LICENSE

TEspeX.py

@@ -295,7 +295,7 @@ def star_ind(genome, r_length):
   os.mkdir("index")
   os.chdir("index")
   # then we can call the STAR index function using the number of threads that is passed from command line
-  starCmd = bin_path + "STAR-2.6.0c/bin/tespex/STAR --runThreadN " +str(num_threads)+ " --runMode genomeGenerate --genomeDir " +os.path.abspath(".")+ " --genomeFastaFiles " +genome+ " --genomeSAindexNbases " +str(genomeSAindexNbase)+ " --genomeChrBinNbits " +str(genomeChrBinNbits)
+  starCmd = bin_path + "STAR-2.6.0c/STAR --runThreadN " +str(num_threads)+ " --runMode genomeGenerate --genomeDir " +os.path.abspath(".")+ " --genomeFastaFiles " +genome+ " --genomeSAindexNbases " +str(genomeSAindexNbase)+ " --genomeChrBinNbits " +str(genomeChrBinNbits)
   bash(starCmd)
 
   os.chdir(dir)
@@ -313,9 +313,9 @@ def star_aln(fq_list, strandn, fastaReference, pair, rm, *index_dir):
   # otherwise each directory has its own index
   if index_dir:
     index = index_dir[0]
-    command = bin_path + "STAR-2.6.0c/bin/tespex/STAR --outSAMunmapped None --outSAMprimaryFlag AllBestScore --outFilterMismatchNoverLmax 0.04 --outMultimapperOrder Random --outSAMtype BAM Unsorted --outStd BAM_Unsorted --runThreadN " +str(num_threads)+ " --genomeDir " +index
+    command = bin_path + "STAR-2.6.0c/STAR --outSAMunmapped None --outSAMprimaryFlag AllBestScore --outFilterMismatchNoverLmax 0.04 --outMultimapperOrder Random --outSAMtype BAM Unsorted --outStd BAM_Unsorted --runThreadN " +str(num_threads)+ " --genomeDir " +index
   else:
-    command = bin_path + "STAR-2.6.0c/bin/tespex/STAR --outSAMunmapped None --outSAMprimaryFlag AllBestScore --outFilterMismatchNoverLmax 0.04 --outMultimapperOrder Random --outSAMtype BAM Unsorted --outStd BAM_Unsorted --runThreadN " +str(num_threads)+ " --genomeDir " +os.path.abspath("index")
+    command = bin_path + "STAR-2.6.0c/STAR --outSAMunmapped None --outSAMprimaryFlag AllBestScore --outFilterMismatchNoverLmax 0.04 --outMultimapperOrder Random --outSAMtype BAM Unsorted --outStd BAM_Unsorted --runThreadN " +str(num_threads)+ " --genomeDir " +os.path.abspath("index")
   # for every line of the file launch the analysis
   with open(fq_list) as reads:
     for line in reads:

index.py

@@ -182,7 +182,7 @@ def star_ind(genome, r_length):
   os.mkdir("index")
   os.chdir("index")
   # then we can call the STAR index function using the number of threads that is passed from command line
-  starCmd = bin_path + "STAR-2.6.0c/bin/tespex/STAR --runThreadN " +str(num_threads)+ " --runMode genomeGenerate --genomeDir " +os.path.abspath(".")+ " --genomeFastaFiles " +genome+ " --genomeSAindexNbases " +str(genomeSAindexNbase)+ " --genomeChrBinNbits " +str(genomeChrBinNbits)
+  starCmd = bin_path + "STAR-2.6.0c/STAR --runThreadN " +str(num_threads)+ " --runMode genomeGenerate --genomeDir " +os.path.abspath(".")+ " --genomeFastaFiles " +genome+ " --genomeSAindexNbases " +str(genomeSAindexNbase)+ " --genomeChrBinNbits " +str(genomeChrBinNbits)
   bash(starCmd)
 
   os.chdir(dir)

wrapper_slurm.py

@@ -161,7 +161,7 @@ def fileTrue(file):
   parser.add_argument('--ncrna', type=str, help='fa/fa.gz file containing ncrna Ensembl sequences in fasta format [required]', required=True)
   parser.add_argument('--sample', type=str, help='txt file containing fq/fq.gz FULL PATHS. If reads are single end, one path should be written in each line. If reads are paired end the two mates should be written in the same line separated by \\t [required]', required=True)
   parser.add_argument('--paired', type=str, help='T (true) or F (false). T means the reads are paired and consequently the sample file is expected to contain 2 columns. F means the reads are not paired, sample file is expected to contain  1 single column [required]', required=True)
-  parser.add_argument('--length', type=int, help='length of the read given as input. This is used to calculate STAR index parameters. If your fq/fq.gz file contains reads with different length specify the most frequent read length [required]', required=True)
+  parser.add_argument('--length', type=int, help='length of the read given as input. This is used to calculateSTAR index parameters. If your fq/fq.gz file contains reads with different length specify the most frequent read length [required]', required=True)
   parser.add_argument('--out', type=str, help='directory where the output files will be written. This directory is created by the pipeline, specificy a non-yet-existing directory', required=True)
   parser.add_argument('--strand', type=str, help='strandeness of the RNAseq library. no = unstranded/htseqcount \'no\', yes = htseqcount \'yes\', reverse = htseqcount \'reverse\'', required=True)
   parser.add_argument('--job', type=str, help='number of jobs that can be run at the same time', required=True)