Commit 3dd46446 authored by Jerome Mariette's avatar Jerome Mariette
Browse files

check formats

parent 86b67132
...@@ -28,8 +28,9 @@ import copy as _copy ...@@ -28,8 +28,9 @@ import copy as _copy
from urlparse import urlparse from urlparse import urlparse
from jflow.config_reader import JFlowConfigReader from jflow.config_reader import JFlowConfigReader
# import custom types # import custom types and custom formats
from workflows.types import * from workflows.types import *
from workflows.formats import *
# define all input type available # define all input type available
...@@ -71,18 +72,6 @@ def inputfile(file): ...@@ -71,18 +72,6 @@ def inputfile(file):
else: else:
return urlfile(file) return urlfile(file)
class Formats(object):
ANY = "any"
BAM = "bam"
FASTQ = "fastq"
FASTA = "fasta"
SFF = "sff"
QUAL = "qual"
FLOW = "flow"
HTML = "html"
class MultipleParameters(object): class MultipleParameters(object):
def __init__(self, types, required, choices, excludes, default, actions): def __init__(self, types, required, choices, excludes, default, actions):
self.types = types self.types = types
...@@ -627,6 +616,9 @@ class AbstractInputFile(AbstractIOFile): ...@@ -627,6 +616,9 @@ class AbstractInputFile(AbstractIOFile):
except: except:
return [input, False] return [input, False]
def check(self, ifile):
eval(self.file_format)(ifile)
class AbstractOutputFile(AbstractIOFile): class AbstractOutputFile(AbstractIOFile):
""" """
...@@ -667,6 +659,7 @@ class InputFile(StrParameter, AbstractInputFile): ...@@ -667,6 +659,7 @@ class InputFile(StrParameter, AbstractInputFile):
jflow_config_reader = JFlowConfigReader() jflow_config_reader = JFlowConfigReader()
new_path = os.path.join(jflow_config_reader.get_tmp_directory(), input) new_path = os.path.join(jflow_config_reader.get_tmp_directory(), input)
if is_local: new_path = input if is_local: new_path = input
self.check(new_path)
return new_path return new_path
...@@ -752,6 +745,9 @@ class InputFileList(ParameterList, AbstractInputFile): ...@@ -752,6 +745,9 @@ class InputFileList(ParameterList, AbstractInputFile):
for path in path2test: for path in path2test:
jflow_config_reader = JFlowConfigReader() jflow_config_reader = JFlowConfigReader()
new_vals.append(os.path.join(jflow_config_reader.get_tmp_directory(), path)) new_vals.append(os.path.join(jflow_config_reader.get_tmp_directory(), path))
# now that all files are downloaded and ok, check the format
for cfile in new_vals:
self.check(cfile)
return new_vals return new_vals
class OutputFileList(ParameterList, AbstractOutputFile): class OutputFileList(ParameterList, AbstractOutputFile):
......
...@@ -17,6 +17,8 @@ ...@@ -17,6 +17,8 @@
from jflow.workflow import Workflow from jflow.workflow import Workflow
from jflow.parameter import InputFileList, InputFile from jflow.parameter import InputFileList, InputFile
from workflows.formats import Formats
class Alignment (Workflow): class Alignment (Workflow):
...@@ -24,9 +26,9 @@ class Alignment (Workflow): ...@@ -24,9 +26,9 @@ class Alignment (Workflow):
return "Align reads against a reference genome" return "Align reads against a reference genome"
def define_parameters(self, function="process"): def define_parameters(self, function="process"):
self.add_input_file_list("read_1", "Which read1 files should be used", required=True) self.add_input_file_list("read_1", "Which read1 files should be used", file_format=Formats.FASTQ, required=True)
self.add_input_file_list("read_2", "Which read2 files should be used (if single end, leave empty)") self.add_input_file_list("read_2", "Which read2 files should be used (if single end, leave empty)", file_format=Formats.FASTQ)
self.add_input_file("reference_genome", "Which genome should the read being align on", required=True) self.add_input_file("reference_genome", "Which genome should the read being align on", required=True, file_format=Formats.FASTA)
def process(self): def process(self):
# index the reference genome # index the reference genome
......
...@@ -19,7 +19,7 @@ import os ...@@ -19,7 +19,7 @@ import os
from subprocess import Popen, PIPE from subprocess import Popen, PIPE
from jflow.component import Component from jflow.component import Component
from jflow.parameter import Formats from workflows.formats import Formats
from weaver.function import ShellFunction from weaver.function import ShellFunction
from weaver.abstraction import Map from weaver.abstraction import Map
......
...@@ -19,7 +19,7 @@ import os ...@@ -19,7 +19,7 @@ import os
from subprocess import Popen, PIPE from subprocess import Popen, PIPE
from jflow.component import Component from jflow.component import Component
from jflow.parameter import Formats from workflows.formats import Formats
from weaver.function import PythonFunction, ShellFunction from weaver.function import PythonFunction, ShellFunction
......
#
# Copyright (C) 2012 INRA
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
from jflow import seqio
import os
import sys
class Formats(object):
ANY = "any"
BAM = "bam"
FASTQ = "fastq"
FASTA = "fasta"
SFF = "sff"
def fastq(ifile):
try:
reader = seqio.FastqReader(ifile)
nb_seq = 0
for id, desc, seq, qualities in reader:
nb_seq += 1
# only check the first 10 sequences
if nb_seq == 10: break
except:
sys.stderr.write("Error: The provided file '" + ifile + "' is not a fastq file!\n")
sys.exit(1)
def fasta(ifile):
try:
reader = seqio.FastaReader(ifile, wholefile=True)
nb_seq = 0
for id, desc, seq, qualities in reader:
nb_seq += 1
# only check the first 10 sequences
if nb_seq == 10: break
except:
sys.stderr.write("Error: The provided file '" + ifile + "' is not a fasta file!\n")
sys.exit(1)
def sff(ifile):
try:
reader = seqio.SFFReader(ifile)
nb_seq = 0
for id, desc, seq, qualities in reader:
nb_seq += 1
# only check the first 10 sequences
if nb_seq == 10: break
except:
sys.stderr.write("Error: The provided file '" + ifile + "' is not a sff file!\n")
sys.exit(1)
\ No newline at end of file
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