = []
for i in range( number_of_points - 1 ):
for j in range( len( score_points ) ):
tmp_array.append( int( score_points[j][i] ) )
score_matrix.append( tmp_array )
tmp_array = []
for j in range( len( score_points ) ):
try:
tmp_array.append( int( score_points[j][i] ) )
except:
invalid_lines += 1
score_matrix.append( tmp_array )
# generate pdf figures
#outfile_R_pdf = outfile_R_name
@@ -268,6 +257,8 @@ def __main__():
if invalid_scores > 0:
print 'Skipped %d invalid scores. ' % invalid_scores
if invalid_lines > 0:
print 'Skipped %d invalid lines. ' % invalid_lines
if empty_score_matrix_columns > 0:
print '%d missing scores in score_matrix. ' % empty_score_matrix_columns