def buildWorkSpace(outfile, workspace):
'''write genomic workspace.
Available workspaces are:
genomic
the full genome
intronic
introns (requires annotator_regions to be set)
exonic
exonic (requires annotator_regions to be set)
intergenic
introns (requires annotator_regions to be set)
geneterritories
introns (requires annotator_geneterritories to be set)
mappable
mappable part of genome (requires annotator_mappability to be set )
alignable
only the alignable part of a genome (requires annotator_alignment to be set)
If ``gc_control`` is True, the chromosomes will be divided into isochores
(requiers the paramater ``annotator_gc_workspace`` to be set).
'''
to_cluster = True
job_options = "-l mem_free=4000M"
workspace = workspace.lower()
if workspace == "genomic":
P.checkParameter("genome")
statement = '''
python %(scriptsdir)s/index2bed.py
--genome=%(genome)s
--log=%(outfile)s.log
--remove-regex='%(enrichment_remove_pattern)s'
> %(outfile)s
'''
elif workspace in ("intergenic", "intronic", "cds"):
P.checkParameter("enrichment_regions")
workspace_upper = workspace.upper()
statement = '''
gunzip < %(enrichment_regions)s
| awk 'BEGIN {printf("track name=%(workspace)s\\n"); }
($3 == "%(workspace)s"
|| $3 == "%(workspace_upper)s")
&& !( $1 ~ /%(enrichment_remove_pattern)s/)
{ printf("%%s\\t%%i\\t%%i\\n", $1, $4-1, $5); }'
> %(outfile)s
'''
elif workspace == "unknown":
P.checkParameter("enrichment_regions")
statement = '''
awk '($3 == "intronic" || $3 == "intergenic" )'
< %(enrichment_regions)s
| python %(scriptsdir)s/gff2enrichment.py
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(enrichment_remove_pattern)s'
> %(outfile)s
'''
elif workspace == "known":
P.checkParameter("enrichment_regions")
statement = '''
awk '($3 == "CDS" || $3 ~ /UTR/ || $3 ~ /flank/)'
< %(enrichment_regions)s
| python %(scriptsdir)s/gff2enrichment.py
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(enrichment_remove_pattern)s'
> %(outfile)s
'''
elif workspace == "alignable":
P.checkParameter("enrichment_alignment")
statement = '''gunzip
< %(enrichment_alignment)s
| sort -k10,10
| awk '$10 !~ /%(enrichment_remove_pattern)s/ \
{if ($10!=l) {printf("\\n##Work\\t%%s", $10); l=$10;} \
printf("\\t(%%i,%%i)", $12,$13); }; \
END {printf ("\\n");}'\
> %(outfile)s
'''
elif workspace == "gene-territories":
P.checkParameter("enrichment_geneterritories")
statement = '''
python %(scriptsdir)s/gff2enrichment.py \
--section=workspace \
--max-length=0 \
--log=%(outfile)s.log \
--remove-regex='%(enrichment_remove_pattern)s'
< %(enrichment_geneterritories)s > %(outfile)s
'''
elif workspace == "mappable":
P.checkParameter("enrichment_mappability")
statement = '''
python %(scriptsdir)s/bed2gff.py < %(enrichment_mappability)s
| python %(scriptsdir)s/gff2enrichment.py
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(enrichment_remove_pattern)s'
> %(outfile)s
'''
else:
raise P.PipelineError("unknown workspace '%s'" % workspace)
P.run()
def buildAnnotatorWorkSpace(tmpdir,
outfile,
workspaces=("genomic", ),
gc_control=False):
'''write genomic workspace.
Available workspaces are:
genomic
the full genome
all
is ignored
intronic
introns (requires annotator_regions to be set)
intergenic
introns (requires annotator_regions to be set)
geneterritories
introns (requires annotator_geneterritories to be set)
mappable
mappable part of genome (requires annotator_mappability to be set )
alignable
only the alignable part of a genome (requires annotator_alignment to be set)
If ``gc_control`` is True, the chromosomes will be divided into isochores
(requiers the paramater ``annotator_gc_workspace`` to be set).
'''
to_cluster = True
job_options = "-l mem_free=4000M"
tmpworkspaces = []
if gc_control:
P.checkParameter("annotator_gc_workspace")
tmpsynonyms = PARAMS["annotator_gc_workspace"] + ".synonyms"
tmpworkspaces.append(PARAMS["annotator_gc_workspace"])
else:
tmpsynonyms = None
for workspace in workspaces:
tmpworkspace = os.path.join(tmpdir, "workspace_%s" % workspace)
if workspace == "all":
continue
elif workspace == "genomic":
P.checkParameter("genome")
statement = '''
python %(scriptsdir)s/index2gff.py
--genome=%(genome)s
--log=%(outfile)s.log
| python %(scriptsdir)s/gff2annotator2tsv.py
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(annotator_remove_pattern)s'
> %(tmpworkspace)s
'''
elif workspace in ("intergenic", "intronic", "CDS"):
P.checkParameter("annotator_regions")
statement = '''
awk '$3 == "%(workspace)s"'
< %(annotator_regions)s
| python %(scriptsdir)s/gff2annotator2tsv.py
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(annotator_remove_pattern)s'
> %(tmpworkspace)s
'''
elif workspace == "unknown":
P.checkParameter("annotator_regions")
statement = '''
awk '($3 == "intronic" || $3 == "intergenic" )'
< %(annotator_regions)s
| python %(scriptsdir)s/gff2annotator2tsv.py
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(annotator_remove_pattern)s'
> %(tmpworkspace)s
'''
elif workspace == "known":
P.checkParameter("annotator_regions")
statement = '''
awk '($3 == "CDS" || $3 ~ /UTR/ || $3 ~ /flank/)'
< %(annotator_regions)s
| python %(scriptsdir)s/gff2annotator2tsv.py
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(annotator_remove_pattern)s'
> %(tmpworkspace)s
'''
elif workspace == "alignable":
P.checkParameter("annotator_alignment")
statement = '''gunzip
< %(annotator_alignment)s
| sort -k10,10
| awk '$10 !~ /%(annotator_remove_pattern)s/ \
{if ($10!=l) {printf("\\n##Work\\t%%s", $10); l=$10;} \
printf("\\t(%%i,%%i)", $12,$13); }; \
END {printf ("\\n");}'\
> %(tmpworkspace)s
'''
elif workspace == "gene-territories":
P.checkParameter("annotator_geneterritories")
statement = '''
python %(scriptsdir)s/gff2annotator2tsv.py \
--section=workspace \
--max-length=0 \
--log=%(outfile)s.log \
--remove-regex='%(annotator_remove_pattern)s'
< %(annotator_geneterritories)s > %(tmpworkspace)s
'''
elif workspace == "mappable":
P.checkParameter("annotator_mappability")
statement = '''
python %(scriptsdir)s/bed2gff.py < %(annotator_mappability)s
| python %(scriptsdir)s/gff2annotator2tsv.py
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(annotator_remove_pattern)s'
> %(tmpworkspace)s
'''
else:
raise P.PipelineError("unknown workspace '%s'" % workspace)
P.run()
tmpworkspaces.append(tmpworkspace)
return tmpworkspaces, tmpsynonyms
def buildWorkSpace(outfile, workspace):
'''write genomic workspace.
Available workspaces are:
genomic
the full genome
intronic
introns (requires annotator_regions to be set)
exonic
exonic (requires annotator_regions to be set)
intergenic
introns (requires annotator_regions to be set)
geneterritories
introns (requires annotator_geneterritories to be set)
mappable
mappable part of genome (requires annotator_mappability to be set )
alignable
only the alignable part of a genome (requires annotator_alignment to be set)
If ``gc_control`` is True, the chromosomes will be divided into isochores
(requiers the paramater ``annotator_gc_workspace`` to be set).
'''
to_cluster = True
job_options = "-l mem_free=4000M"
workspace = workspace.lower()
if workspace == "genomic":
P.checkParameter("genome")
statement = '''
python %(scriptsdir)s/index2bed.py
--genome=%(genome)s
--log=%(outfile)s.log
--remove-regex='%(enrichment_remove_pattern)s'
> %(outfile)s
'''
elif workspace in ("intergenic", "intronic", "cds"):
P.checkParameter("enrichment_regions")
workspace_upper = workspace.upper()
statement = '''
gunzip < %(enrichment_regions)s
| awk 'BEGIN {printf("track name=%(workspace)s\\n"); }
($3 == "%(workspace)s"
|| $3 == "%(workspace_upper)s")
&& !( $1 ~ /%(enrichment_remove_pattern)s/)
{ printf("%%s\\t%%i\\t%%i\\n", $1, $4-1, $5); }'
> %(outfile)s
'''
elif workspace == "unknown":
P.checkParameter("enrichment_regions")
statement = '''
awk '($3 == "intronic" || $3 == "intergenic" )'
< %(enrichment_regions)s
| python %(scriptsdir)s/gff2enrichment.py
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(enrichment_remove_pattern)s'
> %(outfile)s
'''
elif workspace == "known":
P.checkParameter("enrichment_regions")
statement = '''
awk '($3 == "CDS" || $3 ~ /UTR/ || $3 ~ /flank/)'
< %(enrichment_regions)s
| python %(scriptsdir)s/gff2enrichment.py
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(enrichment_remove_pattern)s'
> %(outfile)s
'''
elif workspace == "alignable":
P.checkParameter("enrichment_alignment")
statement = '''gunzip
< %(enrichment_alignment)s
| sort -k10,10
| awk '$10 !~ /%(enrichment_remove_pattern)s/ \
{if ($10!=l) {printf("\\n##Work\\t%%s", $10); l=$10;} \
printf("\\t(%%i,%%i)", $12,$13); }; \
END {printf ("\\n");}'\
> %(outfile)s
'''
elif workspace == "gene-territories":
P.checkParameter("enrichment_geneterritories")
statement = '''
python %(scriptsdir)s/gff2enrichment.py \
--section=workspace \
--max-length=0 \
--log=%(outfile)s.log \
--remove-regex='%(enrichment_remove_pattern)s'
< %(enrichment_geneterritories)s > %(outfile)s
'''
elif workspace == "mappable":
P.checkParameter("enrichment_mappability")
statement = '''
python %(scriptsdir)s/bed2gff.py < %(enrichment_mappability)s
| python %(scriptsdir)s/gff2enrichment.py
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(enrichment_remove_pattern)s'
> %(outfile)s
'''
else:
raise P.PipelineError("unknown workspace '%s'" % workspace)
P.run()
def buildAnnotatorWorkSpace(tmpdir,
outfile,
workspaces=("genomic",),
gc_control = False):
'''write genomic workspace.
Available workspaces are:
genomic
the full genome
all
is ignored
intronic
introns (requires annotator_regions to be set)
intergenic
introns (requires annotator_regions to be set)
geneterritories
introns (requires annotator_geneterritories to be set)
mappable
mappable part of genome (requires annotator_mappability to be set )
alignable
only the alignable part of a genome (requires annotator_alignment to be set)
If ``gc_control`` is True, the chromosomes will be divided into isochores
(requiers the paramater ``annotator_gc_workspace`` to be set).
'''
to_cluster = True
job_options = "-l mem_free=4000M"
tmpworkspaces = []
if gc_control:
P.checkParameter("annotator_gc_workspace")
tmpsynonyms = PARAMS["annotator_gc_workspace"] + ".synonyms"
tmpworkspaces.append(PARAMS["annotator_gc_workspace"])
else:
tmpsynonyms = None
for workspace in workspaces:
tmpworkspace = os.path.join(tmpdir, "workspace_%s" % workspace)
if workspace == "all":
continue
elif workspace == "genomic":
P.checkParameter("genome")
statement = '''
python %(scriptsdir)s/index2gff.py
--genome=%(genome)s
--log=%(outfile)s.log
| python %(scriptsdir)s/gff2annotator2tsv.py
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(annotator_remove_pattern)s'
> %(tmpworkspace)s
'''
elif workspace in ("intergenic", "intronic", "CDS"):
P.checkParameter("annotator_regions")
statement = '''
awk '$3 == "%(workspace)s"'
< %(annotator_regions)s
| python %(scriptsdir)s/gff2annotator2tsv.py
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(annotator_remove_pattern)s'
> %(tmpworkspace)s
'''
elif workspace == "unknown":
P.checkParameter("annotator_regions")
statement = '''
awk '($3 == "intronic" || $3 == "intergenic" )'
< %(annotator_regions)s
| python %(scriptsdir)s/gff2annotator2tsv.py
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(annotator_remove_pattern)s'
> %(tmpworkspace)s
'''
elif workspace == "known":
P.checkParameter("annotator_regions")
statement = '''
awk '($3 == "CDS" || $3 ~ /UTR/ || $3 ~ /flank/)'
< %(annotator_regions)s
| python %(scriptsdir)s/gff2annotator2tsv.py
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(annotator_remove_pattern)s'
> %(tmpworkspace)s
'''
elif workspace == "alignable":
P.checkParameter("annotator_alignment")
statement = '''gunzip
< %(annotator_alignment)s
| sort -k10,10
| awk '$10 !~ /%(annotator_remove_pattern)s/ \
{if ($10!=l) {printf("\\n##Work\\t%%s", $10); l=$10;} \
printf("\\t(%%i,%%i)", $12,$13); }; \
END {printf ("\\n");}'\
> %(tmpworkspace)s
'''
elif workspace == "gene-territories":
P.checkParameter("annotator_geneterritories")
statement = '''
python %(scriptsdir)s/gff2annotator2tsv.py \
--section=workspace \
--max-length=0 \
--log=%(outfile)s.log \
--remove-regex='%(annotator_remove_pattern)s'
< %(annotator_geneterritories)s > %(tmpworkspace)s
'''
elif workspace == "mappable":
P.checkParameter("annotator_mappability")
statement = '''
python %(scriptsdir)s/bed2gff.py < %(annotator_mappability)s
| python %(scriptsdir)s/gff2annotator2tsv.py
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(annotator_remove_pattern)s'
> %(tmpworkspace)s
'''
else:
raise P.PipelineError("unknown workspace '%s'" % workspace)
P.run()
tmpworkspaces.append(tmpworkspace)
return tmpworkspaces, tmpsynonyms