def loadDistances(infile, outfile):
'''load annotations'''
P.load(
infile, outfile,
"--index=gene_id --map=gene_id:str --index=closest_id --map=closest_id:str"
)
table = outfile[:-len(".load")]
def loadFilteredContigLengths(infile, outfile):
'''
load contig lengths
'''
outname = P.snip(os.path.dirname(infile), ".dir") + "_" + P.snip(os.path.basename(infile), ".tsv") + ".load"
P.load(infile, outname)
P.touch(outfile)
def loadTranscriptSummary(infile, outfile):
'''summarize binding information per transcript.'''
dbh = connect()
table = P.toTable(outfile)
cc = dbh.cursor()
# sqlite can not do full outer join
cc.execute( """DROP TABLE IF EXISTS %(table)s""" % locals() )
transcripts = [x[0] for x in cc.execute(
"SELECT DISTINCT(transcript_id) FROM annotations.transcript_info").fetchall()]
tmpf = P.getTempFile()
tables = ("tata", "cpg")
titles = tables
vals = []
for table in tables:
t = set([x[0] for x in cc.execute(
"SELECT DISTINCT(transcript_id) FROM %(table)s" % locals()).fetchall()])
vals.append(t)
tmpf.write("transcript_id\t%s\n" % "\t".join(titles))
for transcript_id in transcripts:
tmpf.write("%s\t%s\n" % (transcript_id,
"\t".join([str(int(transcript_id in v)) for v in vals])))
tmpf.close()
P.load(tmpf.name, outfile)
os.unlink(tmpf.name)
def loadContigSummary(infile, outfile):
'''
load contig summary stats for each assembler
'''
outname = P.snip(os.path.dirname(infile), ".dir") + "_" + os.path.basename(infile) + ".load"
P.load(infile, outname)
P.touch(outfile)
def loadGeneTables(infile, outfile):
'''
load genes from metagenemaek analysis
'''
if infile.find("gff") != -1:
P.load(infile, outfile)
else:
P.load(infile, outfile)
def loadExonValidation(infiles, outfile):
"""merge alignment stats into single tables."""
suffix = suffix = ".exon.validation.tsv.gz"
mergeAndLoad(infiles, outfile, suffix=suffix)
for infile in infiles:
track = P.snip(infile, suffix)
o = "%s_overrun.load" % track
P.load(infile + ".overrun.gz", o)
def loadContigLengths(infile, outfile):
'''
load contig lengths
'''
outname = P.snip(os.path.dirname(infile), ".dir") + "_" + P.snip(
os.path.basename(infile), ".tsv") + ".load"
P.load(infile, outname)
P.touch(outfile)
def loadContigSummary(infile, outfile):
'''
load contig summary stats for each assembler
'''
outname = P.snip(os.path.dirname(infile), ".dir") + \
"_" + os.path.basename(infile) + ".load"
P.load(infile, outname)
P.touch(outfile)
def loadExonValidation(infiles, outfile):
'''merge alignment stats into single tables.'''
suffix = suffix = ".exon.validation.tsv.gz"
mergeAndLoad(infiles, outfile, suffix=suffix)
for infile in infiles:
track = P.snip(infile, suffix)
o = "%s_overrun.load" % track
P.load(infile + ".overrun.gz", o)
def loadContigGCContent(infile, outfile):
'''
load contig GC content
'''
outname = P.snip(os.path.dirname(infile), ".dir") + \
"_" + P.snip(os.path.basename(infile), ".tsv") + ".load"
P.load(infile, outname, "--index=id")
P.touch(outfile)
def loadContigLengths(infile, outfile):
'''
load contig lengths
'''
outname = P.snip(os.path.dirname(infile), ".dir") + \
"_" + P.snip(os.path.basename(infile), ".tsv") + ".load"
P.load(infile, outname, "--index=scaffold_name")
P.touch(outfile)
def loadHypergeometricAnalysis(infile, outfile):
'''load GO results.'''
track = P.toTable(outfile)
tablename = 'hypergeometric_%s_summary' % track
P.load(infile, outfile, tablename=tablename)
dbh = connect()
ontologies = [x[0] for x in Database.executewait(
dbh,
'''SELECT DISTINCT ontology FROM %s''' % tablename).fetchall()]
genelists = [x[0] for x in Database.executewait(
dbh,
'''SELECT DISTINCT genelist FROM %s''' % tablename).fetchall()]
# output files from runGO.py
sections = ('results', 'parameters', 'withgenes')
for section in sections:
tablename = 'hypergeometric_%s_%s' % (track, section)
statement = '''
python %(scriptsdir)s/combine_tables.py
--cat=track
--regex-filename="hypergeometric.dir/%(track)s.tsv.dir/(\S+).%(section)s"
hypergeometric.dir/%(track)s.tsv.dir/*.%(section)s
| python %(scriptsdir)s/csv2db.py
%(csv2db_options)s
--table=%(tablename)s
>> %(outfile)s'''
P.run()
for ontology in ontologies:
fn = os.path.join(infile + ".dir", "all_alldesc.%s.l2fold" % ontology)
if not os.path.exists(fn):
E.warn("file %s does not exist" % fn)
continue
P.load(fn,
outfile,
tablename='hypergeometric_%s_%s_l2fold' % (track, ontology),
options='--allow-empty')
fn = os.path.join(
infile + ".dir", "all_alldesc.%s.l10pvalue" % ontology)
P.load(fn,
outfile,
tablename='hypergeometric_%s_%s_l10pvalue' % (track, ontology),
options='--allow-empty')
fn = os.path.join(
infile + ".dir", "all_alldesc.%s.l10qvalue" % ontology)
P.load(fn,
outfile,
tablename='hypergeometric_%s_%s_l10qvalue' % (track, ontology),
options='--allow-empty')
def loadEdgeR( infile, outfile ):
'''load EdgeR per-chunk summary stats.'''
prefix = P.snip( outfile, ".load" )
for fn in glob.glob( infile + "*_summary.tsv" ):
prefix = P.snip(fn[len(infile)+1:], "_summary.tsv")
P.load( fn,
prefix + ".deseq_summary.load",
collapse = 0,
transpose = "sample")
P.touch( outfile )
def loadCufflinks( infile, outfile ):
'''load expression level measurements.'''
track = P.snip( outfile, ".load" )
P.load( infile + ".genes_tracking.gz",
outfile = track + "_genefpkm.load",
options = "--index=gene_id --ignore-column=tracking_id --ignore-column=class_code --ignore-column=nearest_ref_id" )
track = P.snip( outfile, ".load" )
P.load( infile + ".fpkm_tracking.gz",
outfile = track + "_fpkm.load",
options = "--index=tracking_id --ignore-column=nearest_ref_id --rename-column=tracking_id:transcript_id" )
P.touch( outfile )
def loadReadCounts(infiles, outfile):
'''load read counts into database.'''
outf = P.getTempFile()
outf.write("track\ttotal_reads\n")
for infile in infiles:
track = P.snip(infile, ".nreads")
lines = IOTools.openFile(infile).readlines()
nreads = int(lines[0][:-1].split("\t")[1])
outf.write("%s\t%i\n" % (track, nreads))
outf.close()
P.load(outf.name, outfile)
os.unlink(outf.name)
def loadReadCounts( infiles, outfile ):
'''load read counts into database.'''
outf = P.getTempFile()
outf.write( "track\ttotal_reads\n")
for infile in infiles:
track = P.snip(infile, ".nreads")
lines = IOTools.openFile( infile ).readlines()
nreads = int( lines[0][:-1].split("\t")[1])
outf.write( "%s\t%i\n" % (track,nreads))
outf.close()
P.load( outf.name, outfile )
os.unlink(outf.name)
def loadMotifInformation( infiles, outfile ):
'''load information about motifs into database.'''
outf = P.getTempFile(".")
outf.write("motif\n" )
for infile in infiles:
if IOTools.isEmpty( infile ): continue
motif = P.snip( infile, ".motif" )
outf.write( "%s\n" % motif )
outf.close()
P.load( outf.name, outfile, "--allow-empty" )
os.unlink( outf.name )
def loadMemeSummary( infiles, outfile ):
'''load information about motifs into database.'''
outf = P.getTempFile(".")
outf.write("track\n" )
for infile in infiles:
if IOTools.isEmpty( infile ): continue
motif = P.snip( infile, ".meme" )
outf.write( "%s\n" % motif )
outf.close()
P.load( outf.name, outfile )
os.unlink( outf.name )
def loadCufflinks(infile, outfile):
'''load expression level measurements.'''
track = P.snip(outfile, ".load")
P.load(infile + ".genes_tracking.gz",
outfile=track + "_genefpkm.load",
options="--index=gene_id "
"--ignore-column=tracking_id "
"--ignore-column=class_code "
"--ignore-column=nearest_ref_id")
track = P.snip(outfile, ".load")
P.load(infile + ".fpkm_tracking.gz",
outfile=track + "_fpkm.load",
options="--index=tracking_id "
"--ignore-column=nearest_ref_id "
"--rename-column=tracking_id:transcript_id")
P.touch(outfile)
def loadMemeChipSummary( infiles, outfile ):
'''load information about motifs into database.'''
outf = P.getTempFile(".")
outf.write("track\tnpeaks\twidth\tmasking\tpath\n" )
for infile in infiles:
if IOTools.isEmpty( infile ): continue
fn = P.snip(os.path.basename( infile ), ".memechip" )
track, npeaks, width, masking = fn.split(".")
outf.write( "\t".join( map(str,(track, npeaks, width, masking, fn)) ) + "\n" )
outf.close()
P.load( outf.name, outfile )
os.unlink( outf.name )
def loadTomTom(infile, outfile):
'''load tomtom results'''
tablename = P.toTable(outfile)
resultsdir = os.path.join(os.path.abspath(PARAMS["exportdir"]), "tomtom",
infile)
xml_file = os.path.join(resultsdir, "tomtom.xml")
if not os.path.exists(xml_file):
E.warn("no tomtom output - skipped loading ")
P.touch(outfile)
return
# get the motif name from the xml file
tree = xml.etree.ElementTree.ElementTree()
tree.parse(xml_file)
motifs = tree.find("targets")
name2alt = {}
for motif in motifs.getiterator("motif"):
name = motif.get("name")
alt = motif.get("alt")
name2alt[name] = alt
tmpfile = P.getTempFile(".")
# parse the text file
for line in IOTools.openFile(infile):
if line.startswith("#Query"):
tmpfile.write(
"target_name\tquery_id\ttarget_id\toptimal_offset\tpvalue\tevalue\tqvalue\tOverlap\tquery_consensus\ttarget_consensus\torientation\n"
)
continue
data = line[:-1].split("\t")
target_name = name2alt[data[1]]
tmpfile.write("%s\t%s" % (target_name, line))
tmpfile.close()
P.load(tmpfile.name, outfile)
os.unlink(tmpfile.name)
def loadDESeq( infile, outfile ):
'''load DESeq per-chunk summary stats.'''
prefix = P.snip( outfile, ".load" )
if os.path.exists( infile + "_size_factors.tsv" ):
P.load( infile + "_size_factors.tsv",
prefix + "_deseq_size_factors.load",
collapse = True,
transpose = "sample")
for fn in glob.glob( infile + "*_summary.tsv" ):
prefix = P.snip(fn[len(infile)+1:], "_summary.tsv")
P.load( fn,
prefix + ".deseq_summary.load",
collapse = 0,
transpose = "sample")
P.touch( outfile )
def loadMissedReadCounts(infiles, outfile):
"""load summary table of numbers of missed reads."""
def _getlines(inf):
return len(IOTools.openFile(inf).readlines()) - 1
tmpfile = P.getTempFile()
infiles = sorted(infiles)
tmpfile.write("track\tmapped_genome\tmissed_junctions\tmissed_transcriptome\n")
for x in range(0, len(infiles), 2):
junctions, transcriptome = infiles[x], infiles[x + 1]
track = P.snip(junctions, ".missed_junctions.gz")
mapped_genome = _getlines(track + ".mapped_reads.gz")
tmpfile.write("%s\t%i\t%i\t%i\n" % (track, mapped_genome, _getlines(junctions), _getlines(transcriptome)))
tmpfile.close()
P.load(tmpfile.name, outfile)
os.unlink(tmpfile.name)
def loadTomTom(infile, outfile):
'''load tomtom results'''
tablename = P.toTable(outfile)
resultsdir = os.path.join(
os.path.abspath(PARAMS["exportdir"]), "tomtom", infile)
xml_file = os.path.join(resultsdir, "tomtom.xml")
if not os.path.exists(xml_file):
E.warn("no tomtom output - skipped loading ")
P.touch(outfile)
return
# get the motif name from the xml file
tree = xml.etree.ElementTree.ElementTree()
tree.parse(xml_file)
motifs = tree.find("targets")
name2alt = {}
for motif in motifs.getiterator("motif"):
name = motif.get("name")
alt = motif.get("alt")
name2alt[name] = alt
tmpfile = P.getTempFile(".")
# parse the text file
for line in IOTools.openFile(infile):
if line.startswith("#Query"):
tmpfile.write(
"target_name\tquery_id\ttarget_id\toptimal_offset\tpvalue\tevalue\tqvalue\tOverlap\tquery_consensus\ttarget_consensus\torientation\n")
continue
data = line[:-1].split("\t")
target_name = name2alt[data[1]]
tmpfile.write("%s\t%s" % (target_name, line))
tmpfile.close()
P.load(tmpfile.name, outfile)
os.unlink(tmpfile.name)
def loadMissedReadCounts(infiles, outfile):
'''load summary table of numbers of missed reads.'''
def _getlines(inf):
return len(IOTools.openFile(inf).readlines()) - 1
tmpfile = P.getTempFile()
infiles = sorted(infiles)
tmpfile.write(
"track\tmapped_genome\tmissed_junctions\tmissed_transcriptome\n")
for x in range(0, len(infiles), 2):
junctions, transcriptome = infiles[x], infiles[x + 1]
track = P.snip(junctions, ".missed_junctions.gz")
mapped_genome = _getlines(track + ".mapped_reads.gz")
tmpfile.write("%s\t%i\t%i\t%i\n" %
(track, mapped_genome, _getlines(junctions),
_getlines(transcriptome)))
tmpfile.close()
P.load(tmpfile.name, outfile)
os.unlink(tmpfile.name)
def loadIdbaStats(infile, outfile):
'''
load the idba stats
'''
P.load(infile, outfile)
def loadGeneLevelReadCounts(infile, outfile):
P.load(infile, outfile, options="--index=gene_id")
def loadCufflinksFPKM(infile, outfile):
'''load fkpm data into table.'''
P.load(infile, outfile,
"--index=gene_id --index=transcript_id")
def loadDESeqStats(infile, outfile):
P.load(infile, outfile)
def loadBlastOnAminoAcidSequences(infile, outfile):
'''
load blastp results
'''
P.load(infile, outfile)
def loadChimericityScores(infile, outfile):
'''
load the chimericity scores
'''
P.load(infile, outfile)
def loadFilteredContigStats(infile, outfile):
'''
load the filtered contig stats
'''
P.load(infile, outfile)
def loadTATABox(infile, outfile):
'''load TATA box information.'''
P.load(infile + ".table.gz", outfile, "--index=transcript_id")
def loadDummyTask(infile, outfile):
'''load results of word counting into database.'''
P.load(infile, outfile, "--index=word")
def loadAlignmentStats(infile, outfile):
'''
load bam2stats results
'''
P.load(infile, outfile)
def loadMetavelvetRawStats(infile, outfile):
'''
load the assembly stats for meta-velvet
'''
inf = P.snip(infile, ".contigs.fa") + ".stats.txt"
P.load(inf, outfile)
def loadMetavelvetStats(infile, outfile):
'''
load the metavelvet stats
'''
P.load(infile, outfile)
def loadCpGIslands(infile, outfile):
'''load CpG Islands information.'''
P.load(infile, outfile, "--index=transcript_id")
def loadMACSsoloSummary(infile, outfile):
'''load macs summary.'''
P.load(infile, outfile, "--index=track")
def loadExpectedAndObservedGenomeCoverage(infile, outfile):
'''
load the combined table for observed and expected
genome coverage
'''
P.load(infile, outfile)
def loadFeatureCounts(infile, outfile):
'''load individual feature counts into database'''
P.load(infile, outfile, "--index=gene_id")
def loadFastqcSummary(infile, outfile):
P.load(infile, outfile, options="--index=track")
def loadEssentialGeneAssignments(infile, outfile):
'''
load assignments of essential genes
'''
P.load(infile, outfile, "--index=contig")
def loadTranscriptLevelReadCounts(infile, outfile):
P.load(infile, outfile, options="--index=transcript_id")
def loadMACSsoloSummary(infile, outfile):
'''load macs summary.'''
P.load(infile, outfile, "--index=track")
def loadTagCountSummary(infile, outfile):
'''load windows summary.'''
P.load(infile, outfile)
P.load(P.snip(infile, ".tsv") + "_correlation.tsv",
P.snip(outfile, "_stats.load") + "_correlation.load",
options="--first-column=track")
def loadOverrun(infile, outfile):
'''load annotations'''
P.load(infile, outfile, "--index=gene_id --map=gene_id:str")
def loadEdgeRStats(infile, outfile):
P.load(infile, outfile)
def loadFilteringSummary(infile, outfile):
'''load filtering summary.'''
P.load(infile, outfile)
def loadCuffdiffStats(infile, outfile):
'''import cuffdiff results.'''
P.load(infile, outfile)
def loadRepeats(infile, outfile):
'''load repeat overlap'''
P.load(infile, outfile, "--index=gene_id --map=gene_id:str")
def loadDummyTask( infile, outfile ):
'''load results of word counting into database.'''
P.load( infile, outfile, "--index=word" )
def loadContigStats(infile, outfile):
'''
load the contig stats
'''
P.load(infile, outfile)
