diff --git a/bin/preprocess_dataset b/bin/preprocess_dataset
index f13be0a..b14954e 100755
--- a/bin/preprocess_dataset
+++ b/bin/preprocess_dataset
@@ -29,7 +29,7 @@ def parseArguments(args):
description="""Prepare a CLIP-Seq dataset in BED format for the training of an ssHMM. The following preprocessing steps are taken:
1 - Filter (positive) BED file, 2 - Shuffle (positive) BED file to generate negative dataset, 3 - Elongate positive and negative BED files for later structure prediction, 4 - Fetch genomic sequences for elongated BED files, 5 - Produce FASTA files with genomic sequences in viewpoint format, 6 - Calculate RNA shapes, 7 - Calculate RNA structures
-This script requires awk, bedtools (shuffle, slop, getfasta), RNAshapes, and RNAstructures.
+This script requires bedtools (shuffle, slop, getfasta), RNAshapes, and RNAstructures.
A root directory for the datasets and a dataset name (e.g., the protein name) has to be given. The following files will be created in the root directory and its subdirectories:
- /bed/<dataset_name>/positive_raw.bed - positive BED file from CLIP-Seq experiment
@@ -90,12 +90,6 @@ def checkPrereqs():
# Something else went wrong while trying to run `bedtools`
raise
- try:
- check_call(["which", "awk"], stdout=devnull, stderr=devnull)
- except CalledProcessError as e:
- print>>sys.stderr, "ERROR: awk not found. Tried to execute 'which awk'."
- return False
-
try:
check_call(["RNAshapes", "-v"], stdout=devnull, stderr=devnull)
except OSError as e:
@@ -107,15 +101,11 @@ def checkPrereqs():
raise
try:
- check_call(["Fold", "-v"], stdout=devnull, stderr=devnull)
- check_call(["ct2dot", "-v"], stdout=devnull, stderr=devnull)
- except OSError as e:
- if e.errno == os.errno.ENOENT:
- print>>sys.stderr, "ERROR: RNAstructures not found. Tried to execute 'Fold -v' and 'ct2dot -v'."
- return False
- else:
- # Something else went wrong while trying to run `RNAstructures`
- raise
+ check_call(["which", "Fold"], stdout=devnull, stderr=devnull)
+ check_call(["which", "ct2dot"], stdout=devnull, stderr=devnull)
+ except CalledProcessError:
+ print>>sys.stderr, "ERROR: RNAstructure not found. Tried to execute 'which Fold' and 'which ct2dot'."
+ return False
return True
@@ -140,11 +130,19 @@ def filteringBed(filteredBedFileName, rawBedFileName, lowest_score, min_length,
print>>sys.stderr, 'INPUT:', rawBedFileName
print>>sys.stderr, 'OUTPUT:', filteredBedFileName
- filteredBedFile = open(filteredBedFileName, 'w')
+ rawBed = open(rawBedFileName, 'r')
+ filteredBed = open(filteredBedFileName, 'w')
+ num_filtered = 0
+ for line in rawBed:
+ fields = line.strip().split()
+ siteLength = int(fields[2]) - int(fields[1])
+ if siteLength <= max_length and siteLength >= min_length and float(fields[4]) >= lowest_score:
+ print>>filteredBed, line.strip()
+ num_filtered += 1
+
#filter for max length, min length, and min score
- call(['awk', '{{if ($3-$2 <= {0} && $3-$2 >= {1} && $5 >= {2}) {{print $0}}}}'.format(max_length, min_length, lowest_score), rawBedFileName], stdout=filteredBedFile)
- filteredBedFile.close()
- num_filtered = sum(1 for line in open(filteredBedFileName))
+ rawBed.close()
+ filteredBed.close()
print>>sys.stderr, 'STEP 1 finished (filtering resulted in {0} good binding sites)'.format(num_filtered)
@@ -239,7 +237,7 @@ def formatFasta(fastaFormattedFileName, bedIntervalFileName, bedIntervalLongFile
def main(args):
options = parseArguments(args)
- #Check required programs bedtools, awk, RNAshapes, and RNAstructures
+ #Check required programs bedtools, RNAshapes, and RNAstructures
if not checkPrereqs():
return