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biopet.biopet
Commits
64f71be7
Commit
64f71be7
authored
Jan 13, 2015
by
Peter van 't Hof
Browse files
Remove old scripts
parent
d4cad0b9
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/scripts/prefixFastq.py
deleted
100755 → 0
View file @
d4cad0b9
#!/usr/bin/env python
#
# Biopet is built on top of GATK Queue for building bioinformatic
# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
# should also be able to execute Biopet tools and pipelines.
#
# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
#
# Contact us at: sasc@lumc.nl
#
# A dual licensing mode is applied. The source code within this project that are
# not part of GATK Queue is freely available for non-commercial use under an AGPL
# license; For commercial users or users who do not want to follow the AGPL
# license, please contact us to obtain a separate license.
#
# prep_deepsage.py
#
# Script for preprocessing deepSAGE sequencing samples.
#
# Adapted from: http://galaxy.nbic.nl/u/pacthoen/w/deepsagelumc
import
argparse
from
Bio
import
SeqIO
PREFIX
=
'CATG'
def
prep_deepsage
(
input_fastq
,
output_fastq
,
is_gzip
,
seq
):
if
is_gzip
:
import
gzip
opener
=
gzip
.
GzipFile
else
:
opener
=
open
with
opener
(
input_fastq
,
'r'
)
as
in_handle
,
open
(
output_fastq
,
'w'
)
as
\
out_handle
:
# adapted from fastools.fastools.add
# not importing since we also need to cut away parts of the sequence
for
rec
in
SeqIO
.
parse
(
in_handle
,
'fastq'
):
qual
=
rec
.
letter_annotations
[
'phred_quality'
]
rec
.
letter_annotations
=
{}
rec
.
seq
=
seq
+
rec
.
seq
rec
.
letter_annotations
=
{
'phred_quality'
:
[
40
]
*
len
(
seq
)
+
qual
}
SeqIO
.
write
(
rec
,
out_handle
,
"fastq"
)
if
__name__
==
'__main__'
:
parser
=
argparse
.
ArgumentParser
()
parser
.
add_argument
(
'input_fastq'
,
type
=
str
,
help
=
"Path to input FASTQ file"
)
parser
.
add_argument
(
'-o'
,
'--output'
,
type
=
str
,
dest
=
'output_fastq'
,
default
=
"prep_deepsage_output.fq"
,
help
=
"Path to output FASTQ file"
)
parser
.
add_argument
(
'--gzip'
,
dest
=
'gzip'
,
action
=
'store_true'
,
help
=
"Whether input FASTQ file is gzipped or not."
)
parser
.
add_argument
(
'--prefix'
,
dest
=
'prefix'
,
type
=
str
,
default
=
PREFIX
,
help
=
"Whether input FASTQ file is gzipped or not."
)
args
=
parser
.
parse_args
()
prep_deepsage
(
args
.
input_fastq
,
args
.
output_fastq
,
args
.
gzip
,
args
.
prefix
)
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/prefixFastq.scala
deleted
100644 → 0
View file @
d4cad0b9
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.scripts
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
,
Argument
}
import
java.io.File
class
PrefixFastq
(
val
root
:
Configurable
)
extends
PythonCommandLineFunction
{
setPythonScript
(
"prefixFastq.py"
)
@Input
(
doc
=
"Input file"
)
var
input
:
File
=
_
@Output
(
doc
=
"output File"
)
var
output
:
File
=
_
@Argument
(
doc
=
"Prefix sequence"
)
var
prefix
:
String
=
"CATG"
@Argument
(
doc
=
"Input file is gziped"
,
required
=
false
)
var
gzip
:
Boolean
=
_
override
def
beforeCmd
{
if
(
input
.
getName
.
endsWith
(
".gzip"
)
||
input
.
getName
.
endsWith
(
"gz"
))
gzip
=
true
}
def
cmdLine
=
getPythonCommand
+
required
(
"-o"
,
output
)
+
required
(
"--prefix"
,
prefix
)
+
required
(
input
)
}
object
PrefixFastq
{
def
apply
(
root
:
Configurable
,
input
:
File
,
outputDir
:
String
)
:
PrefixFastq
=
{
val
prefixFastq
=
new
PrefixFastq
(
root
)
prefixFastq
.
input
=
input
prefixFastq
.
output
=
new
File
(
outputDir
,
input
.
getName
+
".prefix.fastq"
)
return
prefixFastq
}
}
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