argparse 在调用脚本时有效,但在合并到新脚本时无效
argparse works when calling script but not when incorporated to new script
这是我的基本问题:
我有以下内容:
文件名:parseFastq.py
执行:通过命令行
代码 运行 它:python3 parseFastq.py --fastq /Users/remaining_dir/test1.fastq
此代码有效!!!
但是,当我复制 parseFastq.py 的组件时,出现了问题。
代码如下:
Class 是第一个定义的...这部分有效并且 运行 在我的新脚本上没问题。
import argparse
import gzip
#Example use is
# python parseFastq.py --fastq /Users/remaining_dir/test1.fastq
################################################
# You can use this code and put it in your own script
class ParseFastQ(object):
"""Returns a read-by-read fastQ parser analogous to file.readline()"""
def __init__(self,filePath,headerSymbols=['@','+']):
"""Returns a read-by-read fastQ parser analogous to file.readline().
Exmpl: parser.__next__()
-OR-
Its an iterator so you can do:
for rec in parser:
... do something with rec ...
rec is tuple: (seqHeader,seqStr,qualHeader,qualStr)
"""
if filePath.endswith('.gz'):
self._file = gzip.open(filePath)
else:
self._file = open(filePath, 'rU')
self._currentLineNumber = 0
self._hdSyms = headerSymbols
def __iter__(self):
return self
def __next__(self):
"""Reads in next element, parses, and does minimal verification.
Returns: tuple: (seqHeader,seqStr,qualHeader,qualStr)"""
# ++++ Get Next Four Lines ++++
elemList = []
for i in range(4):
line = self._file.readline()
self._currentLineNumber += 1 ## increment file position
if line:
elemList.append(line.strip('\n'))
else:
elemList.append(None)
# ++++ Check Lines For Expected Form ++++
trues = [bool(x) for x in elemList].count(True)
nones = elemList.count(None)
# -- Check for acceptable end of file --
if nones == 4:
raise StopIteration
# -- Make sure we got 4 full lines of data --
assert trues == 4,\
"** ERROR: It looks like I encountered a premature EOF or empty line.\n\
Please check FastQ file near line number %s (plus or minus ~4 lines) and try again**" % (self._currentLineNumber)
# -- Make sure we are in the correct "register" --
assert elemList[0].startswith(self._hdSyms[0]),\
"** ERROR: The 1st line in fastq element does not start with '%s'.\n\
Please check FastQ file near line number %s (plus or minus ~4 lines) and try again**" % (self._hdSyms[0],self._currentLineNumber)
assert elemList[2].startswith(self._hdSyms[1]),\
"** ERROR: The 3rd line in fastq element does not start with '%s'.\n\
Please check FastQ file near line number %s (plus or minus ~4 lines) and try again**" % (self._hdSyms[1],self._currentLineNumber)
# -- Make sure the seq line and qual line have equal lengths --
assert len(elemList[1]) == len(elemList[3]), "** ERROR: The length of Sequence data and Quality data of the last record aren't equal.\n\
Please check FastQ file near line number %s (plus or minus ~4 lines) and try again**" % (self._currentLineNumber)
# ++++ Return fatsQ data as tuple ++++
return tuple(elemList)
##########################################################################
这是在同一个脚本中调用时不起作用的代码;它与将碎片放入有关:
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='Process fasq files and seperaate into 4 categories')
parser.add_argument("-f", "--fastq", required=True, help="Place fastq inside here")
args = parser.parse_args()
fastqfile = ParseFastQ(args.fastq)
我尝试了以下方法,但我无法获得 fastqfile,它应该包含一个包含以下内容的元组:(seqHeader,seqStr,qualHeader,qualStr)
尝试:
parser.add_argument("-/Users/remaining_dir/test1.fastq", "--fastq", required=True, help="Place fastq inside here")
错误:
argument -/Users/remaining_dir/test1.fastq/--fastq: conflicting option string: --fastq
尝试:
parser.add_argument("-/Users/remaining_dir/test1.fastq", "-@", required=True, help="Place fastq inside here")
输出[332]:
_StoreAction(option_strings=['-/Users/remaining_dir/test1.fastq', '-@'], dest='/Users/remaining_dir/test1.fastq', nargs=None, const=None, default=None, type=None, choices=None, help='Place fastq inside here', metavar=None)
下一行:
错误:
usage: [-h] -/Users/remaining_dir/test1.fastq
/USERS/REMAINING_DIR/TEST1.FASTQ
: error: the following arguments are required: -/Users/remaining_dir/test1.fastq/-@
An exception has occurred, use %tb to see the full traceback.
SystemExit: 2
when %tb selected the following info was give:
File "/Users/brownbear/opt/anaconda3/lib/python3.7/argparse.py", line 2508, in error
self.exit(2, _('%(prog)s: error: %(message)s\n') % args)
File "/Users/brownbear/opt/anaconda3/lib/python3.7/argparse.py", line 2495, in exit
_sys.exit(status)
如果有帮助,我将提供一些示例 fastq 数据
@seq13534-419
GCAGTAGCGGTCATAAGTGGTACATTACGAGATTCGGAGTACCATAGATTCGCATGAATCCCTGTGGATACGAGAGTGTGAGATATATGTACGCCAATCCAGTGTGATACCCATGAGATTTAGGACCGATGATGGTTGAGGACCAAGGATTGACCCGATGGATGCAGATTTGACCCCAGATAGAATAAATGCGATGAGATGATTTGGCCGATAGATAGATAGTGTCGTGAGGTGACGTCCGTCACTGGACGAA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFDFFDFFDDFDFDFFFFDDFFDDFDDFF
@seq86249-867
GGATTAGCGGTCATAAGTCGTACATTACGAGATTCGGAGTACCATAGATTCGCATGAATCCCTGTGGATACGAGAGTGTGAGATATATGTACGCCAATCCAGTGTGATACCCATGAGATTTAGGACCGATGATGGTTGAGGACCAAGGATTGACCCGATGGATGCAGATTTGACCCCAGATAGAATAAATGCGATGAGATGATTTGGCCGATAGATAGATAGAGGTCAGTATAACCTCTCAAAGCTTTATCTACGGATGGATCCGCGC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDDFDDDDDDFFDFDDFDDDFDFFDDFFFFFFFFFDDFDFFDDFDDF
@seq46647-928
GACCTAGCGGTCATAAGTGGTACATTACGAGATTCGGAGTACCATAGATTCGCATGAATCCCTGTGGATACGAGAGTGTGAGATATATGTACGCCAATCCAGTGTGATACCCATGAGATTTAGGACCGATGATGGTTGACGACCAAGGATTGACCCGATGGATGCAGATTTGACCCCAGATAGAATAAATGCGATGAGATGATTTGGCCGATAGATAGATAGTAAGTAAATGCCACGGACTCGTCACGTG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDDDFDFDFFFFFDFFDFDFDDDDDFDFF
任何帮助将不胜感激为什么当我 运行 脚本但现在当我尝试并入脚本
根据我的理解回答你的问题,你可以像这样简单地向解析器添加另一个参数。
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='Process fasq files and seperaate into 4
categories')
parser.add_argument("-f", "--fastq", required=True, help="Place fastq inside here")
parser.add_argument("-t", "--type", required=True, help="The type of file")
args = parser.parse_args()
print(args.fastq)
print(args.type)
然后像这样调用它。
python3 parseFastq.py --fastq /Users/remaining_dir/test1.fastq --type fastq
解决方案有两个主要部分
我试图通过 IDE (Spyder) 运行 argparse,并且 运行 仅选择代码而不是整个脚本。
对于 python 的新手和第一次使用 argparse 的人...此工具仅在从命令行调用时有效。
因此,一旦您创建了参数 table
你会运行如下L
从命令行:
python3 parseFastq.py --fastq test1.fastq
为了从初始设置中进一步分解它,您基本上是在标记您的 test1.fastq 文件,标记为 --fastq... 这很关键,如果您收到错误提示它是必需的一种特殊的格式是你必须将它们成对添加......在这个特定的例子中,你也可以用“-f”的缩写来标记。因此,它也可以是 运行 as...
从命令行:
python3 parseFastq.py -f test1.fastq
只要您的 py 脚本 运行 与您调用的文件位于同一目录中,您就不需要完整的扩展名。
这是我的基本问题:
我有以下内容: 文件名:parseFastq.py 执行:通过命令行 代码 运行 它:python3 parseFastq.py --fastq /Users/remaining_dir/test1.fastq
此代码有效!!!
但是,当我复制 parseFastq.py 的组件时,出现了问题。
代码如下:
Class 是第一个定义的...这部分有效并且 运行 在我的新脚本上没问题。
import argparse
import gzip
#Example use is
# python parseFastq.py --fastq /Users/remaining_dir/test1.fastq
################################################
# You can use this code and put it in your own script
class ParseFastQ(object):
"""Returns a read-by-read fastQ parser analogous to file.readline()"""
def __init__(self,filePath,headerSymbols=['@','+']):
"""Returns a read-by-read fastQ parser analogous to file.readline().
Exmpl: parser.__next__()
-OR-
Its an iterator so you can do:
for rec in parser:
... do something with rec ...
rec is tuple: (seqHeader,seqStr,qualHeader,qualStr)
"""
if filePath.endswith('.gz'):
self._file = gzip.open(filePath)
else:
self._file = open(filePath, 'rU')
self._currentLineNumber = 0
self._hdSyms = headerSymbols
def __iter__(self):
return self
def __next__(self):
"""Reads in next element, parses, and does minimal verification.
Returns: tuple: (seqHeader,seqStr,qualHeader,qualStr)"""
# ++++ Get Next Four Lines ++++
elemList = []
for i in range(4):
line = self._file.readline()
self._currentLineNumber += 1 ## increment file position
if line:
elemList.append(line.strip('\n'))
else:
elemList.append(None)
# ++++ Check Lines For Expected Form ++++
trues = [bool(x) for x in elemList].count(True)
nones = elemList.count(None)
# -- Check for acceptable end of file --
if nones == 4:
raise StopIteration
# -- Make sure we got 4 full lines of data --
assert trues == 4,\
"** ERROR: It looks like I encountered a premature EOF or empty line.\n\
Please check FastQ file near line number %s (plus or minus ~4 lines) and try again**" % (self._currentLineNumber)
# -- Make sure we are in the correct "register" --
assert elemList[0].startswith(self._hdSyms[0]),\
"** ERROR: The 1st line in fastq element does not start with '%s'.\n\
Please check FastQ file near line number %s (plus or minus ~4 lines) and try again**" % (self._hdSyms[0],self._currentLineNumber)
assert elemList[2].startswith(self._hdSyms[1]),\
"** ERROR: The 3rd line in fastq element does not start with '%s'.\n\
Please check FastQ file near line number %s (plus or minus ~4 lines) and try again**" % (self._hdSyms[1],self._currentLineNumber)
# -- Make sure the seq line and qual line have equal lengths --
assert len(elemList[1]) == len(elemList[3]), "** ERROR: The length of Sequence data and Quality data of the last record aren't equal.\n\
Please check FastQ file near line number %s (plus or minus ~4 lines) and try again**" % (self._currentLineNumber)
# ++++ Return fatsQ data as tuple ++++
return tuple(elemList)
##########################################################################
这是在同一个脚本中调用时不起作用的代码;它与将碎片放入有关:
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='Process fasq files and seperaate into 4 categories')
parser.add_argument("-f", "--fastq", required=True, help="Place fastq inside here")
args = parser.parse_args()
fastqfile = ParseFastQ(args.fastq)
我尝试了以下方法,但我无法获得 fastqfile,它应该包含一个包含以下内容的元组:(seqHeader,seqStr,qualHeader,qualStr)
尝试:
parser.add_argument("-/Users/remaining_dir/test1.fastq", "--fastq", required=True, help="Place fastq inside here")
错误:
argument -/Users/remaining_dir/test1.fastq/--fastq: conflicting option string: --fastq
尝试:
parser.add_argument("-/Users/remaining_dir/test1.fastq", "-@", required=True, help="Place fastq inside here")
输出[332]:
_StoreAction(option_strings=['-/Users/remaining_dir/test1.fastq', '-@'], dest='/Users/remaining_dir/test1.fastq', nargs=None, const=None, default=None, type=None, choices=None, help='Place fastq inside here', metavar=None)
下一行:
错误:
usage: [-h] -/Users/remaining_dir/test1.fastq
/USERS/REMAINING_DIR/TEST1.FASTQ
: error: the following arguments are required: -/Users/remaining_dir/test1.fastq/-@
An exception has occurred, use %tb to see the full traceback.
SystemExit: 2
when %tb selected the following info was give:
File "/Users/brownbear/opt/anaconda3/lib/python3.7/argparse.py", line 2508, in error
self.exit(2, _('%(prog)s: error: %(message)s\n') % args)
File "/Users/brownbear/opt/anaconda3/lib/python3.7/argparse.py", line 2495, in exit
_sys.exit(status)
如果有帮助,我将提供一些示例 fastq 数据
@seq13534-419
GCAGTAGCGGTCATAAGTGGTACATTACGAGATTCGGAGTACCATAGATTCGCATGAATCCCTGTGGATACGAGAGTGTGAGATATATGTACGCCAATCCAGTGTGATACCCATGAGATTTAGGACCGATGATGGTTGAGGACCAAGGATTGACCCGATGGATGCAGATTTGACCCCAGATAGAATAAATGCGATGAGATGATTTGGCCGATAGATAGATAGTGTCGTGAGGTGACGTCCGTCACTGGACGAA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFDFFDFFDDFDFDFFFFDDFFDDFDDFF
@seq86249-867
GGATTAGCGGTCATAAGTCGTACATTACGAGATTCGGAGTACCATAGATTCGCATGAATCCCTGTGGATACGAGAGTGTGAGATATATGTACGCCAATCCAGTGTGATACCCATGAGATTTAGGACCGATGATGGTTGAGGACCAAGGATTGACCCGATGGATGCAGATTTGACCCCAGATAGAATAAATGCGATGAGATGATTTGGCCGATAGATAGATAGAGGTCAGTATAACCTCTCAAAGCTTTATCTACGGATGGATCCGCGC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDDFDDDDDDFFDFDDFDDDFDFFDDFFFFFFFFFDDFDFFDDFDDF
@seq46647-928
GACCTAGCGGTCATAAGTGGTACATTACGAGATTCGGAGTACCATAGATTCGCATGAATCCCTGTGGATACGAGAGTGTGAGATATATGTACGCCAATCCAGTGTGATACCCATGAGATTTAGGACCGATGATGGTTGACGACCAAGGATTGACCCGATGGATGCAGATTTGACCCCAGATAGAATAAATGCGATGAGATGATTTGGCCGATAGATAGATAGTAAGTAAATGCCACGGACTCGTCACGTG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDDDFDFDFFFFFDFFDFDFDDDDDFDFF
任何帮助将不胜感激为什么当我 运行 脚本但现在当我尝试并入脚本
根据我的理解回答你的问题,你可以像这样简单地向解析器添加另一个参数。
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='Process fasq files and seperaate into 4
categories')
parser.add_argument("-f", "--fastq", required=True, help="Place fastq inside here")
parser.add_argument("-t", "--type", required=True, help="The type of file")
args = parser.parse_args()
print(args.fastq)
print(args.type)
然后像这样调用它。
python3 parseFastq.py --fastq /Users/remaining_dir/test1.fastq --type fastq
解决方案有两个主要部分
我试图通过 IDE (Spyder) 运行 argparse,并且 运行 仅选择代码而不是整个脚本。
对于 python 的新手和第一次使用 argparse 的人...此工具仅在从命令行调用时有效。
因此,一旦您创建了参数 table
你会运行如下L
从命令行:
python3 parseFastq.py --fastq test1.fastq
为了从初始设置中进一步分解它,您基本上是在标记您的 test1.fastq 文件,标记为 --fastq... 这很关键,如果您收到错误提示它是必需的一种特殊的格式是你必须将它们成对添加......在这个特定的例子中,你也可以用“-f”的缩写来标记。因此,它也可以是 运行 as...
从命令行:
python3 parseFastq.py -f test1.fastq
只要您的 py 脚本 运行 与您调用的文件位于同一目录中,您就不需要完整的扩展名。