def loadTranscriptClassification(infiles, outfile):
P.concatenate_and_load(infiles,
outfile,
regex_filename=".+/(.+).class.gz",
options="-i transcript_id -i gene_id"
" -i match_gene_id -i match_transcript_id"
" -i source",
job_memory="64G")
def loadCramQuality(infiles, outfile):
''' Load the quality scores for the different cells
into the database (summarized table).
'''
quality_files = [
fn for filenames in infiles for fn in filenames
if fn.endswith(".quality")
]
P.concatenate_and_load(quality_files,
outfile,
regex_filename="validate.cram.dir/(.*).quality",
cat="track",
has_titles=False,
header="cramID,number_reads,cram_quality_score")
def mergeAllQuants(infiles, outfile):
job_threads = 3
P.concatenate_and_load(
infiles,
outfile,
regex_filename="quantification.dir/(.*)_agg-agg-agg.sf",
options="-i Name -i Length -i EffectiveLength"
" -i TPM -i NumReads -i track"
" -i source",
job_memory="64G")
if not os.path.isfile("mapping_rates.txt"):
statement = ''' bash /shared/sudlab1/General/projects/UTRONs/MyFiles/scripts/mapping_rates_script.sh '''
P.run(statement)
else:
pass
def loadUtronIDs(infiles, outfile):
job_threads = 3
header = "track,transcript_id"
options = "-i track -i transcript_id"
if not outfile == "all_utrons_ids.load":
header += ",match_transcript_id"
options += " -i match_transcript_id"
P.concatenate_and_load(infiles,
outfile,
regex_filename=".+/(.+)\..+\.ids.gz",
has_titles=False,
cat="track",
header=header,
options=options,
job_memory="64G")
def loadSeedTables(infiles, outfile):
P.concatenate_and_load(infiles, outfile,
regex_filename=".+/(.+)\.(?:meme|dreme|memechip).tsv")
def mergeAndLoadTrackComparisons(infiles, outfile):
P.concatenate_and_load(infiles, outfile,
regex_filename=(".+/(.+)_to_(.+).tomtom"),
cat="track1,track2",
options="-i track1 -i track2")
