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python-interface/mspy/parser_fasta.py at master · astams/python-interface · GitHub
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parser_fasta.py
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# -------------------------------------------------------------------------
# Copyright (C) 2005-2013 Martin Strohalm <www.mmass.org>
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# Complete text of GNU GPL can be found in the file LICENSE.TXT in the
# main directory of the program.
# -------------------------------------------------------------------------
# load libs
import
re
import
os
.
path
# load stopper
from
mod_stopper
import
CHECK_FORCE_QUIT
# load objects
import
obj_sequence
# compile basic patterns
spPattern
=
re
.
compile
(
'^(sp\|[A-Z][A-Z0-9]+)\|(.*)'
)
giPattern
=
re
.
compile
(
'^(gi\|[0-9]+[\.0-9]*)\|(.*)'
)
gbPattern
=
re
.
compile
(
'^(gb\|[A-Z]{3}[0-9]{5}[\.0-9]*)\|(.*)'
)
refPattern
=
re
.
compile
(
'^(ref\|[A-Z]{2}_[0-9]+[\.0-9]*)\|(.*)'
)
# PARSE FASTA SEQUENCE FILE
# -------------------------
class
parseFASTA
():
"""Parse data from FASTA."""
def
__init__
(
self
,
path
):
self
.
path
=
path
# check path
if
not
os
.
path
.
exists
(
path
):
raise
IOError
,
'File not found! --> '
+
self
.
path
# ----
def
sequences
(
self
):
"""Get sequences from document."""
# open document
try
:
document
=
file
(
self
.
path
)
rawData
=
document
.
readlines
()
document
.
close
()
except
IOError
:
return
False
# read data
reading
=
False
data
=
[]
for
line
in
rawData
:
line
=
line
.
strip
()
# discard comments and empty lines
if
not
line
or
line
[
0
]
==
';'
:
continue
# new sequence started
if
line
[
0
]
==
'>'
:
# store previous sequence
if
reading
:
try
:
sequence
=
obj_sequence
.
sequence
(
chain
,
title
=
title
,
accession
=
accession
)
data
.
append
(
sequence
)
except
:
pass
# start new sequence
title
=
line
[
1
:]
accession
=
''
chain
=
''
reading
=
True
# get accession
if
spPattern
.
match
(
title
):
match
=
spPattern
.
match
(
title
)
accession
=
match
.
group
(
1
)
title
=
match
.
group
(
2
)
elif
giPattern
.
match
(
title
):
match
=
giPattern
.
match
(
title
)
accession
=
match
.
group
(
1
)
title
=
match
.
group
(
2
)
elif
gbPattern
.
match
(
title
):
match
=
gbPattern
.
match
(
title
)
accession
=
match
.
group
(
1
)
title
=
match
.
group
(
2
)
elif
refPattern
.
match
(
title
):
match
=
refPattern
.
match
(
title
)
accession
=
match
.
group
(
1
)
title
=
match
.
group
(
2
)
# get sequence chain
elif
reading
:
for
char
in
(
'
\t
'
,
'
\n
'
,
'
\r
'
,
'
\f
'
,
'
\v
'
,
' '
,
'*'
):
line
=
line
.
replace
(
char
,
''
)
chain
+=
line
.
upper
()
# store last sequence
if
reading
:
try
:
sequence
=
obj_sequence
.
sequence
(
chain
,
title
=
title
,
accession
=
accession
)
data
.
append
(
sequence
)
except
:
pass
return
data
# ----
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