From f6e605c80b200e5d7d08a4d1b83538702b271023 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Fri, 5 Nov 2010 16:27:02 -0700 Subject: [PATCH] Update to the new UCSC DAF file. We are submitting 3 different types of expression data, one for Gencode v3c, one for Gencode v4, and one for the de novo cufflinks assembly. As a result I needed to update the file name to ucsc view map to describe these new, more specific datasets. Also I modified the name of the archival and upload condor scripts to include a username. --- extra/ucsc_encode_submission/ucsc_gather.py | 37 +++++++++++---------- 1 file changed, 20 insertions(+), 17 deletions(-) diff --git a/extra/ucsc_encode_submission/ucsc_gather.py b/extra/ucsc_encode_submission/ucsc_gather.py index 3edc9bf..f8d598f 100755 --- a/extra/ucsc_encode_submission/ucsc_gather.py +++ b/extra/ucsc_encode_submission/ucsc_gather.py @@ -423,7 +423,7 @@ arguments = czvf ../%(archivename)s %(filelist)s Error = compress.err.$(Process).log Output = compress.out.$(Process).log -Log = /tmp/submission-compress.log +Log = /tmp/submission-compress-%(user)s.log initialdir = %(initialdir)s queue @@ -434,7 +434,8 @@ queue context = {'archivename': make_submission_name(ininame), 'filelist': " ".join(files), - 'initialdir': os.getcwd()} + 'initialdir': os.getcwd(), + 'user': os.getlogin()} condor_script = make_condor_name(ininame, 'archive') condor_stream = open(condor_script,'w') @@ -447,17 +448,18 @@ def make_condor_upload_script(ininame): script = """Universe = vanilla Executable = /usr/bin/lftp -arguments = -c put ../%(archivename)s -o ftp://detrout@encodeftp.cse.ucsc.edu/ +arguments = -c put ../%(archivename)s -o ftp://detrout@encodeftp.cse.ucsc.edu/%(archivename)s Error = upload.err.$(Process).log Output = upload.out.$(Process).log -Log = /tmp/submission-upload.log +Log = /tmp/submission-upload-%(user)s.log initialdir = %(initialdir)s queue """ context = {'archivename': make_submission_name(ininame), - 'initialdir': os.getcwd()} + 'initialdir': os.getcwd(), + 'user': os.getlogin()} condor_script = make_condor_name(ininame, 'upload') condor_stream = open(condor_script,'w') @@ -597,13 +599,14 @@ class NameToViewMap(object): ('*.condor', None), ('*.daf', None), ('*.ddf', None), - ('*denovo.genes.expr', 'GeneDeNovo'), - ('*denovo.transcripts.expr','TranscriptDeNovo'), - ('*novel.genes.expr', 'GeneDeNovo'), - ('*novel.transcripts.expr', 'TranscriptDeNovo'), - ('*genes.expr', 'GeneFPKM'), - ('*transcripts.expr', 'TranscriptFPKM'), - ('*transcript.expr', 'TranscriptFPKM'), + ('cufflinks-0.9.0-genes.expr', 'GeneDeNovo'), + ('cufflinks-0.9.0-transcripts.expr', 'TranscriptDeNovo'), + ('cufflinks-0.9.0-transcripts.gtf', 'GeneModel'), + ('GENCODE-v3c-genes.expr', 'GeneGencV3c'), + ('GENCODE-v3c-transcripts.expr', 'TranscriptGencV3c'), + ('GENCODE-v4-genes.expr', 'GeneGencV4'), + ('GENCODE-v4-transcripts.expr', 'TranscriptGencV4'), + ('GENCODE-v4-transcript.expr', 'TranscriptGencV4'), ('*_r1.fastq', 'FastqRd1'), ('*_r2.fastq', 'FastqRd2'), ('*.fastq', 'Fastq'), @@ -625,13 +628,13 @@ class NameToViewMap(object): "PlusSignal": {"MapAlgorithm": ma}, "MinusSignal": {"MapAlgorithm": ma}, "Signal": {"MapAlgorithm": ma}, + "GeneModel": {"MapAlgorithm": ma}, "GeneDeNovo": {"MapAlgorithm": ma}, "TranscriptDeNovo": {"MapAlgorithm": ma}, - "GeneDeNovo": {"MapAlgorithm": ma}, - "TranscriptDeNovo": {"MapAlgorithm": ma}, - "GeneFPKM": {"MapAlgorithm": ma}, - "TranscriptFPKM": {"MapAlgorithm": ma}, - "TranscriptFPKM": {"MapAlgorithm": ma}, + "GeneGencV3c": {"MapAlgorithm": ma}, + "TranscriptGencV3c": {"MapAlgorithm": ma}, + "GeneGencV4": {"MapAlgorithm": ma}, + "TranscriptGencV4": {"MapAlgorithm": ma}, "FastqRd1": {"MapAlgorithm": "NA", "type": "fastq"}, "FastqRd2": {"MapAlgorithm": "NA", "type": "fastq"}, "Fastq": {"MapAlgorithm": "NA", "type": "fastq" }, -- 2.30.2