vjcitn
commented
5 years ago Apparently if python 2.7 is used these issues do not crop up
Closed vjcitn closed 5 years ago
vjcitn
commented
5 years ago Apparently if python 2.7 is used these issues do not crop up
trying out phaser at NHGRI Computational medicine hackation
is the example at https://stephanecastel.wordpress.com/2017/02/15/how-to-generate-ase-data-with-phaser/ known to work with current code?
################################################## Welcome to phASER v1.1.1 Author: Stephane Castel (scastel@nygenome.org) Updated by: Bishwa K. Giri (bkgiri@uncg.edu) ##################################################
Completed the check of dependencies and input files availability...
STARTED "Read backed phasing and ASE/haplotype analyses" ... DATE, TIME : 2019-06-10, 18:17:09
1. Loading heterozygous variants into intervals...
Processing sample named NA06986 using all the chromosomes ... removing blacklisted variants and processing VCF...
1b. Loading haplotypic count blacklist intervals...
Traceback (most recent call last): File "REDO/phaser/phaser/phaser.py", line 2358, in
main();
File "REDO/phaser/phaser/phaser.py", line 170, in main
parse_sample(sample_name, map_sample_column, args.bam, args.o, contig_ban)
File "REDO/phaser/phaser/phaser.py", line 235, in parse_sample
for line in raw_interval.split("\n"):
TypeError: a bytes-like object is required, not 'str'