def main_align(args, stdout, stderr) :
if args.outDir is None :
args.outDir = "."
for fastaFile in args.input :
pyalign.ungapFastaFile(fastaFile, fastaFile + ".ungap.tmp")
pyalign.runMafft(fastaFile + ".ungap.tmp", fastaFile + ".tmp", args.nthreads)
out = os.path.join(args.outDir, os.path.basename(fastaFile))
os.rename(fastaFile + ".tmp", out)
os.remove(fastaFile + ".ungap.tmp")
def main_ungap(args, stdout, stderr) :
if args.all :
assert args.position is None and args.seq is None and args.syncNtDir is None
for inputFile in args.input :
stderr.write("Processing file " + inputFile + "\n")
outFile = os.path.join(args.outDir, inputFile)
pyalign.ungapFastaFile(inputFile, outFile)
if args.position is not None or args.seq is not None :
if args.position is None :
args.position = 1
if args.seq is None :
args.seq = 0
for inputFile in args.input :
stderr.write("Processing file " + inputFile + "\n")
if args.outDir is None :
outFile = inputFile
else :
outFile = os.path.join(args.outDir, os.path.basename(inputFile))
try :
inputAln = AlignIO.read(inputFile, "fasta")
loaded = True
except ValueError :
loaded = False
if args.outDir == "." :
os.remove(outFile)
if loaded :
ungapResult = pyalign.ungapAln(inputAln, args.position, args.seq)
outputAln = ungapResult["ungappedAln"]
with open(outFile, "w") as fo :
for seq in outputAln :
fo.write(">" + seq.description + "\n")
fo.write(str(seq.seq) + "\n")
if args.syncNtDir is not None :
ntFile = os.path.join(args.syncNtDir,
os.path.basename(inputFile) + ".alnNt")
pyalign.ungapNtAlnFile(ntFile, ungapResult["removedSeq"],
ungapResult["removedPos"], ntFile)
def test_gapInSeqs_000(self) :
mod.ungapFastaFile(tf("inputFile3.fa"), tf("_testFile3.fa"))
self.assertFileEqual(tf("_testFile3.fa"), tf("outputFile3.fa"))
def test_noGap_000(self) :
mod.ungapFastaFile(tf("inputFile1.fa"), tf("_testFile1.fa"))
self.assertFileEqual(tf("_testFile1.fa"), tf("outputFile1.fa"))