| Traceback (most recent call last): | |
| File "pymcjointModel.py", line 148, in <module> | |
| estimateBayesFactor(Data_and_Disp) | |
| File "pymcjointModel.py", line 135, in estimateBayesFactor | |
| H_0, H_1, H_2, H_3 = run_pymc(x_u_r1,y_u_r1,x_t_r1,y_t_r1,r_1,r_2) | |
| File "pymcjointModel.py", line 112, in run_pymc | |
| step = Metropolis() | |
| File "/usr/local/lib/python2.7/dist-packages/pymc3/step_methods/arraystep.py", line 60, in __new__ | |
| step.__init__([var], *args, **kwargs) | |
| File "/usr/local/lib/python2.7/dist-packages/pymc3/step_methods/metropolis.py", line 98, in __init__ |
| a = [1,4,5,10] | |
| cache = {} | |
| for i in a: | |
| cache[i] = 1 | |
| counter = 0 | |
| #okay khub bhalo code hoyeche | |
| def coin(x): | |
| if not x in cache: |
| DROP TABLE IF EXISTS emp; | |
| CREATE TABLE emp ( | |
| empno decimal(4,0) NOT NULL, | |
| ename varchar(10) default NULL, | |
| job varchar(9) default NULL, | |
| mgr decimal(4,0) default NULL, | |
| hiredate date default NULL, | |
| sal decimal(7,2) default NULL, | |
| comm decimal(7,2) default NULL, |
| #API created by @apfejes (Anthony Fejes) on top of my half-cooked script | |
| #python ebi_url_from_srr.py --file srr_list.txt | xargs -I {} wget {} | |
| import argparse | |
| def prepareURL(srr_name, prefix="ftp://ftp.sra.ebi.ac.uk/vol1/fastq/"): | |
| dir_1=srr_name[:6] | |
| dir_2="" | |
| url="" | |
| num_digits=sum(s.isdigit() for s in srr_name) | |
| if(num_digits == 6): |
| import argparse | |
| default_prefix = "ftp.sra.ebi.ac.uk/vol1/fastq/" | |
| ascp_prefix = "ftp.sra.ebi.ac.uk:/vol1/fastq/" | |
| default_protocol = "ftp://" | |
| default_suffix = "*.fastq.gz" | |
| default_ascp_line = "ascp -QT -l 300m -i ~/.ssh/asperaweb_id_dsa.openssh anonftp@ftp.ncbi.nlm.nih.gov:{} {}" | |
| def prepare_url(srr_name, prefix): |
SAM and BAM filtering one-liners
@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/
Please extend with additional/faster/better solutions via a pull request!
BWA mapping (using piping for minimal disk I/O)
| #!/bin/bash | |
| #################################### | |
| USAGE: bash auto_sub.sh <QUEUE_LIM> <MAX_JOB_NUM> | |
| ################################### | |
| USER="$(whoami)" | |
| MAX_LIMIT=$1 | |
| MAX_JOB_NUM=$2 |