Python Pipeline.publish_report示例

示例#1

文件： pipeline_rnaseqdiffexpression.py 项目： BioinformaticsArchive/cgat

def publish():
    '''publish files.'''
    # publish web pages
    P.publish_report()

    # publish additional data
    web_dir = PARAMS["web_dir"]
    project_id = P.getProjectId()

    # directory, files
    exportfiles = {
        "bamfiles" : glob.glob( "*.bam" ) + glob.glob( "*.bam.bai" ),
        "genesets": [ "lincrna.gtf.gz", "abinitio.gtf.gz" ],
        "classification": glob.glob("*.class.tsv.gz") ,
        "differential_expression" : glob.glob( "*.cuffdiff.dir" ),
        }
    
    bams = []

    for targetdir, filenames in exportfiles.iteritems():
        for src in filenames:
            dest = "%s/%s/%s" % (web_dir, targetdir, src)
            if dest.endswith( ".bam"): bams.append( dest )
            dest = os.path.abspath( dest )
            if not os.path.exists( dest ):
                os.symlink( os.path.abspath(src), dest )
    
    # output ucsc links
    for bam in bams: 
        filename = os.path.basename( bam )
        track = P.snip( filename, ".bam" )
        print """track type=bam name="%(track)s" bigDataUrl=http://www.cgat.org/downloads/%(project_id)s/bamfiles/%(filename)s""" % locals()

示例#2

文件： pipeline_cufflinks_optimization.py 项目： jmadzo/cgat

def publish():
    '''publish files.'''
    # publish web pages
    patterns = [(re.compile("/ifs/projects/proj012/report/html"),
                 "http://www.cgat.org/downloads/KW0ok5WWly/report"),
                ]

    P.publish_report(patterns=patterns)

示例#3

def publish():
    '''publish files.'''
    # publish web pages
    patterns = [
        (re.compile("/ifs/projects/proj012/report/html"),
         "http://www.cgat.org/downloads/KW0ok5WWly/report"),
    ]

    P.publish_report(patterns=patterns)

示例#4

文件： pipeline_rnaseqlncrna.py 项目： yangjl/cgat

def publish():
    '''publish files.'''
    # publish web pages
    P.publish_report()

    # publish additional data - i.e. the final lncRNA gtf file
    web_dir = PARAMS["web_dir"]

    if not os.path.exists(os.path.join(web_dir), "lncrna_final.class.gtf.gz"):
        os.symlink("lncrna_final.class.gtf.gz", os.path.abspath(os.path.join(os.path.join(web_dir), "lncrna_final.class.gtf.gz")))

示例#5

文件： pipeline_windows.py 项目： pombredanne/cgat

def publish():
    '''publish files.'''

    # directory : files
    export_files = { "bamfiles": glob.glob("*.bam") + glob.glob("*.bam.bai"),
                     "bigwigfiles": glob.glob("*.bw"),
                     "bedfiles": glob.glob("deseq.dir/*.bed.gz") + glob.glob("edger.dir/*.bed.gz"),
                     }

    # publish web pages
    P.publish_report( export_files = export_files )

示例#6

文件： pipeline_rnaseqlncrna.py 项目： lesheng/cgat

def publish():
    '''publish files.'''
    # publish web pages
    P.publish_report()

    # publish additional data - i.e. the final lncRNA gtf file
    web_dir = PARAMS["web_dir"]

    if not os.path.exists(os.path.join(web_dir), "lncrna_final.class.gtf.gz"):
        os.symlink(
            "lncrna_final.class.gtf.gz",
            os.path.abspath(
                os.path.join(os.path.join(web_dir),
                             "lncrna_final.class.gtf.gz")))

示例#7

文件： pipeline_medip.py 项目： lesheng/cgat

def publish():
    '''publish files.'''

    # publish web pages
    P.publish_report()

    # publish additional data
    web_dir = PARAMS["web_dir"]
    project_id = P.getProjectId()

    ucsc_urls = {
        "bam":
        """track type=bam name="%(track)s" bigDataUrl=http://www.cgat.org/downloads/%(project_id)s/%(dirname)s/%(filename)s""",
        "bigwig":
        """track type=bigWig name="%(track)s" bigDataUrl=http://www.cgat.org/downloads/%(project_id)s/%(dirname)s/%(filename)s""",
    }

    # directory, files
    exportfiles = (
        ("bamfiles", glob.glob("*/*.genome.bam") +
         glob.glob("*/*.genome.bam.bai"), "bam"),
        ("bamfiles", glob.glob("*/*.prep.bam") +
         glob.glob("*/*.prep.bam.bai"), "bam"),
        ("medips", glob.glob("*/*.bigwig"), "bigwig"),
    )

    ucsc_files = []

    for targetdir, filenames, datatype in exportfiles:
        for src in filenames:
            filename = os.path.basename(src)
            dest = "%s/%s/%s" % (web_dir, targetdir, filename)
            suffix = os.path.splitext(src)
            if suffix in ucsc_urls:
                ucsc_files.append((datatype, targetdir, filename))
            dest = os.path.abspath(dest)
            if not os.path.exists(dest):
                os.symlink(os.path.abspath(src), dest)

    # output ucsc links
    for ucsctype, dirname, filename in ucsc_files:
        filename = os.path.basename(filename)
        track = P.snip(filename, ucsctype)
        print ucsc_urls[ucsctype] % locals()

示例#8

文件： pipeline_motifs.py 项目： santayana/cgat

def publish():
    '''publish files.'''
    # publish web pages

    P.publish_report()

    # publish additional data
    web_dir = PARAMS["web_dir"]
    project_id = P.getProjectId()

    # directory, files
    exportfiles = {
        "intervals":
        glob.glob(os.path.join(PARAMS["exportdir"], "bed", "*.bed.gz")) +
        glob.glob(os.path.join(PARAMS["exportdir"], "bed", "*.bed.gz.tbi")),
    }

    bams = []

    for targetdir, filenames in exportfiles.iteritems():
        if len(filenames) == 0:
            E.warn("no files for target '%s'" % targetdir)
        for src in filenames:
            dest = "%s/%s/%s" % (web_dir, targetdir, os.path.basename(src))
            if dest.endswith(".bam"):
                bams.append(dest)
            dest = os.path.abspath(dest)
            destdir = os.path.dirname(dest)
            if not os.path.exists(destdir):
                os.makedirs(destdir)

            if not os.path.exists(dest):
                E.debug("creating symlink from %s to %s" % (src, dest))
                os.symlink(os.path.abspath(src), dest)

    # output ucsc links
    for bam in bams:
        filename = os.path.basename(bam)
        track = P.snip(filename, ".bam")
        print """track type=bam name="%(track)s" bigDataUrl=http://www.cgat.org/downloads/%(project_id)s/bamfiles/%(filename)s""" % locals(
        )

示例#9

文件： pipeline_motifs.py 项目： jmadzo/cgat

def publish():
    '''publish files.'''
    # publish web pages

    P.publish_report()

    # publish additional data
    web_dir = PARAMS["web_dir"]
    project_id = P.getProjectId()

    # directory, files
    exportfiles = {
        "intervals": glob.glob(os.path.join(PARAMS["exportdir"], "bed", "*.bed.gz")) +
        glob.glob(os.path.join(PARAMS["exportdir"], "bed", "*.bed.gz.tbi")),
    }

    bams = []

    for targetdir, filenames in exportfiles.iteritems():
        if len(filenames) == 0:
            E.warn("no files for target '%s'" % targetdir)
        for src in filenames:
            dest = "%s/%s/%s" % (web_dir, targetdir, os.path.basename(src))
            if dest.endswith(".bam"):
                bams.append(dest)
            dest = os.path.abspath(dest)
            destdir = os.path.dirname(dest)
            if not os.path.exists(destdir):
                os.makedirs(destdir)

            if not os.path.exists(dest):
                E.debug("creating symlink from %s to %s" % (src, dest))
                os.symlink(os.path.abspath(src), dest)

    # output ucsc links
    for bam in bams:
        filename = os.path.basename(bam)
        track = P.snip(filename, ".bam")
        print """track type=bam name="%(track)s" bigDataUrl=http://www.cgat.org/downloads/%(project_id)s/bamfiles/%(filename)s""" % locals()

示例#10

文件： pipeline_readqc.py 项目： lesheng/cgat

def publish():
    '''publish files.'''
    P.publish_report()

示例#11

文件： pipeline_template.py 项目： jmadzo/cgat

def publish_report():
    '''publish report.'''

    E.info("publishing report")
    P.publish_report()

示例#12

def publish_report():
    '''publish report.'''

    E.info("publishing report")
    P.publish_report()

示例#13

def publish():
    '''publish report and data.'''

    E.info("publishing report")
    P.publish_report()

示例#14

文件： pipeline_readqc.py 项目： Charlie-George/cgat

def publish():
    '''publish files.'''
    P.publish_report()

示例#15

文件： pipeline_ancestral_repeats.py 项目： nishantthakur/cgat

def publish_report():
    """publish report."""

    E.info("publishing report")
    P.publish_report()

示例#16

文件： pipeline_rnaseqdiffexpression.py 项目： lesheng/cgat

def publish():
    '''publish files.'''
    # publish web pages
    P.publish_report()

示例#17

文件： pipeline_rnaseqdiffexpression.py 项目： jmadzo/cgat

def publish():
    '''publish files.'''
    # publish web pages
    P.publish_report()

示例#18

文件： pipeline_template.py 项目： BioinformaticsArchive/cgat

def publish():
    '''publish report and data.'''

    E.info( "publishing report" )
    P.publish_report()

示例#19

文件： pipeline_benchmark_rnaseqmappers.py 项目： nishantthakur/cgat

def publish():
    """publish files."""
    P.publish_report()