updated funcations to use jar files, also updated some reference sequ…

…ences

.gitignore

@@ -6,6 +6,8 @@ config_office.ini
 config_pssb.ini
 config.ini
 .svn
+nbproject
+README.TXT
 *.stk
 *.sto
 *.bin

config_skel.ini

@@ -8,7 +8,13 @@ cmalign_cmd = /path/to/cmalign
 hmmalign_cmd = /path/to/hmmalign
 blast_cmd = /path/to/blastall
 formatdb_cmd = /path/to/formatdb
-parse_error_analysis_cmd = /path/to/AlignmentTools/parseErrorAnalysis.py
+parse_error_analysis_cmd = /path/to/parseErrorAnalysis.py
 usearch_cmd=/path/to/usearch6.0
 
 #gridware_env_path=/usr/bin:/usr/sbin:/Software/bin  #unsed
+
+process_class_jar = /path/to/RDPTools/SeqFilters.jar
+cluster_jar = /path/to/RDPTools/Clustering.jar
+framebot_jar = /path/to/RDPTools/FrameBot.jar
+alignment_tools_jar = /path/to/RDPTools/AlignmentTools/dist/AlignmentTools.jar
+abundance_jar = /path/to/RDPTools/AbundanceStats.jar

fgp_wrapper.py

@@ -18,13 +18,22 @@ def check_seq_counts(seq_files):
 
 def check_seq_counts_file(seq_file):
 	total_seqs = 0
-	for seq in SeqIO.parse(open(seq_file), "fasta"):
+	stream = open(seq_file)
+	first_char = stream.read(1)
+	if first_char == "@":
+		format = "fastq"
+	else:
+		format = "fasta"
+	stream.close()
+
+	for seq in SeqIO.parse(open(seq_file), format):
 		if seq.id[0] != "#":
 			total_seqs += 1
 	return total_seqs
 
 def send_mail(email_address, subject, mail_file):
-	pass
+	cmd = ["cafe", mail_wrapper_class, "--to_email", email_address, "--subject_name", subject, "--message_file", mail_file]
+	subprocess.call(cmd)
 
 def main(options_file, command_file, infiles):
 	seq_files = []

resources/nifh/README

@@ -1 +1,4 @@
 Model and reference sequences obtained from fungene, >95% coverage, aligned and model built 20 times to smooth variance
+
+framebot.fasta contains the nifH region flanked by Poly primers
+framebot_full_nifh.fasta contains the full nifH region