From 144bd3f40986befbbff726339bfddb4532ef3a08 Mon Sep 17 00:00:00 2001
From: Beibei Chen <beibei.chen@utsouthwestern.edu>
Date: Wed, 26 Apr 2017 09:40:17 -0500
Subject: [PATCH] modify runMEME and set default for toppeak
---
astrocyte_pkg.yml | 2 +-
workflow/scripts/runMemechip.py | 18 +++++++++---------
2 files changed, 10 insertions(+), 10 deletions(-)
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index 71ca977..398bd04 100644
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -114,7 +114,7 @@ workflow_parameters:
required: true
description: |
The number of top peaks to use for motif discovery.
-
+ default: 200
# -----------------------------------------------------------------------------
# SHINY APP CONFIGURATION
diff --git a/workflow/scripts/runMemechip.py b/workflow/scripts/runMemechip.py
index 5dddd2f..1838e17 100644
--- a/workflow/scripts/runMemechip.py
+++ b/workflow/scripts/runMemechip.py
@@ -9,7 +9,6 @@ import string
import argparse as ap
import logging
import twobitreader
-import pybedtools
import subprocess
import pandas as pd
from Bio import SeqIO
@@ -52,7 +51,7 @@ def run_wrapper(args):
def run(infile, genome, limit, output):
- infile = pybedtools.BedTool(infile)
+ infile = open(infile).readlines()
logging.debug(len(infile))
genome = twobitreader.TwoBitFile(genome)
outfile = open(output+".fa","w")
@@ -65,19 +64,20 @@ def run(infile, genome, limit, output):
rowcount += 1
#logging.debug(record)
if rowcount <=limit:
- #logging.debug(rowcount)
+ seqbuf = record.rstrip().split("\t")
try:
#logging.debug(record.chrom)
- seq = genome[record.chrom][record.start:record.stop]
+ seq = genome[seqbuf[0]][int(seqbuf[1]):int(seqbuf[2])]
except:
pass
else:
- if record.strand == "-":
- seq = rc(seq)
- if len(record.fields)>=4:
- newfa_name = record.name
+ if len(seqbuf)>=5:
+ if seqbuf[5] == "-":
+ seq = rc(seq)
+ if len(seqbuf)>=4:
+ newfa_name = seqbuf[3]
else:
- newfa_name = "_".join(record.fields)
+ newfa_name = "_".join(seqbuf)
newfa = SeqRecord(Seq(seq),newfa_name,description="")
#logging.debug(seq)
SeqIO.write(newfa,outfile,"fasta")
--
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