From 3d4fcb9d0965e4b2566910950cd364e73017f5b7 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Tue, 16 Nov 2010 21:39:25 -0800 Subject: [PATCH] Cache the attributes for each type of fastq file. Previously it was just using whatever was last as the set of attributes. Which led to everything being flagged as FastqRd2 --- extra/ucsc_encode_submission/ucsc_gather.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/extra/ucsc_encode_submission/ucsc_gather.py b/extra/ucsc_encode_submission/ucsc_gather.py index 72d7f32..d160b21 100755 --- a/extra/ucsc_encode_submission/ucsc_gather.py +++ b/extra/ucsc_encode_submission/ucsc_gather.py @@ -268,6 +268,7 @@ def make_submission_ini(host, apidata, library_result_map, paired=True): # write other lines submission_files = os.listdir(result_dir) fastqs = {} + fastq_attributes = {} for f in submission_files: attributes = view_map.find_attributes(f, lib_id) if attributes is None: @@ -278,6 +279,7 @@ def make_submission_ini(host, apidata, library_result_map, paired=True): continue elif attributes.get("type", None) == 'fastq': fastqs.setdefault(ext, set()).add(f) + fastq_attributes[ext] = attributes else: inifile.extend( make_submission_section(line_counter, @@ -287,13 +289,13 @@ def make_submission_ini(host, apidata, library_result_map, paired=True): ) inifile += [''] line_counter += 1 + # add in fastqs on a single line. - # add in fastqs on a single line. - for extension, fastq_set in fastqs.items(): + for extension, fastq_files in fastqs.items(): inifile.extend( make_submission_section(line_counter, - fastq_set, - attributes[extension]) + fastq_files, + fastq_attributes[extension]) ) inifile += [''] line_counter += 1 -- 2.30.2