diff --git a/scripts/get_sequencing_read_data.py b/scripts/get_sequencing_read_data.py index e8e16f7..687fbf4 100755 --- a/scripts/get_sequencing_read_data.py +++ b/scripts/get_sequencing_read_data.py @@ -10,7 +10,7 @@ def get_sequencing_read_data(sequencer_path): """ method to check the read lengths in the RunInfo.xml file """ # compare tag - atac_reads = [[51, 8, 24, 50], [51, 8, 16, 50]] + atac_reads = [[51, 8, 24, 50], [51, 8, 16, 50], [51, 8, 24, 51]] # set variables to parge the XML file @@ -31,7 +31,9 @@ def get_sequencing_read_data(sequencer_path): detected_reads = [y[1] for y in reads_tag] # check the read lengths. if they equal the atacReads list, then set atac variable to True - if ((detected_reads == atac_reads[0]) or (detected_reads == atac_reads[1])): + # if ((detected_reads == atac_reads[0]) or (detected_reads == atac_reads[1]) or (detected_reads == atac_reads[2])) + # making a simpler if statement to check for reads + if (detected_reads in atac_reads): atac = True use_bases_mask = "Y" + str(reads_tag[0][1]) + ",I" + str(reads_tag[1][1]) + ",Y" + str(reads_tag[2][1]) + ",Y" + str(reads_tag[3][1]) else: