def addIllumina(readsetfh, orgname, rundata, nembasedir, outlog):
"""Add Illumina experiments to our readset."""
index = 1
for exp in rundata.expsIllumina:
trinsetsingle = os.path.join(nembasedir, "illumina", "_trinityASM_%s" % exp, \
"assemblydir", "single", "Trinity.fasta")
trinsetpaired = os.path.join(nembasedir, "illumina", "_trinityASM_%s" % exp, \
"assemblydir", "paired", "Trinity.fasta")
oasset = os.path.join(nembasedir, "illumina", "_oasesASM_%s" % exp, \
"assemblydir", "transcripts.fa")
if not (os.path.exists(trinsetsingle) and os.path.exists(trinsetpaired) and \
os.path.exists(oasset)):
print "Warning: Experiment %s not found for %s" % (exp, orgname)
outlog.write("Warning: Experiment %s not found for %s\n" % (exp, orgname))
continue
elif os.stat(trinsetsingle)[6] == 0 and os.stat(trinsetpaired)[6] == 0:
print "Trinity assembly empty, using Oases"
for rec in fasta_itr(oasset):
rec.header = "Contig_Illumina_%s" % index
writeSeq(rec, readsetfh)
index += 1
else:
for rec in fasta_itr(trinsetsingle):
rec.header = "Contig_Illumina_%s" % index
writeSeq(rec, readsetfh)
index += 1
for rec in fasta_itr(trinsetpaired):
rec.header = "Contig_Illumina_%s" % index
writeSeq(rec, readsetfh)
index += 1
def getFromFastaByName(cf):
"""Print records where names match their header. If partial is true, check for
partial matches. names can also be a list of compiled regular expressions (or
objects that have a findall method)."""
names, status = getNames(cf, cf.get_parameter('regexp', 'boolean'))
if not status == constants.OK:
return status
fastafile = cf.get_input('fastafile')
outputfile = open(cf.get_output('outputfile'), 'w')
partial = cf.get_parameter('partial', 'boolean')
negate = cf.get_parameter('negate', 'boolean')
for rec in fasta_itr(fastafile):
found = False
for name in names:
if hasattr(name, 'findall'):
matches = name.findall(rec.header)
if len(matches) > 0:
found = True; break
elif partial and rec.header.find(name) >= 0 or \
rec.header == name:
found = True; break
if not negate and found or \
negate and not found:
outputfile.write(str(rec) + "\n")
outputfile.close()
return constants.OK
def getOverRepClusters(cf):
"""Identify over represented clusters in a fastqfile and write the cluster seed
to a file."""
fastqfile = cf.get_input('fastqfile')
resultsuc = cf.get_input('resultsuc')
resultsfa = cf.get_input('resultsfa')
percRep = cf.get_parameter('percRep', 'float')
output = cf.get_output('resultsfa')
totalSeqs = 0
fqp = FastqParser()
for rec in fqp.parse(open(fastqfile, 'rb')):
totalSeqs += 1
clusterCounts = {}
reader = csv.reader(open(resultsuc, 'rb'), quoting=csv.QUOTE_NONE, delimiter='\t')
for row in reader:
if row[0] == 'H':
if not clusterCounts.has_key(row[-1]):
clusterCounts[row[-1]] = 0
clusterCounts[row[-1]] += 1
outfh = open(output, 'wb')
for rec in fasta_itr(resultsfa):
if not clusterCounts.has_key(rec.header):
continue
clusterRep = (float(clusterCounts[rec.header]) / float(totalSeqs)) * 100
if clusterRep >= percRep:
outfh.write(str(rec) + '\n')
outfh.close()
return constants.OK
def fasta_read(file_name):
"""read the sequence from a file in fasta format"""
seq_dict = dict()
for record in fasta.fasta_itr(file_name):
header = record.header
seq_dict[header] = record.sequence
return seq_dict
def getAllData(dataFile):
allData = []
for record in fasta.fasta_itr(dataFile): #Create parallel arrays for negative sequence/headers
sequence = re.sub('[()\'\']', '', record.sequence.strip());
header = re.sub('[()\'\']', '', record.header.strip());
allData.append([header, sequence]);
return allData;
def printMIRAContigs(orgdir): """Print the assembled mira contigs to an output file.""" outputfile = os.path.join(orgdir, "contigs.fa") outfh = open(outputfile, 'w') miraasm = os.path.join(orgdir, "mira_assembly", "mira_d_results", \ "mira_out.unpadded.fasta") for rec in fasta_itr(miraasm): outfh.write(str(rec) + "\n") outfh.close()
def fasta_read(file_name): """read the sequence from a file in fasta format""" seq_dict = dict() for record in fasta.fasta_itr(file_name): header = record.header seq_dict[header] = record.sequence; return seq_dict;
def getAllData(dataFile):
allData = []
for record in fasta.fasta_itr(
dataFile): #Create parallel arrays for negative sequence/headers
sequence = re.sub('[()\'\']', '', record.sequence.strip())
header = re.sub('[()\'\']', '', record.header.strip())
allData.append([header, sequence])
return allData
def appendUnassembledReads(orgdir, asmreads): """Append the unassembled reads to the final contig file.""" outputfile = os.path.join(orgdir, "contigs.fa") outfh = open(outputfile, 'a') readfile = os.path.join(orgdir, "reads.fa") for rec in fasta_itr(readfile): if asmreads.has_key(rec.header): continue outfh.write(str(rec) + "\n") outfh.close()
def fasta_merge(cf):
"""Merge an array of fastafiles."""
outfh = open(cf.get_output("output"), "w")
fastafiles = get_array(cf, "fastafiles")
cf.write_log(str(fastafiles))
for key, fastafile in fastafiles:
for rec in fasta_itr(fastafile):
outfh.write(str(rec) + "\n")
outfh.close()
return constants.OK
def CreateNegDict(NegativeFileName): NegSequences = [] NegHeaders = [] NegativeFile = open(NegativeFileName, "r") for record in fasta.fasta_itr(NegativeFileName): #Create parallel arrays for negative sequence/headers sequence = record.sequence header = record.header NegSequences.append(sequence) NegHeaders.append(header) return NegSequences, NegHeaders;
def addESTs(readsetfh, orgname, nembasedir, outlog):
"""Add a set of ESTs to our readset."""
estset = os.path.join(nembasedir, "est", "_outputCtgSet_%s" % orgname, "output")
if not os.path.exists(estset):
outlog.write("ESTs for %s not found \n" % orgname)
return
index = 1
for rec in fasta_itr(estset):
rec.header = "Contig_EST_%s" % index
writeSeq(rec, readsetfh)
index += 1
def add454(readsetfh, orgname, rundata, nembasedir, outlog):
"""Add 454 experiments to our readset."""
index = 1
for exp in rundata.exps454:
cap3contigs = os.path.join(nembasedir, "454", "_cap3Asm_%s" % exp, "assemblydir", \
"output.cap.contigs")
cap3singlets = os.path.join(nembasedir, "454", "_cap3Asm_%s" % exp, "assemblydir", \
"output.cap.singlets")
if not (os.path.exists(cap3contigs) and os.path.exists(cap3singlets)):
print "Warning: Experiment %s not found for %s" % (exp, orgname)
outlog.write("Warning: Experiment %s not found for %s\n" % (exp, orgname))
continue
for rec in fasta_itr(cap3contigs):
rec.header = "Contig_454_%s" % index
writeSeq(rec, readsetfh)
index += 1
for rec in fasta_itr(cap3singlets):
rec.header = "Contig_454_%s" % index
writeSeq(rec, readsetfh)
index += 1
def get_seqs(f):
seqs = []
fg_gc_list = []
fg_lengths = []
stream = open(f)
for record in fasta.fasta_itr(f):
record.sequence= record.sequence.upper()
seqs.append(record)
fg_gc_list.append(GC(record.sequence))
fg_lengths.append(len(record.sequence))
stream.close()
return seqs, fg_gc_list, fg_lengths
def renameContigs(indir, outdir): """Rename the contigs in indir and write them to outdir.""" for d in os.listdir(indir): code = getSpeciesCode(d) os.mkdir(os.path.join(outdir, d)) infile = os.path.join(indir, d, "contigs.fa") outfile = os.path.join(outdir, d, "contigs.fa") outfh = open(outfile, 'w') index = 1 for rec in fasta_itr(infile): rec.header = code + "_" + str(index) index += 1 outfh.write(str(rec) + "\n") outfh.close()
#!/usr/bin/python
#
# This software is freely provided for any use.
#
# erik garrison <*****@*****.**>
import fasta
from fasta import fasta_itr
import sys
if len(sys.argv) < 3:
print "usage:", sys.argv[0], "<contig_file> <contig length cutoff>"
exit()
contig_file = sys.argv[1]
cutoff = int(sys.argv[2])
for rec in fasta_itr(contig_file):
if len(rec.sequence) > cutoff:
print rec
import re
import os
#Prepare and open files
PositiveFileName = sys.argv[1]
NegativeFileName = sys.argv[2]
PosFileBaseName = os.path.basename(PositiveFileName)
print PosFileBaseName
OutputFileName = "NON" + PosFileBaseName
print OutputFileName
PositiveFile = open(PositiveFileName, "r")
NegativeFile = open(NegativeFileName, "r")
OutputFile = open(OutputFileName, "w")
PosLengths = []
for record in fasta.fasta_itr(
PositiveFileName): #Remember lengths of positive sequences
seqLength = len(record.sequence)
PosLengths.append(seqLength)
NegSequences = []
NegHeaders = []
for record in fasta.fasta_itr(
NegativeFileName
): #Create parallel arrays for negative sequence/headers
sequence = record.sequence
header = record.header
NegSequences.append(sequence)
NegHeaders.append(header)
indexArr = []
import fasta
import sys
import random
PositiveFileName = sys.argv[1]
NegativeFileName = sys.argv[2]
OutputFileName = sys.argv[3]
#OutputFileName = PositiveFileName.lstrip("TTP_PARCLIP_ConversionSpecificity")
#OutputFileName = OutputFileName.rstrip(".txt")
#OutputFileName = "Non_TTPPARCLIP" + OutputFileName + ".txt"
PositiveFile = open(PositiveFileName, "r")
NegativeFile = open(NegativeFileName, "r")
OutputFile = open(OutputFileName, "w")
PosLengths = []
for record in fasta.fasta_itr(
PositiveFileName): #Remember lengths of positive sequences
seqLength = len(record.sequence)
PosLengths.append(seqLength)
NegSequences = []
NegHeaders = []
for record in fasta.fasta_itr(NegativeFileName):
sequence = record.sequence
header = record.header
NegSequences.append(sequence)
NegHeaders.append(header)
for number in PosLengths:
gotLength = False
seqLength = 0
import re import os #Prepare and open files PositiveFileName = sys.argv[1] NegativeFileName = sys.argv[2] PosFileBaseName = os.path.basename(PositiveFileName); print PosFileBaseName OutputFileName = "NON" + PosFileBaseName print OutputFileName; PositiveFile = open(PositiveFileName, "r") NegativeFile = open(NegativeFileName, "r") OutputFile = open(OutputFileName , "w") PosLengths = [] for record in fasta.fasta_itr(PositiveFileName): #Remember lengths of positive sequences seqLength = len(record.sequence) PosLengths.append(seqLength) NegSequences = [] NegHeaders = [] for record in fasta.fasta_itr(NegativeFileName): #Create parallel arrays for negative sequence/headers sequence = record.sequence header = record.header NegSequences.append(sequence) NegHeaders.append(header) indexArr = [] #Iterate through lengths in positive length array, picking a random negative sequence #and picking LENGTH nucleotides at random start point
import fasta
import sys
import random
PositiveFileName = sys.argv[1]
NegativeFileName = sys.argv[2]
OutputFileName = sys.argv[3];
#OutputFileName = PositiveFileName.lstrip("TTP_PARCLIP_ConversionSpecificity")
#OutputFileName = OutputFileName.rstrip(".txt")
#OutputFileName = "Non_TTPPARCLIP" + OutputFileName + ".txt"
PositiveFile = open(PositiveFileName, "r")
NegativeFile = open(NegativeFileName, "r")
OutputFile = open(OutputFileName , "w")
PosLengths = []
for record in fasta.fasta_itr(PositiveFileName): #Remember lengths of positive sequences
seqLength = len(record.sequence)
PosLengths.append(seqLength)
NegSequences = []
NegHeaders = []
for record in fasta.fasta_itr(NegativeFileName):
sequence = record.sequence
header = record.header
NegSequences.append(sequence)
NegHeaders.append(header)
for number in PosLengths:
gotLength = False
#
# erik garrison <*****@*****.**>
import fasta
from fasta import fasta_itr
import sys
if len(sys.argv) < 2:
print "usage:", sys.argv[0], "<fasta file>"
exit()
fasta_file = sys.argv[1]
print '\t'.join(["header", "length", "a", "t", "g", "c", "at", "gc", "other"])
for rec in fasta_itr(fasta_file):
l = len(rec.sequence)
a,t,g,c,at,gc,other = 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
for bp in rec.sequence:
if bp == 'A':
a += 1
elif bp == 'T':
t += 1
elif bp == 'G':
g += 1
elif bp == 'C':
c += 1
else:
other += 1
at = a + t
gc = g + c
#os.environ["HMMERDB"] += ":"+os.path.abspath(options.hmm_path)
#print os.environ["HMMERDB"]
out_fname = os.path.abspath(options.out_fname)
out_dir = os.path.dirname(out_fname)
fname = os.path.abspath(options.input_fasta)
tr = string.maketrans("gatcryswkmbdhvnGATCRYSWKMBDHVN",
"ctagyrswmkvhdbnCTAGYRSWMKVHDBN")
def rev_record(record):
return ">" + record.header + "|rev\n" + format(
record.sequence[::-1].translate(tr))
records = [rec for rec in fasta.fasta_itr(fname)]
headers = [[rec.header, len(rec.sequence)] for rec in records]
ff = open(out_fname + '.fa', 'w')
for (i, rec) in enumerate(records):
ff.write('>s' + str(i) + '\n' + format(rec.sequence) + '\n')
ff.write('>s' + str(i) + '|rev\n' +
format(rec.sequence[::-1].translate(tr)) + '\n')
ff.close()
#sys.exit(1)
# a temporary fasta file, use s(int) to easy the parsing
def parse_hmmsearch(kingdom, moltype, src):
# function to parse hmmsearch output
resu = []
parser.print_help()
sys.exit(1)
#print "%s"% os.path.abspath(options.hmm_path)
#os.environ["HMMERDB"] += ":"+os.path.abspath(options.hmm_path)
#print os.environ["HMMERDB"]
fname = os.path.abspath(options.input_fasta)
tr = string.maketrans("gatcryswkmbdhvnGATCRYSWKMBDHVN","ctagyrswmkvhdbnCTAGYRSWMKVHDBN")
def rev_record(record):
return ">"+record.header+"|rev\n"+format(record.sequence[::-1].translate(tr))
records = [rec for rec in fasta.fasta_itr(fname)]
headers = [[rec.header,len(rec.sequence)] for rec in records]
temp_fasta = tempfile.NamedTemporaryFile(delete=False)
ff = open(temp_fasta.name,'w')
for (i, rec) in enumerate(records):
ff.write('>s'+str(i)+'\n'+format(rec.sequence)+'\n')
ff.write('>s'+str(i)+'|rev\n'+format(rec.sequence[::-1].translate(tr))+'\n')
ff.close()
#sys.exit(1)
# a temporary fasta file, use s(int) to easy the parsing
def parse_hmmsearch(kingdom, moltype, src):
# function to parse hmmsearch output
resu = []
#os.environ["HMMERDB"] += ":"+os.path.abspath(options.hmm_path)
#print os.environ["HMMERDB"]
out_fname = os.path.abspath(options.out_fname)
out_dir = os.path.dirname(out_fname)
fname = os.path.abspath(options.input_fasta)
tr = string.maketrans("gatcryswkmbdhvnGATCRYSWKMBDHVN",
"ctagyrswmkvhdbnCTAGYRSWMKVHDBN")
def rev_record(record):
return ">" + record.header + "|rev\n" + format(
record.sequence[::-1].translate(tr))
records = [rec for rec in fasta.fasta_itr(fname)]
headers = [[rec.header, len(rec.sequence)] for rec in records]
ff = open(out_fname + '.fa', 'w')
for (i, rec) in enumerate(records):
ff.write('>s' + str(i) + '\n' + format(rec.sequence) + '\n')
ff.write('>s' + str(i) + '|rev\n' +
format(rec.sequence[::-1].translate(tr)) + '\n')
ff.close()
#sys.exit(1)
# a temporary fasta file, use s(int) to easy the parsing
def parse_hmmsearch(kingdom, moltype, src):
# function to parse hmmsearch output
resu = []
