Updated path for all scripts to /nfs/pathogen/sh16_scripts

Aga.py

@@ -221,7 +221,7 @@ def filter_repeats(contigfile, tmpname):
 
 
 	if options.mapping:
-		os.system("~sh16/scripts/multiple_mappings_to_bam.py -M 2 -z 0.9 -p smalt -v latest -X -r "+core_file+" "+' '.join(args)+' > '+tmpname+'jobstring')
+		os.system("/nfs/pathogen/sh16_scripts/multiple_mappings_to_bam.py -M 2 -z 0.9 -p smalt -v latest -X -r "+core_file+" "+' '.join(args)+' > '+tmpname+'jobstring')
 
 		jobnum=open(tmpname+'jobstring', "rU").readlines()[-4].split(">")[0].split("<")[1]
 
@@ -261,9 +261,9 @@ def filter_repeats(contigfile, tmpname):
 			continue
 		donefolders.append(folder)
 
-		os.system("~sh16/scripts/Aga/bam_filter.py -t notpaired -b "+folder+"_SMALT/"+folder+".bam -o "+folder+"_SMALT/"+folder+"_unmapped")
+		os.system("/nfs/pathogen/sh16_scripts/Aga/bam_filter.py -t notpaired -b "+folder+"_SMALT/"+folder+".bam -o "+folder+"_SMALT/"+folder+"_unmapped")
 
-		contigdepths=os.popen("~sh16/scripts/Aga/contig_stats.py -b "+folder+"_SMALT/"+folder+".bam -H" )#.readlines()
+		contigdepths=os.popen("/nfs/pathogen/sh16_scripts/Aga/contig_stats.py -b "+folder+"_SMALT/"+folder+".bam -H" )#.readlines()
 		totlen=0.0
 		totdepth=0.0
 		for contigdepth in contigdepths:
@@ -311,7 +311,7 @@ def filter_repeats(contigfile, tmpname):
 			sys.exit()
 
 
-		#os.system("~sh16/scripts/multiple_mappings_to_bam.py -r "+acc_file+" -f -X -y -p smalt -L "+tmpname+"_[12].fastq")# >  /dev/null 2>&1")
+		#os.system("/nfs/pathogen/sh16_scripts/multiple_mappings_to_bam.py -r "+acc_file+" -f -X -y -p smalt -L "+tmpname+"_[12].fastq")# >  /dev/null 2>&1")
 
 		os.system("samtools faidx "+acc_file)
 		os.system("smalt index -k 13 -s 1 "+acc_file+".index "+acc_file)
@@ -322,7 +322,7 @@ def filter_repeats(contigfile, tmpname):
 		os.system("rm -f "+tmpname+".1.bam "+tmpname+".sam "+acc_file+".fai "+acc_file+".index.*")
 
 
-		contigstats=os.popen("~sh16/scripts/Aga/contig_stats.py -b "+tmpname+".bam -H" )#.readlines()
+		contigstats=os.popen("/nfs/pathogen/sh16_scripts/Aga/contig_stats.py -b "+tmpname+".bam -H" )#.readlines()
 		contiglist=[]
 
 		for contigstat in contigstats:
@@ -336,19 +336,19 @@ def filter_repeats(contigfile, tmpname):
 		if len(contiglist)>0:
 			contigstring=','.join(contiglist)
 			print contigstring
-			os.system("~sh16/scripts/Aga/bam_filter.py -t aga -c "+contigstring+" -b "+tmpname+".bam -o "+tmpname+"_unmapped")
+			os.system("/nfs/pathogen/sh16_scripts/Aga/bam_filter.py -t aga -c "+contigstring+" -b "+tmpname+".bam -o "+tmpname+"_unmapped")
 		else:
-			os.system("~sh16/scripts/Aga/bam_filter.py -t notpaired -b "+tmpname+".bam -o "+tmpname+"_unmapped")
+			os.system("/nfs/pathogen/sh16_scripts/Aga/bam_filter.py -t notpaired -b "+tmpname+".bam -o "+tmpname+"_unmapped")
 
 
 
-		os.system('~sh16/scripts/iterative_assembler.py -L 500 -n 0 -f '+tmpname+"_unmapped_1.fastq -r "+tmpname+"_unmapped_2.fastq -o "+folder+"_contigs.mfa")
+		os.system('/nfs/pathogen/sh16_scripts/iterative_assembler.py -L 500 -n 0 -f '+tmpname+"_unmapped_1.fastq -r "+tmpname+"_unmapped_2.fastq -o "+folder+"_contigs.mfa")
 
 
 		os.system("cat "+folder+"_contigs.mfa >> "+acc_file)
-		os.system("~sh16/scripts/Contig_summary.py "+folder+"_contigs.mfa "+acc_file)
+		os.system("/nfs/pathogen/sh16_scripts/Contig_summary.py "+folder+"_contigs.mfa "+acc_file)
 		filter_repeats(acc_file, tmpname)
-		os.system("~sh16/scripts/Contig_summary.py "+acc_file)
+		os.system("/nfs/pathogen/sh16_scripts/Contig_summary.py "+acc_file)
 
 
 	os.system("mv "+acc_file+" "+options.prefix+"_accessory_genome.fasta")	
@@ -362,13 +362,13 @@ def filter_repeats(contigfile, tmpname):
 	else:
 		refname=tmpname
 
-	os.system("~sh16/scripts/fasta2fastq_shredder.py "+options.ref+" "+refname+" 76 3 c 200")
+	os.system("/nfs/pathogen/sh16_scripts/fasta2fastq_shredder.py "+options.ref+" "+refname+" 76 3 c 200")
 
 	#final mapping of all isolates against ref+accessory
 	if options.embl!="":
-		os.system("~sh16/scripts/multiple_mappings_to_bam.py -p smalt -v latest -G -O pan_genome -E -f -x -r "+options.prefix+"_pan_genome.fasta -e "+options.embl+" "+' '.join(args)+' '+refname+'_[12].fastq')
+		os.system("/nfs/pathogen/sh16_scripts/multiple_mappings_to_bam.py -p smalt -v latest -G -O pan_genome -E -f -x -r "+options.prefix+"_pan_genome.fasta -e "+options.embl+" "+' '.join(args)+' '+refname+'_[12].fastq')
 	else:
-		os.system("~sh16/scripts/multiple_mappings_to_bam.py -p smalt -v latest -G -O pan_genome -E -f -x -r "+options.prefix+"_pan_genome.fasta "+' '.join(args)+' '+refname+'_[12].fastq')
+		os.system("/nfs/pathogen/sh16_scripts/multiple_mappings_to_bam.py -p smalt -v latest -G -O pan_genome -E -f -x -r "+options.prefix+"_pan_genome.fasta "+' '.join(args)+' '+refname+'_[12].fastq')
 
 
 

Aga/Aga.py

@@ -221,7 +221,7 @@ def filter_repeats(contigfile, tmpname):
 	sys.exit()
 
 	if options.mapping:
-		os.system("~sh16/scripts/multiple_mappings_to_bam.py -M 2 -z 0.9 -p smalt -v latest -X -r "+core_file+" "+' '.join(args)+' > '+tmpname+'jobstring')
+		os.system("/nfs/pathogen/sh16_scripts/multiple_mappings_to_bam.py -M 2 -z 0.9 -p smalt -v latest -X -r "+core_file+" "+' '.join(args)+' > '+tmpname+'jobstring')
 
 		jobnum=open(tmpname+'jobstring', "rU").readlines()[-4].split(">")[0].split("<")[1]
 
@@ -264,9 +264,9 @@ def filter_repeats(contigfile, tmpname):
 		if options.mapping or (not os.path.isfile(folder+"_SMALT/"+folder+"_unmapped_1.fastq") and not os.path.isfile(folder+"_SMALT/"+folder+"_unmapped_1.fastq.gz")) or (not os.path.isfile(folder+"_SMALT/"+folder+"_unmapped_2.fastq") and not os.path.isfile(folder+"_SMALT/"+folder+"_unmapped_2.fastq.gz")):
 			print "Identifying reads not in proper pairs for", folder
 			sys.stdout.flush()
-			os.system("~sh16/scripts/Aga/bam_filter.py -t atleastoneunmapped -b "+folder+"_SMALT/"+folder+".bam -o "+folder+"_SMALT/"+folder+"_unmapped")
+			os.system("/nfs/pathogen/sh16_scripts/Aga/bam_filter.py -t atleastoneunmapped -b "+folder+"_SMALT/"+folder+".bam -o "+folder+"_SMALT/"+folder+"_unmapped")
 
-		contigdepths=os.popen("~sh16/scripts/Aga/contig_stats.py -b "+folder+"_SMALT/"+folder+".bam -H" )#.readlines()
+		contigdepths=os.popen("/nfs/pathogen/sh16_scripts/Aga/contig_stats.py -b "+folder+"_SMALT/"+folder+".bam -H" )#.readlines()
 		totlen=0.0
 		totdepth=0.0
 		for contigdepth in contigdepths:
@@ -315,7 +315,7 @@ def filter_repeats(contigfile, tmpname):
 			sys.exit()
 
 
-		#os.system("~sh16/scripts/multiple_mappings_to_bam.py -r "+acc_file+" -f -X -y -p smalt -L "+tmpname+"_[12].fastq")# >  /dev/null 2>&1")
+		#os.system("/nfs/pathogen/sh16_scripts/multiple_mappings_to_bam.py -r "+acc_file+" -f -X -y -p smalt -L "+tmpname+"_[12].fastq")# >  /dev/null 2>&1")
 
 		os.system("samtools faidx "+acc_file)
 		os.system("smalt index -k 13 -s 1 "+acc_file+".index "+acc_file)
@@ -326,7 +326,7 @@ def filter_repeats(contigfile, tmpname):
 		os.system("rm -f "+tmpname+".1.bam "+tmpname+".sam "+acc_file+".fai "+acc_file+".index.*")
 
 
-		contigstats=os.popen("~sh16/scripts/Aga/contig_stats.py -b "+tmpname+".bam -H" )#.readlines()
+		contigstats=os.popen("/nfs/pathogen/sh16_scripts/Aga/contig_stats.py -b "+tmpname+".bam -H" )#.readlines()
 		contiglist=[]
 
 		for contigstat in contigstats:
@@ -342,30 +342,30 @@ def filter_repeats(contigfile, tmpname):
 		if len(contiglist)>0:
 			contigstring=','.join(contiglist)
 			print contigstring
-			os.system("~sh16/scripts/Aga/bam_filter.py -t aga -c "+contigstring+" -b "+tmpname+".bam -o "+tmpname+"_unmapped")
+			os.system("/nfs/pathogen/sh16_scripts/Aga/bam_filter.py -t aga -c "+contigstring+" -b "+tmpname+".bam -o "+tmpname+"_unmapped")
 		else:
-			os.system("~sh16/scripts/Aga/bam_filter.py -t atleastoneunmapped -b "+tmpname+".bam -o "+tmpname+"_unmapped")
+			os.system("/nfs/pathogen/sh16_scripts/Aga/bam_filter.py -t atleastoneunmapped -b "+tmpname+".bam -o "+tmpname+"_unmapped")
 
 
 
-		#os.system('~sh16/scripts/iterative_assembler.py -L 500 -n 0 -f '+tmpname+"_unmapped_1.fastq -r "+tmpname+"_unmapped_2.fastq -o "+folder+"_contigs.mfa")
-		os.system('~sh16/scripts/velvet_assembly.sh -p -n -i 300 -e '+str(exp)+' -f '+tmpname+"_unmapped_1.fastq -r "+tmpname+"_unmapped_2.fastq -s "+folder+".fastq")
+		#os.system('/nfs/pathogen/sh16_scripts/iterative_assembler.py -L 500 -n 0 -f '+tmpname+"_unmapped_1.fastq -r "+tmpname+"_unmapped_2.fastq -o "+folder+"_contigs.mfa")
+		os.system('/nfs/pathogen/sh16_scripts/velvet_assembly.sh -p -n -i 300 -e '+str(exp)+' -f '+tmpname+"_unmapped_1.fastq -r "+tmpname+"_unmapped_2.fastq -s "+folder+".fastq")
 		os.system("rm -rf "+tmpname+".fasta "+folder+"_contigs.mfa")
 		os.system("cp "+folder+"_velvet/contigs.fa "+folder+"_contigs.mfa")
 		os.system("rm -rf "+folder+"_velvet")
 		os.system("cat "+core_file+" "+acc_file+" > "+tmpname+".fasta")
-		os.system("~sh16/scripts/fasta2fastq_shredder.py "+tmpname+".fasta "+tmpname+" 76 3 l 250")
+		os.system("/nfs/pathogen/sh16_scripts/fasta2fastq_shredder.py "+tmpname+".fasta "+tmpname+" 76 3 l 250")
 		os.system("rm -rf "+tmpname+".fasta")
 		os.system("smalt index -k 13 -s 1 "+folder+"_contigs.mfa.index "+folder+"_contigs.mfa")
 		os.system("smalt map -r "+str(randrange(1,99999))+" -f samsoft -o "+tmpname+".sam "+folder+"_contigs.mfa.index "+tmpname+"_1.fastq "+tmpname+"_2.fastq")
 		os.system("samtools view -b -o "+tmpname+".bam -t "+folder+"_contigs.mfa -S "+tmpname+".sam")
 		os.system("samtools sort "+tmpname+".bam "+tmpname+"_sort")
 		os.system("samtools index "+tmpname+"_sort.bam")
 
-		os.system("~sh16/scripts/Contig_summary.py "+folder+"_contigs.mfa")
-		os.system("~sh16/scripts/Contig_summary.py "+acc_file)
+		os.system("/nfs/pathogen/sh16_scripts/Contig_summary.py "+folder+"_contigs.mfa")
+		os.system("/nfs/pathogen/sh16_scripts/Contig_summary.py "+acc_file)
 
-		contigstats=os.popen("~sh16/scripts/Aga/contig_stats.py -b "+tmpname+"_sort.bam -H" )#.readlines()
+		contigstats=os.popen("/nfs/pathogen/sh16_scripts/Aga/contig_stats.py -b "+tmpname+"_sort.bam -H" )#.readlines()
 		os.system("rm -rf "+tmpname+".[sb]am")
 		contiglist=[]
 
@@ -386,9 +386,9 @@ def filter_repeats(contigfile, tmpname):
 				print >> output, ''.join(line.split("\n")[1:])
 		output.close()
 		os.system("cat "+tmpname+".fasta >> "+acc_file)
-#		os.system("~sh16/scripts/Contig_summary.py "+folder+"_contigs.mfa "+acc_file)
+#		os.system("/nfs/pathogen/sh16_scripts/Contig_summary.py "+folder+"_contigs.mfa "+acc_file)
 #		filter_repeats(acc_file, tmpname)
-		os.system("~sh16/scripts/Contig_summary.py "+acc_file)
+		os.system("/nfs/pathogen/sh16_scripts/Contig_summary.py "+acc_file)
 
 
 	os.system("mv "+acc_file+" "+options.prefix+"_accessory_genome.fasta")	
@@ -402,13 +402,13 @@ def filter_repeats(contigfile, tmpname):
 	else:
 		refname=tmpname
 
-	os.system("~sh16/scripts/fasta2fastq_shredder.py "+options.ref+" "+refname+" 76 3 c 250")
+	os.system("/nfs/pathogen/sh16_scripts/fasta2fastq_shredder.py "+options.ref+" "+refname+" 76 3 c 250")
 
 	#final mapping of all isolates against ref+accessory
 	if options.embl!="":
-		os.system("~sh16/scripts/multiple_mappings_to_bam.py -p smalt -v latest -G -O "+options.prefix+" -E -f -x -r "+options.prefix+"_pan_genome.fasta -e "+options.embl+" "+' '.join(args)+' '+refname+'_[12].fastq')
+		os.system("/nfs/pathogen/sh16_scripts/multiple_mappings_to_bam.py -p smalt -v latest -G -O "+options.prefix+" -E -f -x -r "+options.prefix+"_pan_genome.fasta -e "+options.embl+" "+' '.join(args)+' '+refname+'_[12].fastq')
 	else:
-		os.system("~sh16/scripts/multiple_mappings_to_bam.py -p smalt -v latest -G -O "+options.prefix+" -E -f -x -r "+options.prefix+"_pan_genome.fasta "+' '.join(args)+' '+refname+'_[12].fastq')
+		os.system("/nfs/pathogen/sh16_scripts/multiple_mappings_to_bam.py -p smalt -v latest -G -O "+options.prefix+" -E -f -x -r "+options.prefix+"_pan_genome.fasta "+' '.join(args)+' '+refname+'_[12].fastq')
 
 
 

Aga/Aga2.py

@@ -12,14 +12,14 @@
 from Bio.Seq import Seq
 from shutil import copyfile
 import mimetypes
-sys.path.extend(map(os.path.abspath, ['/nfs/users/nfs_s/sh16/scripts/modules/']))
+sys.path.extend(map(os.path.abspath, ['/nfs/pathogen/sh16_scripts/modules/']))
 import farm
 import subprocess
 import gzip
 
 SMALT_LOC="/software/pathogen/external/apps/usr/bin/smalt"
 SAMTOOLS_LOC="/software/pathogen/external/apps/usr/bin/samtools"
-AGA_DIR="/nfs/users/nfs_s/sh16/scripts/Aga/"
+AGA_DIR="/nfs/pathogen/sh16_scripts/Aga/"
 
 
 ##########################

Aga/Aga2_restart_after_assemblies.py

@@ -12,12 +12,12 @@
 from Bio.Seq import Seq
 from shutil import copyfile
 import mimetypes
-sys.path.extend(map(os.path.abspath, ['/nfs/users/nfs_s/sh16/scripts/modules/']))
+sys.path.extend(map(os.path.abspath, ['/nfs/pathogen/sh16_scripts/modules/']))
 import farm
 
 SMALT_LOC="/software/pathogen/external/apps/usr/bin/smalt"
 SAMTOOLS_LOC="/software/pathogen/external/apps/usr/bin/samtools"
-AGA_DIR="/nfs/users/nfs_s/sh16/scripts/Aga/"
+AGA_DIR="/nfs/pathogen/sh16_scripts/Aga/"
 
 
 ##########################

Aga/Aga3.py

@@ -12,14 +12,14 @@
 from Bio.Seq import Seq
 from shutil import copyfile
 import mimetypes
-sys.path.extend(map(os.path.abspath, ['/nfs/users/nfs_s/sh16/scripts/modules/']))
+sys.path.extend(map(os.path.abspath, ['/nfs/pathogen/sh16_scripts/modules/']))
 import farm
 import subprocess
 import gzip
 
 SMALT_LOC="/software/pathogen/external/apps/usr/bin/smalt"
 SAMTOOLS_LOC="/software/pathogen/external/apps/usr/bin/samtools"
-AGA_DIR="/nfs/users/nfs_s/sh16/scripts/Aga/"
+AGA_DIR="/nfs/pathogen/sh16_scripts/Aga/"
 
 
 ##########################
@@ -546,7 +546,7 @@ def check_input_validity(options, args):
 	for i, assembly in enumerate(args):
 		name=assembly.split("/")[-1].split(".")[0]
 		mummer_file=open(tmpname+"/"+tmpname+"_mummer_"+str(i+1)+".sh", "w")
-		print >> mummer_file, "/nfs/users/nfs_s/sh16/scripts/Aga/align_contigs_with_mummer.py -q "+core_file+" -r "+assembly+" -o "+tmpname+"/"+name+' || error_exit "mummer script failed! Aborting"'
+		print >> mummer_file, "/nfs/pathogen/sh16_scripts/Aga/align_contigs_with_mummer.py -q "+core_file+" -r "+assembly+" -o "+tmpname+"/"+name+' || error_exit "mummer script failed! Aborting"'
 		assembly_list.append(tmpname+"/"+name+"_unmatched.fasta")
 
 		mummer_file.close()

Aga/align_contigs_with_mummer.py

@@ -10,7 +10,7 @@
 import glob
 import shlex, subprocess
 
-sys.path.extend(map(os.path.abspath, ['/nfs/users/nfs_s/sh16/scripts/modules/']))
+sys.path.extend(map(os.path.abspath, ['/nfs/pathogen/sh16_scripts/modules/']))
 from Si_general import *
 from Si_SeqIO import *
 

Aga/better_blast.py

@@ -2,15 +2,15 @@
 
 import os, sys
 from optparse import OptionParser, OptionGroup
-sys.path.extend(map(os.path.abspath, ['/nfs/users/nfs_s/sh16/scripts/modules/']))
+sys.path.extend(map(os.path.abspath, ['/nfs/pathogen/sh16_scripts/modules/']))
 from Si_SeqIO import *
 import subprocess
 import shlex
 import gzip
 import shutil
 from random import *
 import math
-sys.path.extend(map(os.path.abspath, ['/nfs/users/nfs_s/sh16/scripts/modules/']))
+sys.path.extend(map(os.path.abspath, ['/nfs/pathogen/sh16_scripts/modules/']))
 import farm
 
 ##########################

Aga/filter_contigs_with_mummer.py

@@ -10,7 +10,7 @@
 import glob
 import shlex, subprocess
 
-sys.path.extend(map(os.path.abspath, ['/nfs/users/nfs_s/sh16/scripts/modules/']))
+sys.path.extend(map(os.path.abspath, ['/nfs/pathogen/sh16_scripts/modules/']))
 from Si_general import *
 from Si_SeqIO import *
 

Aga/identify_contamination.py

@@ -8,7 +8,7 @@
 from optparse import OptionParser, OptionGroup
 import pysam
 from Bio.Seq import Seq
-sys.path.extend(map(os.path.abspath, ['/nfs/users/nfs_s/sh16/scripts/modules/']))
+sys.path.extend(map(os.path.abspath, ['/nfs/pathogen/sh16_scripts/modules/']))
 from Si_SeqIO import *
 import numpy as np
 import matplotlib.mlab as mlab

Aga/parse_CD-Hit_clusters.py

@@ -183,7 +183,7 @@ def parse_CDHitEST_clstr_file(filehandle):
 		print "Error: samtools sorting failed."
 		sys.exit()
 
-#	returnval=os.system("~sh16/scripts/resistome/filter_doubleclipped_reads.py -b tmp_sort.bam -o "+options.output+"_filtered.bam")
+#	returnval=os.system("/nfs/pathogen/sh16_scripts/resistome/filter_doubleclipped_reads.py -b tmp_sort.bam -o "+options.output+"_filtered.bam")
 #
 #	print "filter_doubleclipped_reads.py return value:", returnval
 #	
@@ -205,7 +205,7 @@ def parse_CDHitEST_clstr_file(filehandle):
 
 		returnval=os.system('grep -A 1 ">'+proposed+'" '+options.db+' > '+proposed+'_ref.fasta')
 
-		returnval=os.system('~sh16/scripts/resistome/bam_filter.py -f pairedfastq -t contigsonemapped -c '+proposed+' -b '+options.output+'.bam -o tmp_proposed')
+		returnval=os.system('/nfs/pathogen/sh16_scripts/resistome/bam_filter.py -f pairedfastq -t contigsonemapped -c '+proposed+' -b '+options.output+'.bam -o tmp_proposed')
 		returnval=os.system('smalt index index '+proposed+'_ref.fasta')
 		if returnval!=0:
 			continue
@@ -221,10 +221,10 @@ def parse_CDHitEST_clstr_file(filehandle):
 		returnval=os.system('samtools index '+proposed+'.bam')
 		if returnval!=0:
 			continue
-		returnval=os.system('~sh16/scripts/resistome/extract_clipping_info.py -b '+proposed+'.bam')
+		returnval=os.system('/nfs/pathogen/sh16_scripts/resistome/extract_clipping_info.py -b '+proposed+'.bam')
 		if returnval!=0:
 			continue
-		returnval=os.system('~sh16/scripts/iCANDY.py '+proposed+'.bam starts.plot '+proposed+'_ref.fasta -d area -l 1 -g 0 -w -Y 0 -o '+proposed+'_coverage.pdf')
+		returnval=os.system('/nfs/pathogen/sh16_scripts/iCANDY.py '+proposed+'.bam starts.plot '+proposed+'_ref.fasta -d area -l 1 -g 0 -w -Y 0 -o '+proposed+'_coverage.pdf')
 		if returnval!=0:
 			continue
 

Aga/subsample_fastq.py

@@ -8,7 +8,7 @@
 from Bio.Seq import Seq
 from Bio.SeqUtils import GC
 import subprocess
-sys.path.extend(map(os.path.abspath, ['/nfs/users/nfs_s/sh16/scripts/modules/']))
+sys.path.extend(map(os.path.abspath, ['/nfs/pathogen/sh16_scripts/modules/']))
 from Si_SeqIO import *
 import gzip
 import mimetypes

Aga/velvet_assembly.sh

@@ -35,7 +35,7 @@ EOF
 }
 
 
-script_dir="/nfs/users/nfs_s/sh16/scripts/"
+script_dir="/nfs/pathogen/sh16_scripts/"
 velvet_dir="/nfs/users/nfs_s/sh16/velvet_1.2.03/"
 
 PAIRED=0

Aga3/Aga3.py

@@ -12,14 +12,14 @@
 from Bio.Seq import Seq
 from shutil import copyfile
 import mimetypes
-sys.path.extend(map(os.path.abspath, ['/nfs/users/nfs_s/sh16/scripts/modules/']))
+sys.path.extend(map(os.path.abspath, ['/nfs/pathogen/sh16_scripts/modules/']))
 import farm
 import subprocess
 import gzip
 
 SMALT_LOC="/software/pathogen/external/apps/usr/bin/smalt"
 SAMTOOLS_LOC="/software/pathogen/external/apps/usr/bin/samtools"
-AGA_DIR="/nfs/users/nfs_s/sh16/scripts/Aga3/"
+AGA_DIR="/nfs/pathogen/sh16_scripts/Aga3/"
 
 
 ##########################

Aga3/align_contigs_with_mummer.py

@@ -10,7 +10,7 @@
 import glob
 import shlex, subprocess
 
-sys.path.extend(map(os.path.abspath, ['/nfs/users/nfs_s/sh16/scripts/modules/']))
+sys.path.extend(map(os.path.abspath, ['/nfs/pathogen/sh16_scripts/modules/']))
 from Si_general import *
 from Si_SeqIO import *
 

Aga3/better_blast.py

@@ -2,7 +2,7 @@
 
 import os, sys
 from optparse import OptionParser, OptionGroup
-sys.path.extend(map(os.path.abspath, ['/nfs/users/nfs_s/sh16/scripts/modules/']))
+sys.path.extend(map(os.path.abspath, ['/nfs/pathogen/sh16_scripts/modules/']))
 from Si_SeqIO import *
 import subprocess
 import shlex
@@ -282,7 +282,7 @@ def check_input_validity(options, args):
 	else:
 		fs="False"
 
-	job2 = farm.Bsub(options.prefix+"_bb_bsub.out", options.prefix+"_bb_bsub.err", tmpname+"_postprocess", "normal", 0.5, "/nfs/users/nfs_s/sh16/scripts/post_process_better_blast.py "+options.tmpdir+" "+tmpname+" "+options.prefix+" "+str(query_file_count)+" "+fs)
+	job2 = farm.Bsub(options.prefix+"_bb_bsub.out", options.prefix+"_bb_bsub.err", tmpname+"_postprocess", "normal", 0.5, "/nfs/pathogen/sh16_scripts/post_process_better_blast.py "+options.tmpdir+" "+tmpname+" "+options.prefix+" "+str(query_file_count)+" "+fs)
 	job2.add_dependency(job1_id) 
 	job2_id = job2.run()
 	print "Job ID =", job2_id

Aga3/filter_contigs_with_mummer.py

@@ -10,7 +10,7 @@
 import glob
 import shlex, subprocess
 
-sys.path.extend(map(os.path.abspath, ['/nfs/users/nfs_s/sh16/scripts/modules/']))
+sys.path.extend(map(os.path.abspath, ['/nfs/pathogen/sh16_scripts/modules/']))
 from Si_general import *
 from Si_SeqIO import *