extend your pipeline

ChiLin is written with python and shell, it’s easy to extend to fit your need.

  • in chilin2/modules/, mkdir chilin2/modules/my_pipe && touch chilin2/modules/my_pipe/
  • write your command into chilin2/modules/my_pipe/ like following:
from samflow.command import ShellCommand
from samflow.workflow import attach_back
def tail(workflow, conf):
    tail = attach_back(workflow,
    """{tool} -50 {input[peaks]} > {output[p]}
    tool = "sort",
    input = {"peaks": conf.prefix + "_sort_peaks.narrowPeak"},
    output = {"p":conf.prefix + "_sort_peaks_tail_50.narrowPeak"},
    name = "get tail lines"))
from chilin2.modules.my_pipe import tail
#at line 349
if need_run(13):

chilin2 – utils package

separate latex template to several object

dc.bwa(workflow, conf)

Use BWA to map reads to genome, call __bwa_sam2bam to post-mapping filter :param workflow: samflow defined class :param conf: parsed config files :return: void

Keep with a stable version of MACS

dc.macs2(workflow, conf)

DC version of ceas

Time: Thu Mar 6 14:30:19 EST 2014

get enrichment ratio on union DHS, exons and promoters

import from frip module using intersectBed

This module is using 4M reads or total reads (specified by –total) to estimate fragment size through latest macs2

Test whether library is mixed by other species

samflow – utils package

class samflow.command.ShellCommand(template=None, tool=None, param={}, input=[], output=[], name='')
class samflow.workflow.Workflow(template=None, tool=None, param={}, input=[], output=[], name='')
class samflow.command.PythonCommand(template=None, tool=None, param={}, input=[], output=[], name='')