Commit a30efe4a authored by Penom Nom's avatar Penom Nom
Browse files

split sff pre-treatment : shhhflows

parent 10ee2e45
......@@ -15,10 +15,8 @@
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
import os,re
from subprocess import Popen, PIPE
# from jflow.component import Component
from jflow.iotypes import OutputFile, OutputFileList, InputFile, InputFileList, Formats
from jflow.abstraction import MultiMap
......@@ -42,8 +40,6 @@ def create_group_file(output_directory,std_out,groups_files_names):
class MothurShhhFlows(Analysis):
"""
"""
def define_parameters(self, sff_files, sample_barcodes=None, bdiffs=0,processors=1):
"""
......@@ -126,6 +122,8 @@ class MothurShhhFlows(Analysis):
self._add_result_element(sample.replace('.','_'), "nb_seq", count)
#global sequences failed and not by sample
ids_failed = self._get_id_seq_failed(self.scrap_flow_files[0])
for ids,count in ids_failed.items():
self._add_result_element(ids, "ids_failed_trim_seqs", count)
#TODO add to the db
# #save barcodes
# self._add_result_element(os.path.basename(self.barcodes_file), "barcodes_file", self._save_file(self.barcodes_file, os.path.basename(self.barcodes_file)+".cfg"))
......
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