Commit b4ac19f8 authored by Maria Bernard's avatar Maria Bernard
Browse files

change Biopython seqio en ng6 seqio

parent 6bac82fa
......@@ -209,11 +209,11 @@ Currently supported enzymes include:
# Tmp output
# Creates list for temporary uncompressed files
tmp_output_read_1 = self.get_outputs('{basename_woext}.fq', self.read1_files)
tmp_output_read_2 = self.get_outputs('{basename_woext}.fq', self.read2_files)
tmp_output_read_1 = self.get_outputs('{basename}', self.read1_files)
tmp_output_read_2 = self.get_outputs('{basename}', self.read2_files)
tmp_discard_read_1 = self.get_outputs('{basename_woext}.notCombined_1.fastq', self.prefixes)
tmp_discard_read_2 = self.get_outputs('{basename_woext}.notCombined_2.fastq', self.prefixes)
tmp_discard_read_1 = self.get_outputs('{basename}.discards', self.prefixes)
tmp_discard_read_2 = self.get_outputs('{basename}.discards', self.prefixes)
# Process radtags read1 files
for i in range(0, len(self.prefixes)):
process_radtag = ShellFunction(self.get_exec_path("process_radtags") + " -f $1 " + self.options + " -o " + self.output_directory + " 2> $2 ", cmd_format='{EXE} {IN} {OUT}')
......@@ -221,11 +221,11 @@ Currently supported enzymes include:
# Recover_mate and recover_discard
recover_mate = PythonFunction(recover_mate_ok, cmd_format="{EXE} {IN} {OUT}")
recover_mate = Map(recover_mate, inputs = [self.output_read_1, self.input_read_2], outputs=[self.output_read_2, self.stderr])
recover_mate = Map(recover_mate, inputs = [self.tmp_output_read_1, self.input_read_2], outputs=[self.tmp_output_read_2, self.stderr])
recover_discard = PythonFunction(recover_mate_discard, cmd_format="{EXE} {IN} {OUT}")
recover_discard = Map(recover_discardn, inputs = [self.discard_read_1, self.input_read_2], outputs=[self.discard_read_2, self.stderr])
recover_discard = Map(recover_discard, inputs = [self.tmp_discard_read_1, self.input_read_2], outputs=[self.tmp_discard_read_2, self.stderr])
# Compress
compress = ShellFunction("gzip $1 $2 $3", cmd_format='{EXE} {IN} {OUT}')
compress = MultiMap(compress, inputs = [tmp_extended_frags, tmp_not_combined_read_1, tmp_not_combined_read_2], outputs = [self.extended_frags, self.not_combined_read_1, self.not_combined_read_2])
compress = MultiMap(compress, inputs = [tmp_output_read_1, tmp_output_read_2, tmp_discard_read_1, tmp_discard_read_2], outputs = [self.out , self.not_combined_read_1, self.not_combined_read_2])
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