details: http://www.bx.psu.edu/hg/galaxy/rev/b7aabc2553fc changeset: 1682:b7aabc2553fc user: wychung date: Fri Dec 19 12:25:52 2008 -0500 description: fixed for short read build distribution tool. remove unused arrays. also update test data output. 3 file(s) affected in this change: test-data/454Score.png test-data/solexaScore.png tools/metag_tools/short_reads_figure_score.py diffs (87 lines): diff -r d38b593a27b4 -r b7aabc2553fc test-data/454Score.png Binary file test-data/454Score.png has changed diff -r d38b593a27b4 -r b7aabc2553fc test-data/solexaScore.png Binary file test-data/solexaScore.png has changed diff -r d38b593a27b4 -r b7aabc2553fc tools/metag_tools/short_reads_figure_score.py --- a/tools/metag_tools/short_reads_figure_score.py Fri Dec 19 11:05:54 2008 -0500 +++ b/tools/metag_tools/short_reads_figure_score.py Fri Dec 19 12:25:52 2008 -0500 @@ -62,6 +62,9 @@ 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 @@ 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 @@ 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 @@ 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 @@ 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 ): + tmp_array = [] for j in range( len( score_points ) ): - tmp_array.append( int( score_points[j][i] ) ) + try: + tmp_array.append( int( score_points[j][i] ) ) + except: + invalid_lines += 1 score_matrix.append( tmp_array ) - tmp_array = [] # generate pdf figures #outfile_R_pdf = outfile_R_name @@ -268,6 +257,8 @@ 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