1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
|
#!/usr/bin/env python3
import os
import logging
class DataFace(object):
""" Some data IFace bowtie can work with.
"""
def size(self):
raise NotImplementedError("size() needs to be implemented!")
class SamFile(DataFace):
def __init__(self,sam_desc):
self.file_desc = sam_desc
def size(self):
if hasattr(self,'no_frags'):
return self.no_frags
count = 0
try:
fh = open(self.file_desc,"r")
for line in fh:
if line[0] != "@":
count += 1
except:
logging.error("Exception reading sam file!")
fh.close()
raise
else:
fh.close()
self.no_frags = count
return count
class FastaQFile(DataFace):
def __init__(self,fastq_desc):
self.file_desc = fastq_desc
def size(self):
if hasattr(self,'no_seqs'):
return self.no_seqs
count = 0
try:
fh = open(self.file_desc,"r")
lno = 0
for line in fh:
if lno == 0:
if line[0] != '@':
raise TypeError("This does not look like a fastq file!")
count += 1
if lno == 2:
if line[0] != '+':
raise TypeError("This does not look like a fastq file!")
lno = (lno + 1) % 4
except:
logging.error("Exception reading fastq file!")
fh.close()
raise
else:
fh.close()
self.no_seqs = count
return self.no_seqs
|
