def ReadSeqs3(FileName, OnSeq, ShowProgress=True):
File = open(FileName)
if ShowProgress:
progress.InitFile(File, FileName)
Label = ""
Seq = ""
while 1:
Line = File.readline()
if len(Line) == 0:
if Seq != "":
OnSeq(Label, Seq)
if ShowProgress:
print >> sys.stderr, "\n"
return
Line = Line.strip()
if len(Line) == 0:
continue
if Line[0] == ">":
if Seq != "":
if ShowProgress:
progress.File()
if TRUNC_LABELS:
Label = Label.split()[0]
OnSeq(Label, Seq)
Label = Line[1:]
Seq = ""
else:
Seq += Line
def ReadSeqs2(FileName, ShowProgress=True):
Seqs = []
Labels = []
File = open(FileName)
if ShowProgress:
progress.InitFile(File, FileName)
while 1:
progress.File()
Line = File.readline()
if len(Line) == 0:
if ShowProgress:
print >> sys.stderr, "\n"
return Labels, Seqs
Line = Line.strip()
if len(Line) == 0:
continue
if Line[0] == ">":
Id = Line[1:]
if TRUNC_LABELS:
Id = Id.split()[0]
Labels.append(Id)
Seqs.append("")
else:
i = len(Seqs) - 1
Seqs[i] = Seqs[i] + Line
def ReadFile(argFileName, OnRecord, ShowProgress=True):
global FileName
FileName = argFileName
File = open(FileName)
if ShowProgress:
progress.InitFile(File, FileName)
while GetRec(File, OnRecord):
if ShowProgress:
progress.File()
if ShowProgress:
progress.FileDone()