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biopet.biopet
Commits
769e3c84
Commit
769e3c84
authored
May 06, 2016
by
Peter van 't Hof
Browse files
Replace VEP with zcat when no variants in vcf file
parent
76992696
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
View file @
769e3c84
...
...
@@ -18,11 +18,10 @@ package nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
nl.lumc.sasc.biopet.utils.Logging
import
nl.lumc.sasc.biopet.utils.
{
Logging
,
VcfUtils
,
tryToParseNumber
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
Version
,
BiopetCommandLineFunction
,
Reference
}
import
nl.lumc.sasc.biopet.utils.tryToParseNumber
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
,
Version
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.io.Source
...
...
@@ -164,105 +163,110 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
}
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
required
(
vepScript
)
+
required
(
"-i"
,
input
)
+
required
(
"-o"
,
output
)
+
conditional
(
v
,
"-v"
)
+
conditional
(
q
,
"-q"
)
+
conditional
(
offline
,
"--offline"
)
+
conditional
(
noProgress
,
"--no_progress"
)
+
conditional
(
everything
,
"--everything"
)
+
conditional
(
force
,
"--force_overwrite"
)
+
conditional
(
noStats
,
"--no_stats"
)
+
conditional
(
statsText
,
"--stats_text"
)
+
conditional
(
html
,
"--html"
)
+
conditional
(
cache
,
"--cache"
)
+
conditional
(
humdiv
,
"--humdiv"
)
+
conditional
(
regulatory
,
"--regulatory"
)
+
conditional
(
cellType
,
"--cel_type"
)
+
conditional
(
phased
,
"--phased"
)
+
conditional
(
alleleNumber
,
"--allele_number"
)
+
conditional
(
numbers
,
"--numbers"
)
+
conditional
(
domains
,
"--domains"
)
+
conditional
(
noEscape
,
"--no_escape"
)
+
conditional
(
hgvs
,
"--hgvs"
)
+
conditional
(
protein
,
"--protein"
)
+
conditional
(
symbol
,
"--symbol"
)
+
conditional
(
ccds
,
"--ccds"
)
+
conditional
(
uniprot
,
"--uniprot"
)
+
conditional
(
tsl
,
"--tsl"
)
+
conditional
(
canonical
,
"--canonical"
)
+
conditional
(
biotype
,
"--biotype"
)
+
conditional
(
xrefRefseq
,
"--xref_refseq"
)
+
conditional
(
checkExisting
,
"--check_existing"
)
+
conditional
(
checkAlleles
,
"--check_alleles"
)
+
conditional
(
checkSvs
,
"--check_svs"
)
+
conditional
(
gmaf
,
"--gmaf"
)
+
conditional
(
maf1kg
,
"--maf_1kg"
)
+
conditional
(
mafEsp
,
"--maf_esp"
)
+
conditional
(
pubmed
,
"--pubmed"
)
+
conditional
(
vcf
,
"--vcf"
)
+
conditional
(
json
,
"--json"
)
+
conditional
(
gvf
,
"--gvf"
)
+
conditional
(
checkRef
,
"--check_ref"
)
+
conditional
(
codingOnly
,
"--coding_only"
)
+
conditional
(
noIntergenic
,
"--no_intergenic"
)
+
conditional
(
pick
,
"--pick"
)
+
conditional
(
pickAllele
,
"--pick_allele"
)
+
conditional
(
flagPick
,
"--flag_pick"
)
+
conditional
(
flagPickAllele
,
"--flag_pick_allele"
)
+
conditional
(
perGene
,
"--per_gene"
)
+
conditional
(
mostSevere
,
"--most_severe"
)
+
conditional
(
summary
,
"--summary"
)
+
conditional
(
filterCommon
,
"--filter_common"
)
+
conditional
(
checkFrequency
,
"--check_frequency"
)
+
conditional
(
allowNonVariant
,
"--allow_non_variant"
)
+
conditional
(
database
,
"--database"
)
+
conditional
(
genomes
,
"--genomes"
)
+
conditional
(
gencodeBasic
,
"--gencode_basic"
)
+
conditional
(
refseq
,
"--refseq"
)
+
conditional
(
merged
,
"--merged"
)
+
conditional
(
allRefseq
,
"--all_refseq"
)
+
conditional
(
lrg
,
"--lrg"
)
+
conditional
(
noWholeGenome
,
"--no_whole_genome"
)
+
conditional
(
skibDbCheck
,
"--skip_db_check"
)
+
optional
(
"--config"
,
vepConfig
)
+
optional
(
"--species"
,
species
)
+
optional
(
"--assembly"
,
assembly
)
+
optional
(
"--format"
,
format
)
+
optional
(
"--dir"
,
dir
)
+
optional
(
"--dir_cache"
,
dirCache
)
+
optional
(
"--dir_plugins"
,
dirPlugins
)
+
optional
(
"--fasta"
,
fasta
)
+
optional
(
"--sift"
,
sift
)
+
optional
(
"--polyphen"
,
polyphen
)
+
repeat
(
"--custom"
,
custom
)
+
repeat
(
"--plugin"
,
plugin
)
+
optional
(
"--individual"
,
individual
)
+
optional
(
"--fields"
,
fields
)
+
optional
(
"--convert"
,
convert
)
+
optional
(
"--terms"
,
terms
)
+
optional
(
"--chr"
,
chr
)
+
optional
(
"--pick_order"
,
pickOrder
)
+
optional
(
"--freq_pop"
,
freqPop
)
+
optional
(
"--freq_gt_lt"
,
freqGtLt
)
+
optional
(
"--freq_filter"
,
freqFilter
)
+
optional
(
"--filter"
,
filter
)
+
optional
(
"--host"
,
host
)
+
optional
(
"--user"
,
user
)
+
optional
(
"--password"
,
password
)
+
optional
(
"--registry"
,
registry
)
+
optional
(
"--build"
,
build
)
+
optional
(
"--compress"
,
compress
)
+
optional
(
"--cache_region_size"
,
cacheRegionSize
)
+
optional
(
"--fork"
,
threads
)
+
optional
(
"--cache_version"
,
cacheVersion
)
+
optional
(
"--freq_freq"
,
freqFreq
)
+
optional
(
"--port"
,
port
)
+
optional
(
"--db_version"
,
dbVersion
)
+
optional
(
"--buffer_size"
,
bufferSize
)
+
optional
(
"--failed"
,
failed
)
def
cmdLine
=
{
if
(
input
.
exists
()
&&
VcfUtils
.
vcfFileIsEmpty
(
input
))
{
val
zcat
=
Zcat
(
this
,
input
,
output
)
zcat
.
cmdLine
}
else
required
(
executable
)
+
required
(
vepScript
)
+
required
(
"-i"
,
input
)
+
required
(
"-o"
,
output
)
+
conditional
(
v
,
"-v"
)
+
conditional
(
q
,
"-q"
)
+
conditional
(
offline
,
"--offline"
)
+
conditional
(
noProgress
,
"--no_progress"
)
+
conditional
(
everything
,
"--everything"
)
+
conditional
(
force
,
"--force_overwrite"
)
+
conditional
(
noStats
,
"--no_stats"
)
+
conditional
(
statsText
,
"--stats_text"
)
+
conditional
(
html
,
"--html"
)
+
conditional
(
cache
,
"--cache"
)
+
conditional
(
humdiv
,
"--humdiv"
)
+
conditional
(
regulatory
,
"--regulatory"
)
+
conditional
(
cellType
,
"--cel_type"
)
+
conditional
(
phased
,
"--phased"
)
+
conditional
(
alleleNumber
,
"--allele_number"
)
+
conditional
(
numbers
,
"--numbers"
)
+
conditional
(
domains
,
"--domains"
)
+
conditional
(
noEscape
,
"--no_escape"
)
+
conditional
(
hgvs
,
"--hgvs"
)
+
conditional
(
protein
,
"--protein"
)
+
conditional
(
symbol
,
"--symbol"
)
+
conditional
(
ccds
,
"--ccds"
)
+
conditional
(
uniprot
,
"--uniprot"
)
+
conditional
(
tsl
,
"--tsl"
)
+
conditional
(
canonical
,
"--canonical"
)
+
conditional
(
biotype
,
"--biotype"
)
+
conditional
(
xrefRefseq
,
"--xref_refseq"
)
+
conditional
(
checkExisting
,
"--check_existing"
)
+
conditional
(
checkAlleles
,
"--check_alleles"
)
+
conditional
(
checkSvs
,
"--check_svs"
)
+
conditional
(
gmaf
,
"--gmaf"
)
+
conditional
(
maf1kg
,
"--maf_1kg"
)
+
conditional
(
mafEsp
,
"--maf_esp"
)
+
conditional
(
pubmed
,
"--pubmed"
)
+
conditional
(
vcf
,
"--vcf"
)
+
conditional
(
json
,
"--json"
)
+
conditional
(
gvf
,
"--gvf"
)
+
conditional
(
checkRef
,
"--check_ref"
)
+
conditional
(
codingOnly
,
"--coding_only"
)
+
conditional
(
noIntergenic
,
"--no_intergenic"
)
+
conditional
(
pick
,
"--pick"
)
+
conditional
(
pickAllele
,
"--pick_allele"
)
+
conditional
(
flagPick
,
"--flag_pick"
)
+
conditional
(
flagPickAllele
,
"--flag_pick_allele"
)
+
conditional
(
perGene
,
"--per_gene"
)
+
conditional
(
mostSevere
,
"--most_severe"
)
+
conditional
(
summary
,
"--summary"
)
+
conditional
(
filterCommon
,
"--filter_common"
)
+
conditional
(
checkFrequency
,
"--check_frequency"
)
+
conditional
(
allowNonVariant
,
"--allow_non_variant"
)
+
conditional
(
database
,
"--database"
)
+
conditional
(
genomes
,
"--genomes"
)
+
conditional
(
gencodeBasic
,
"--gencode_basic"
)
+
conditional
(
refseq
,
"--refseq"
)
+
conditional
(
merged
,
"--merged"
)
+
conditional
(
allRefseq
,
"--all_refseq"
)
+
conditional
(
lrg
,
"--lrg"
)
+
conditional
(
noWholeGenome
,
"--no_whole_genome"
)
+
conditional
(
skibDbCheck
,
"--skip_db_check"
)
+
optional
(
"--config"
,
vepConfig
)
+
optional
(
"--species"
,
species
)
+
optional
(
"--assembly"
,
assembly
)
+
optional
(
"--format"
,
format
)
+
optional
(
"--dir"
,
dir
)
+
optional
(
"--dir_cache"
,
dirCache
)
+
optional
(
"--dir_plugins"
,
dirPlugins
)
+
optional
(
"--fasta"
,
fasta
)
+
optional
(
"--sift"
,
sift
)
+
optional
(
"--polyphen"
,
polyphen
)
+
repeat
(
"--custom"
,
custom
)
+
repeat
(
"--plugin"
,
plugin
)
+
optional
(
"--individual"
,
individual
)
+
optional
(
"--fields"
,
fields
)
+
optional
(
"--convert"
,
convert
)
+
optional
(
"--terms"
,
terms
)
+
optional
(
"--chr"
,
chr
)
+
optional
(
"--pick_order"
,
pickOrder
)
+
optional
(
"--freq_pop"
,
freqPop
)
+
optional
(
"--freq_gt_lt"
,
freqGtLt
)
+
optional
(
"--freq_filter"
,
freqFilter
)
+
optional
(
"--filter"
,
filter
)
+
optional
(
"--host"
,
host
)
+
optional
(
"--user"
,
user
)
+
optional
(
"--password"
,
password
)
+
optional
(
"--registry"
,
registry
)
+
optional
(
"--build"
,
build
)
+
optional
(
"--compress"
,
compress
)
+
optional
(
"--cache_region_size"
,
cacheRegionSize
)
+
optional
(
"--fork"
,
threads
)
+
optional
(
"--cache_version"
,
cacheVersion
)
+
optional
(
"--freq_freq"
,
freqFreq
)
+
optional
(
"--port"
,
port
)
+
optional
(
"--db_version"
,
dbVersion
)
+
optional
(
"--buffer_size"
,
bufferSize
)
+
optional
(
"--failed"
,
failed
)
}
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
...
...
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
View file @
769e3c84
...
...
@@ -134,4 +134,11 @@ object VcfUtils {
else
if
(
name
.
endsWith
(
".vcf.gz"
))
new
File
(
name
+
".tbi"
)
else
throw
new
IllegalArgumentException
(
s
"File given is no vcf file: $vcfFile"
)
}
def
vcfFileIsEmpty
(
file
:
File
)
:
Boolean
=
{
val
reader
=
new
VCFFileReader
(
file
,
false
)
val
hasNext
=
reader
.
iterator
().
hasNext
reader
.
close
()
!
hasNext
}
}
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