Merge branch 'devrefbundle' into 'master'

some comestic changes

See merge request !13

snakecnv/align.snk

@@ -21,7 +21,7 @@ workdir: wdir
 
 snakemake_utils = SnakemakeUtils(samples)
 
-include: "tools/threads.snk"
+include: "tools/utils.snk"
 
 localrules: all_align
 

snakecnv/popsim.snk

 import sys
 import os
 
+include: "tools/utils.snk"
+
+
 ROOTPATH = os.path.dirname(os.path.dirname(workflow.snakefile))
 sys.path.insert(0, os.path.join(ROOTPATH, "lib"))
 os.environ["PYTHONPATH"] = os.path.join(ROOTPATH, "lib")
@@ -70,7 +73,6 @@ bp_inputs, bp_params = buildpop_inputs()
 bp_outputs = buildpop_outputs()
 
 
-include: "tools/threads.snk"
 include: "align.snk"
 include: "referencebundle.snk"
 include: "detection.snk"
@@ -229,4 +231,3 @@ rule buildresults:
             touch results/{wildcards.svtype}/Summarized_results_{wildcards.svtype}.ipynb
             touch results/{wildcards.svtype}/Summarized_results_{wildcards.svtype}.html
         """
-        

snakecnv/referencebundle.snk

@@ -8,6 +8,8 @@ from os.path import join
 from pyfaidx import Fasta
 # from natsort import natsorted
 
+include: "tools/utils.snk"
+
 ROOTPATH = os.path.dirname(workflow.snakefile)
 sys.path.insert(0, os.path.join(ROOTPATH, "lib"))
 os.environ["PYTHONPATH"] = os.path.join(ROOTPATH, "lib")
@@ -30,15 +32,11 @@ SUFF_TYPES = ("gcmask", "svmask", "lcmask")
 p_repeats = re.compile('.*(Satellite|Simple_repeat|Low_complexity).*')
 p_repeats_all = re.compile('.*(Satellite|Simple_repeat|Line|SINE|LTR).*')
 
-def message(mes):
-    sys.stderr.write("|--- " + mes + "\n")
-
-include: "tools/threads.snk"
-
 
 CHROMS = config['chromosomes']
+PERL5LIB = get_perl5lib()
 
-shell.prefix("export PATH=%s/bin:\"$PATH\";" % ROOTPATH)
+shell.prefix("export PATH=%s/bin:\"$PATH\"; export PERL5LIB=%s; " % (ROOTPATH, PERL5LIB))
 
 rule final:
     input:
@@ -54,19 +52,24 @@ rule final:
 
 rule get_fasta:
     input:
-        SUBDIR + PREFIX+"_raw.fasta"
+        fasta=SUBDIR + PREFIX+"_raw.fasta",
+        fai=SUBDIR + PREFIX+"_raw.fasta.fai"
     output:
         SUBDIR + PREFIX+".fasta"
-    run:
-        from Bio import SeqIO
-        with open(input[0], "rU") as handle, open(output[0], "w") as f:
-            for seq in SeqIO.parse(handle, "fasta"):
-                if seq.id in CHROMS:
-                    SeqIO.write([seq], f, "fasta")
-        os.remove(input[0])
-        i_fai = input[0] + ".fai"
-        if os.path.exists(i_fai):
-            os.remove(i_fai)
+    params:
+        chromosomes=CHROMS
+    shell:
+        "samtools faidx {input.fasta} {params.chromosomes} > {output}"
+    # run:
+    #     from Bio import SeqIO
+    #     with open(input[0], "rU") as handle, open(output[0], "w") as f:
+    #         for seq in SeqIO.parse(handle, "fasta"):
+    #             if seq.id in CHROMS:
+    #                 SeqIO.write([seq], f, "fasta")
+    #     os.remove(input[0])
+    #     i_fai = input[0] + ".fai"
+    #     if os.path.exists(i_fai):
+    #         os.remove(i_fai)
 
 rule index:
     input:
@@ -74,7 +77,7 @@ rule index:
     output:
         SUBDIR + "{type}.fasta.fai"
     log:
-        "logs/index/{type}.log"
+        SUBDIR + "logs/index/{type}.log"
     shell:
         "samtools faidx {input} &> {log}"
 
@@ -100,6 +103,8 @@ rule preparesvmask:
         "export PATH=$SV_DIR/bwa:\"$PATH\"; export LD_LIBRARY_PATH=$SV_DIR/bwa:\"$LD_LIBRARY_PATH\"; "
         "ln {input.fasta} {output.seq}; "
         "samtools faidx {output.seq}; "
+        # Checking genome size for bwa index
+        #"genomesize=`cat {output.seq}.fai | awk '{ totsize = totsize +$0}END{ print totsize}'`; "
         "bwa index -a bwtsw {output.seq} 2> {log} || bwa index -a is {output.seq} 2> {log}"
 
 rule mergesvmask:
@@ -151,13 +156,16 @@ rule repeatmask:
     output:
         SUBDIR + "reference.fasta.out"
     params:
-        sp = config['species']
+        sp = config['species'],
+        perl5lib = PERL5LIB
     threads:
         get_threads("repeatmask", 12)
     shell:
-        "export PATH=$SV_DIR/bwa:\"$PATH\"; export LD_LIBRARY_PATH=$SV_DIR/bwa:\"$LD_LIBRARY_PATH\"; "
-        "RepeatMasker -pa {threads} -species {params.sp} -xsmall {input.fasta}"
-        " > {input.fasta}.repeatmasker.log"
+        """
+        export PERL5LIB={params.perl5lib}
+        RepeatMasker -pa {threads} -species {params.sp} -xsmall {input.fasta}
+         > {input.fasta}.repeatmasker.log
+        """
 
 rule rdmask:
     input:

snakecnv/tools/utils.snk

+import os
+import shutil
+
+ROOTPATH = os.path.dirname(os.path.dirname(workflow.snakefile))
+sys.path.insert(0, os.path.join(ROOTPATH, "lib"))
+os.environ["PYTHONPATH"] = os.path.join(ROOTPATH, "lib")
+
+
+def get_threads(rule, default):
+    cluster_config = snakemake.workflow.cluster_config
+    if rule in cluster_config and "threads" in cluster_config[rule]:
+        return cluster_config[rule]["threads"]
+    if "default" in cluster_config and "threads" in cluster_config["default"]:
+        return cluster_config["default"]["threads"]
+    return default
+
+
+def get_perl5lib():
+    condaprefix = os.environ["CONDA_PREFIX"]
+    perllibpath = os.path.join(condaprefix, "lib", "perl5")
+    return perllibpath