bugs fixed in chromosome notation

WGLab · Jan 15, 2021 · 9f0f933 · 9f0f933
1 parent f6e585e
commit 9f0f933
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Showing 3 changed files with 9 additions and 4 deletions.
diff --git a/docs/Usage.md b/docs/Usage.md
@@ -5,7 +5,7 @@
 
 For whole genome variant calling, or calling variants on several chromosomes, use `NanoCaller_WGS.py` to call variants. Assuming all your input files are in a folder `YOUR_INPUT_DIR`, and you want to use `YOUR_OUTPUT_DIR` to store the results. 
 ```
-VERSION=0.3.1
+VERSION=0.3.2
 docker run -itd \
 -v 'YOUR_INPUT_DIR':'/input/' \
 -v 'YOUR_WORKING_DIR':'/output/' \
@@ -23,7 +23,7 @@ python NanoCaller_WGS.py \
 
 For calling variants on single chromosomes, use `NanoCaller.py` to call variants. Assuming all your input files are in a folder `YOUR_INPUT_DIR`, and you want to use `YOUR_OUTPUT_DIR` to store the results. 
 ```
-VERSION=0.3.1
+VERSION=0.3.2
 docker run -itd \
 -v 'YOUR_INPUT_DIR':'/input/' \
 -v 'YOUR_WORKING_DIR':'/output/' \

diff --git a/scripts/NanoCaller.py b/scripts/NanoCaller.py
@@ -126,7 +126,7 @@ def run(args):
                 os.remove('%s.phased.bam' %snp_vcf)
 
             print('%s: Post processing' %(str(datetime.datetime.now())),flush=True)
-            run_cmd('samtools faidx %s %s>%s/%s.fa' %(args.ref,args.chrom,args.output,args.chrom))
+            run_cmd('samtools faidx %s %s > %s/%s.fa' %(args.ref,args.chrom,args.output,args.chrom))
 
             if os.path.exists('%s/ref.sdf' %args.output):
                 if os.path.isdir('%s/ref.sdf' %args.output):

diff --git a/scripts/NanoCaller_WGS.py b/scripts/NanoCaller_WGS.py
@@ -123,7 +123,12 @@
 
             dirname = os.path.dirname(__file__)
 
-            chr_end=chrom_lengths[chrom]
+            try:
+               chr_end=chrom_lengths[chrom]
+
+            except KeyError:
+               print('Contig %s not found in reference' %chrom,flush=True)
+               continue
             for mbase in range(1,chr_end,10000000):
                 out_path=os.path.join(args.output, 'intermediate_files', '%s_%d_%d' %(chrom, mbase, min(chr_end,mbase+10000000-1)))
                 wg_commands.write('python %s -chrom %s %s -cpu 1 --output %s -start %d -end %d -prefix %s_%d_%d\n' %(os.path.join(dirname,'NanoCaller.py'), chrom, cmd, out_path ,mbase, min(chr_end,mbase+10000000-1),chrom, mbase, min(chr_end,mbase+10000000-1)))