Merge pull request #135 from jbelyeu/master

allow csi index for annotation files

Author: ryanlayer

samplot/__init__.py

@@ -1,2 +1,2 @@
 #!/usr/bin/env python
-__version__ = "1.1.5"
+__version__ = "1.1.6"

samplot/samplot.py

@@ -182,7 +182,12 @@ def get_tabix_iter(chrm, start, end, datafile):
     Used to avoid chrX vs. X notation issues when extracting data from
     annotation files
     """
-    tbx = pysam.TabixFile(datafile)
+    try:
+        tbx = pysam.TabixFile(datafile)
+    except:
+        tbx = pysam.TabixFile(datafile, index=datafile+".csi")
+
+
     itr = None
     try:
         itr = tbx.fetch(chrm, max(0, start - 1000), end + 1000)
@@ -2212,7 +2217,9 @@ def gff_file(transcript_file):
 
         idx_file = transcript_file + ".tbi"
         if not os.path.isfile(idx_file):
-            parser.error("transcript file {} is missing .tbi index file".format(transcript_file))
+            idx_file = transcript_file + ".csi"
+            if not os.path.isfile(idx_file):
+                parser.error("transcript file {} is missing .tbi/.csi index file".format(transcript_file))
         return transcript_file
 
     parser.add_argument(
@@ -2250,7 +2257,9 @@ def bed_file(annotation_file):
 
         idx_file = annotation_file + ".tbi"
         if not os.path.isfile(idx_file):
-            parser.error("annotation file {} is missing .tbi index file".format(annotation_file))
+            idx_file = annotation_file + ".csi"
+            if not os.path.isfile(idx_file):
+                parser.error("annotation file {} is missing .tbi index file".format(annotation_file))
         return annotation_file
 
     parser.add_argument(

test/data/Alu.2_X.csionly.bed.gz

@@ -541,4 +541,25 @@ if [ $translocation ]; then
     assert_no_stderr
 fi
 
+
+out_file_name=$func_path"csi-annotation.png"
+bam=$data_path"2_59305747-59505747_X_151018513-151218513.BND.bam"
+run translocation \
+    samplot plot\
+        -c $sv_chrm_1 -s $sv_start_1 -e $sv_end_1 \
+        -c $sv_chrm_2 -s $sv_start_2 -e $sv_end_2 \
+        -b $bam \
+        -o $out_file_name \
+        -t $sv_type \
+        -A $data_path"Alu.2_X.csionly.bed.gz" \
+        -T $data_path"Homo_sapiens.GRCh37.csionly.2_X.gff3.gz" \
+        --zoom 10000
+if [ $translocation ]; then
+    assert_exit_code 0
+    assert_equal $out_file_name $( ls $out_file_name )
+    assert_no_stdout
+    assert_no_stderr
+fi
+
+
 rm -rf $func_path"img/" ssshtest