def __init__(self, alignerDir, matrixFile, gapOpenPenalty,
gapExtendPenalty):
self.alignerDir = alignerDir
self.matrixFile = matrixFile
self.gapOpen = gapOpenPenalty
self.gapExtend = gapExtendPenalty
self.fastaWriter = FastaWriter()
def save(self,fh):
writer=FastaWriter()
id=self.id
data=self.data
deflineExtra=self.deflineExtra
if(self.isDiscrete()):
writer.addToFasta(">"+id+" "+deflineExtra,data,fh)
else:
fh.write("%"+id+" "+deflineExtra+"\n")
n=len(data)
for i in range(0,n): fh.write(str(data[i])+"\n")
def save(self, fh):
writer = FastaWriter()
id = self.id
data = self.data
deflineExtra = self.deflineExtra
if (self.isDiscrete()):
writer.addToFasta(">" + id + " " + deflineExtra, data, fh)
else:
fh.write("%" + id + " " + deflineExtra + "\n")
n = len(data)
for i in range(0, n):
fh.write(str(data[i]) + "\n")
class SmithWaterman:
def __init__(self, alignerDir, matrixFile, gapOpenPenalty,
gapExtendPenalty):
self.alignerDir = alignerDir
self.matrixFile = matrixFile
self.gapOpen = gapOpenPenalty
self.gapExtend = gapExtendPenalty
self.fastaWriter = FastaWriter()
def writeFile(self, defline, seq):
filename = TempFilename.generate("fasta")
self.fastaWriter.writeFasta(defline, seq, filename)
return filename
def swapInsDel(self, cigar):
# This is done because my aligner defines insertions and deletions
# opposite to how they're defined in the SAM specification
newCigar = ""
for x in cigar:
if (x == "I"): x = "D"
elif (x == "D"): x = "I"
newCigar += x
return newCigar
def align(self, seq1, seq2):
file1 = self.writeFile("query", seq1)
file2 = self.writeFile("reference", seq2)
cmd=self.alignerDir+"/smith-waterman -q "+self.matrixFile+" "+\
str(self.gapOpen)+" "+str(self.gapExtend)+" "+file1+" "+file2+" DNA"
output = Pipe.run(cmd)
os.remove(file1)
os.remove(file2)
if (not rex.find("CIGAR=(\S+)", output)):
raise Exception("Can't parse aligner output: " + output)
cigar = rex[1]
cigar = self.swapInsDel(cigar) # because I define cigars differently
return CigarString(cigar)
#!/usr/bin/env python #========================================================================= # This is OPEN SOURCE SOFTWARE governed by the Gnu General Public # License (GPL) version 3, as described at www.opensource.org. # Copyright (C)2016 William H. Majoros ([email protected]). #========================================================================= from __future__ import (absolute_import, division, print_function, unicode_literals, generators, nested_scopes, with_statement) from builtins import (bytes, dict, int, list, object, range, str, ascii, chr, hex, input, next, oct, open, pow, round, super, filter, map, zip) import random import ProgramName import sys from FastaWriter import FastaWriter if(len(sys.argv)!=3): exit(ProgramName.get()+" <length> <id>") L=int(sys.argv[1]) id=sys.argv[2] seq="" alphabet=("A","C","G","T") for i in range(L): index=int(random.random()*4) nuc=alphabet[index] seq+=nuc writer=FastaWriter() writer.addToFasta(">"+id,seq,sys.stdout)
#!/usr/bin/env python #========================================================================= # This is OPEN SOURCE SOFTWARE governed by the Gnu General Public # License (GPL) version 3, as described at www.opensource.org. # Copyright (C)2016 William H. Majoros ([email protected]). #========================================================================= from __future__ import (absolute_import, division, print_function, unicode_literals, generators, nested_scopes, with_statement) from builtins import (bytes, dict, int, list, object, range, str, ascii, chr, hex, input, next, oct, open, pow, round, super, filter, map, zip) import random import ProgramName import sys from FastaWriter import FastaWriter if (len(sys.argv) != 3): exit(ProgramName.get() + " <length> <id>") L = int(sys.argv[1]) id = sys.argv[2] seq = "" alphabet = ("A", "C", "G", "T") for i in range(L): index = int(random.random() * 4) nuc = alphabet[index] seq += nuc writer = FastaWriter() writer.addToFasta(">" + id, seq, sys.stdout)
from FastaWriter import FastaWriter
from GffTranscriptReader import GffTranscriptReader
from Rex import Rex
rex=Rex()
# Process command line
if(len(sys.argv)!=4): exit(sys.argv[0]+" <in.fasta> <in.gff> <out.fasta>")
(fastaFile,gffFile,outFile)=sys.argv[1:]
# Read GFF
reader=GffTranscriptReader()
hash=reader.hashBySubstrate(gffFile)
# Open output file
OUT=open(outFile,"wt")
writer=FastaWriter()
# Process each substrate in the FASTA file
reader=FastaReader(fastaFile)
while(True):
[defline,seq]=reader.nextSequence()
if(not defline): break
if(not rex.find("^\s*>\s*(\S+)",defline)):
exit("Can't parse defline: "+defline)
id=rex[1]
transcripts=hash.get(id,None)
if(not transcripts): continue
for transcript in transcripts:
transSeq=transcript.loadTranscriptSeq(seq)
writer.addToFasta(">"+transcript.getID(),transSeq,OUT)
reader.close()
# The above imports should allow this program to run in both Python 2 and
# Python 3. You might need to update your version of module "future".
import sys
from FastaReader import FastaReader
from FastaWriter import FastaWriter
from GffTranscriptReader import GffTranscriptReader
if(len(sys.argv)!=4):
exit(sys.argv[0]+" <in.fasta> <in.gff> <out.fasta>")
(fastaFile,gffFile,outFile)=sys.argv[1:]
reader=GffTranscriptReader()
transcripts=reader.loadGFF(gffFile)
keep=set()
for transcript in transcripts:
if(transcript.getID()[:3]!="ALT"): continue
keep.add(transcript.getSubstrate())
reader=FastaReader(fastaFile)
writer=FastaWriter()
fh=open(outFile,"wt")
while(True):
(defline,seq)=reader.nextSequence()
if(not defline): break
(id,attr)=FastaReader.parseDefline(defline)
if(id not in keep): continue
writer.addToFasta(defline,seq,fh)
fh.close()
print("[done]",file=sys.stderr)
with_statement)
from builtins import (bytes, dict, int, list, object, range, str, ascii, chr,
hex, input, next, oct, open, pow, round, super, filter,
map, zip)
# The above imports should allow this program to run in both Python 2 and
# Python 3. You might need to update your version of module "future".
import sys
import ProgramName
from FastaReader import FastaReader
from FastaWriter import FastaWriter
from Rex import Rex
rex = Rex()
#=========================================================================
# main()
#=========================================================================
if (len(sys.argv) != 3):
exit(ProgramName.get() + " <in.fasta> <out.fasta>\n")
(infile, outfile) = sys.argv[1:]
OUT = open(outfile, "wt")
writer = FastaWriter()
reader = FastaReader(infile)
while (True):
(defline, seq) = reader.nextSequence()
if (not defline): break
if (not rex.find(">chr", defline)): continue
writer.addToFasta(defline, seq, OUT)
OUT.close()
#filename="/home/bmajoros/1000G/assembly/BRCA1-NA19782.fasta";
filename="/Users/bmajoros/python/test/data/subset.fasta"
print(FastaReader.getSize(filename))
[defline,seq]=FastaReader.firstSequence(filename)
print(len(seq))
#filename="/home/bmajoros/1000G/assembly/test.fasta"
filename="/Users/bmajoros/python/test/data/subset.fasta"
hash=FastaReader.readAllAndKeepDefs(filename)
for key in hash.keys():
[defline,seq]=hash[key]
print(defline)
[id,attrs]=FastaReader.parseDefline(defline)
print("id="+id)
for key,value in attrs.items():
print(key+"="+value)
writer=FastaWriter()
writer.writeFasta(">ABCD","ATCGATCGTAGCTAGTCTGCGCGTATCGTCAGTCTCTATCGATCGTACTGCGATCTAGCTAGCTGATCGTAGCTTCTATGACTGCTAGTCATCTAGCTAGCTGATCGTAGCTGCGCGCGATATATTGCATCTATGCTATCATTGCATGCTAGCTCTAGCTAGTCGATGCTATCTTAGCTAC","test1.fasta")
writer.appendToFasta(">XYZ","GATTACA","test1.fasta")
print(Translation.translate(seq))
print("forward:",seq)
print("revcomp: ",Translation.reverseComplement(seq))
