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fasta.py
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fasta.py
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#!/usr/bin/env python
'''
What is a FASTA format file/string?
This module follows the NCBI conventions: http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
'''
import cStringIO
import re
import math
TEST_FASTA = {'GOOD_TEST': '''>ns|id|a long description
CTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGA
CTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGA
''',
'LONG_TEST': '''>ns|id|a long description
CTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGA
CTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGA
>ns|id2|a long description
CTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGA
CTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGA
''',
'BLANK_IN_TEST': '''>ns|id|a long description
CTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGA
CTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGA
''',
'BLANK_START_TEST': '''
>ns|id|a long description
CTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGA
CTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGA
''',
'DATA_START_TEST': '''CTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGA
>ns|id|a long description
CTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGA
CTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGA
''',
'TWO_NAMELINES_TEST': '''>ns|id|a long description
>ns|id2|a long description
CTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGA
CTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGA
''',
'TRAILING_NAMELINE_TEST': '''>ns|id|a long description
CTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGA
CTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGA
>ns|id2|a long description
'''}
def test():
import traceback, StringIO
for name, testFasta in TEST_FASTA.items():
try:
print
print name
print 'non-strict'
for lines in readFastaLines(StringIO.StringIO(testFasta), strict=False):
print lines
print 'non-strict, all'
for lines in readFastaLines(StringIO.StringIO(testFasta), strict=False, goodOnly=False):
print lines
print 'strict'
for lines in readFastaLines(StringIO.StringIO(testFasta)):
print lines
print 'readFasta'
for lines in readFasta(StringIO.StringIO(testFasta)):
print lines
except Exception:
traceback.print_exc()
def idFromName(line):
'''
line: a fasta nameline
returns: an id parsed from the fasta nameline. The id is the first whitespace separated token after an optional namespace, etc. See the examples below.
This covers a lot of cases that a sane person would put on a nameline. So needless to say it covers very few cases.
Examples in the form nameline => return value:
id => id
id desc => id
>id => id
>id desc => id
>ns|id => id
>ns|id desc => id
>ns|id| => id
>ns|id|desc => id
ns|id => id
ns|id desc => id
ns|id| => id
ns|id|desc => id
ns|id blah|desc => id
Example namelines not covered:
JGI-PSF GENOMES ftp://ftp.jgi-psf.org/pub/JGI_data/Nematostella_vectensis/v1.0/annotation/proteins.Nemve1FilteredModels1.fasta.gz
>jgi|Nemve1|18|gw.48.1.1
>jgi|Nemve1|248885|estExt_fgenesh1_pg.C_76820001
'''
# This could probably be done with one regex, but I am too stupid and this way I can read it.
# remove the leading '>' if there is one.
if line.startswith('>'):
line = line[1:]
# keep only everything after the first pipe. will keep everything if there is no first pipe.
pipe = line.find('|')
if pipe > -1:
line = line[line.find('|')+1:]
# keep everything before the second pipe. will keep everything if there is no second pipe.
pipe = line.find('|')
if pipe > -1:
line = line[:pipe]
# return the first token as the id.
return line.split()[0]
def prettySeq(seq, n=60):
'''
seq: one long bare (no nameline) sequence. e.g. MASNTVSAQGGSNRPVRDFSNIQDVAQFLLFDPIWNEQPGSIVPWKMNREQALAERYPELQTSEPSEDYSGPVESLELLPLEIKLDIMQYLSWEQISWCKHPWLWTRWYKDNVVRVSAITFED
n: maximum length of sequence lines
returns: seq split over multiple lines, all terminated by newlines.
'''
if len(seq) == 0:
raise Exception('zero-length sequence', seq)
seq = ''.join(seq.strip().split())
chunks = int(math.ceil(len(seq)/float(n)))
pretty = ''
for i in range(chunks):
pretty += seq[i*n:(i+1)*n] + '\n'
return pretty
def numSeqsInFastaDb(path):
num = 0
with open(path) as fh:
for line in fh:
if line.startswith('>'):
num += 1
return num
def readIds(fastaFile, strict=True):
'''
fastaFile: a file-like object or a path to a fasta file
yields: id in each nameline.
'''
for nameline in readNamelines(fastaFile, strict):
yield idFromName(nameline)
def readNamelines(fastaFile, strict=True):
'''
fastaFile: a file-like object or a path to a fasta file
yields: each nameline
'''
for nameline, seq in readFasta(fastaFile, strict):
yield nameline
def readFasta(fastaFile, strict=True):
'''
fastaFile: a file-like object or a path to a fasta file
yields: a tuple of (nameline, sequence) for each sequence in the fasta file.
'''
for lines in readFastaLines(fastaFile, strict):
nameline = lines[0].strip()
seq = ''.join((l.strip() for l in lines[1:]))
yield nameline, seq
def readFastaLines(fastaFile, strict=True, goodOnly=True, filterBlankLines=False):
'''
fastaFile: a file-like object or a path to a fasta file
yields: a seq of fasta sequence lines for each sequence in the fasta file.
the first line is the nameline. the other lines are the sequence data lines. lines include newlines.
'''
if isinstance(fastaFile, basestring):
with open(fastaFile) as fh:
for lines in _fastaSeqIter(fh, strict, goodOnly, filterBlankLines):
yield lines
else:
for lines in _fastaSeqIter(fastaFile, strict, goodOnly, filterBlankLines):
yield lines
def splitSeq(seq):
'''
seq: a well-formed fasta sequence string containing a single nameline, including '>' and sequence data lines.
returns: tuple of nameline, including '>', without a newline, and concatenated sequence lines, without newlines
e.g. ['>blahname', 'AFADFDSAFAFAFAFFAFAF']
'''
lines = seq.splitlines()
name = lines[0].strip()
chars = ''.join([l.strip() for l in lines[1:]])
return [name, chars]
def _fastaSeqIter(filehandle, strict=True, goodOnly=True, filterBlankLines=False):
'''
filehandle: file object containing fasta-formatted sequences.
strict: if True, raise an exception when a malformed fasta sequence is encountered.
A malformed sequence is a sequence with a blank line, a sequence line not preceded by a nameline, or a nameline not followed by a sequence line.
E.g. a nameline directly after a nameline, like '>foo\n>bar\nCTAGCTAGGGCA\n'
goodOnly: if True, only yield well-formed fasta sequences, ones with a nameline and one or more sequence datalines and no blank lines.
if False and strict is False, all sequences, malformed or otherwise, will be yielded. there will always be at least one (possibly blank) line.
filterBlankLines: if True, no blank lines (lines only containing whitespace) will be yielded and blank lines will not raise an exception.
Parses the filehandle, yielding one fasta sequence at a time.
yields: a seq of fasta sequence lines. the first line is the nameline. the other lines are the sequence data lines.
'''
for lines in _splitOnNamelines(filehandle, filterBlankLines):
if not lines[0] or lines[0][0] != '>':
if strict:
raise Exception('FASTA error: sequence must start with a nameline.', lines)
elif not goodOnly:
yield lines
elif len(lines) < 2:
if strict:
raise Exception('FASTA error: sequence must contain at least one sequence data line.', lines)
elif not goodOnly:
yield lines
elif '' in (line.strip() for line in lines): # contains a blank line
if strict:
raise Exception('FASTA error: blank lines not allowed')
elif not goodOnly:
yield lines
else: # a good sequence
yield lines
def _splitOnNamelines(filehandle, filterBlankLines=False):
'''
split the lines in filehandle on namelines.
yields: seq of lines, where the first line is a nameline (except if filehandle starts with a non-nameline) the other lines are lines until the next nameline
or the end of the file. lines include newlines. length of yielded seq always contains at least one line.
Said another way, the seq of lines will always contain at least one line. only the first line will ever be a nameline.
filterBlankLines: if True, no blank lines (lines only containing whitespace) will be yielded.
'''
lines = []
for line in filehandle:
if line and line[0] == '>': # a nameline
if lines:
yield lines # yield last sequence
lines = [line] # start new sequence
elif not filterBlankLines:
lines.append(line)
elif line.strip():
lines.append(line)
if lines:
yield lines
def isNameLine(line):
return line.startswith('>')
def _tern(comp, trueVal, falseVal):
''' a tawdry ternary operator '''
if comp:
return trueVal
return falseVal
def head(query, n):
'''returns the first n sequences in query.'''
count = 0
headstr = ''
for line in query.splitlines(keepends=1):
if line.startswith('>'):
count += 1
if count > n: break
headstr += line
return headstr
def dbSize(query):
'''returns the number of sequence characters'''
size = 0
for line in query.splitlines():
if isNameLine(line):
continue
size += len(line.strip())
return size
def numChars(query):
'''
synonym for dbSize(). returns the number of character (e.g. bases or residues for nucleotide or protein sequences).
'''
return dbSize(query)
def numSeqs(query):
'''
synonym for size(), whose name is a little more specific as to what is being measured: the number of sequences.
'''
return size(query)
def size(query):
'''
query: string containing fasta formatted seqeunces
returns: the number of sequences
'''
fh = cStringIO.StringIO(query)
size = numSeqsInFile(fh)
fh.close()
return size
def numSeqsInFile(file):
'''
file: file like object containing fasta formatted sequences
'''
return sum([1 for line in file if isNameLine(line.strip())])
def numSeqsInPath(path):
'''
path: path to fasta formatted db
returns: number of sequences in fasta db
'''
fh = open(path)
size = numSeqsInFile(fh)
fh.close()
return size
def main():
pass
if __name__ == '__main__':
main()
##################
# DECPRECATED CODE
##################
def fastaSeqIterOld(filehandle, strict=True):
'''
filehandle: file object containing fasta-formatted sequences.
ignoreParseError: if True, parsing ignores namelines that do not have sequence character lines. For example, '>foo\n>bar\nABCD\n'
would yield the 'bar' sequence, ignoring the 'foo' sequence that has no sequence characters associated with it.
In all cases blank lines are ignored, no matter where they occur.
Generator function yielding a string representing a single fasta sequence (name line including '>' and sequence lines)
for each fasta sequence in filehandle.
returns: a generator.
notes:
This function was modified from fastaSeqIterStrict to handle bogus fasta input like this:
>ORFP:20136 YOL048C, Contig c378 4079-4399 reverse complement
MLFKVSNFTSLTLLSLIPIVGPILANQLMAPKRTFTYLQRYFLLKGFSKKQAKDFQYEHYASFICFGMSAGLLELIPFFTIVTISSNTVGAAKWCSSLLKGERKKD*
>ORFP:18671 , Contig c238 100299-100300 reverse complement
>ORFP:20137 , Contig c378 4878-5189 reverse complement
MKVGIELISHSQTSHGTHVNSTVLAEKTPQPLEKPSKEHSISKESNINRWLKI
LRRQFDIWFPETIPTMKVRYELLKKNFIKEIFNSRAFIYPFLVSILYYLY*
The old function, even with error handling turned on, would not concatenate all the sequence characters of the 3rd sequence
since they are separated by a blank line.
'''
# states: seeking_nameline, seeking_seqline, in_seq.
state = 'seeking_nameline'
fasta = ''
for line in filehandle:
# ignore all blank lines
if not line.strip():
continue
elif state == 'seeking_nameline' and line.startswith('>'):
state = 'seeking_seqline'
fasta = line
elif state == 'seeking_nameline' and not ignoreParseError:
raise Exception('FASTA parse error. Looking for name line and found line which is neither blank nor nameline. line=%s'%line)
elif state == 'seeking_seqline' and line.startswith('>'):
if ignoreParseError:
# skip nameline without sequence and restart with this nameline.
state = 'seeking_seqline'
fasta = line
else:
raise Exception('FASTA parse error. Looking for sequence line and found name line. line=%s'%line)
elif state == 'seeking_seqline':
state = 'in_seq'
fasta += line
elif state == 'in_seq' and line.startswith('>'):
yield fasta
state = 'seeking_seqline'
fasta = line
elif state == 'in_seq':
fasta += line
else:
raise Exception('FASTA parse error. Unrecognized state. state=%s, line=%s'%(state, line))
if state == 'in_seq':
yield fasta
elif state == 'seeking_seqline' and not ignoreParseError:
raise Exception('FASTA parse error. Looking for sequence line and found end of file.')
elif state == 'seeking_nameline':
pass
else:
raise Exception('FASTA parse error. Unrecognized state found at end of file. state=%s'%state)