Mercurial > repos > iuc > variant_analyzer

diff mut2read.py @ 1:3556001ff2db draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 60dc8db809909edf44d662683b1f392b9d5964bf"
author iuc
date Wed, 04 Dec 2019 16:21:17 -0500
parents 8d29173d49a9
children 3f1dbd2c59bf
line wrap: on
line diff
--- a/mut2read.py	Wed Nov 20 17:47:35 2019 -0500
+++ b/mut2read.py	Wed Dec 04 16:21:17 2019 -0500
@@ -63,7 +63,7 @@
 
     # read mut file
     with open(file1, 'r') as mut:
-        mut_array = np.genfromtxt(mut, skip_header=1, delimiter='\t', comments='#', dtype='string')
+        mut_array = np.genfromtxt(mut, skip_header=1, delimiter='\t', comments='#', dtype=str)
 
     # read dcs bam file
     # pysam.index(file2)
@@ -86,7 +86,7 @@
 
         dcs_len = []
 
-        for pileupcolumn in bam.pileup(chrom.tobytes(), stop_pos - 2, stop_pos, max_depth=100000000):
+        for pileupcolumn in bam.pileup(chrom, stop_pos - 2, stop_pos, max_depth=100000000):
 
             if pileupcolumn.reference_pos == stop_pos - 1:
                 count_alt = 0