I have two text file with a bunch of transcript name and their corresponding
length, it looks like this:
ERCC.txt
ERCC-00002 1061
ERCC-00003 1023
ERCC-00004 523
ERCC-00009 984
ERCC-00012 994
ERCC-00013 808
ERCC-00014 1957
ERCC-00016 844
ERCC-00017 1136
ERCC-00019 644
blast.tx
ERCC-00002 1058
ERCC-00003 1017
ERCC-00004 519
ERCC-00009 977
ERCC-00019 638
ERCC-00022 746
ERCC-00024 134
ERCC-00024 126
ERCC-00024 98
ERCC-00025 445
I want to compare the length of the transcript and see if the length in
blast.txt is at least 90% of the length in ERCC.txt for the corresponding
transcript name ( I hope I am clear!)
So I wrote the following script:
ercctranscript_size = {}
for line in open('ERCC.txt'):
columns = line.strip().split()
transcript = columns[0]
size = columns[1]
ercctranscript_size[transcript] = int(size)
unknown_transcript = open('Not_sequenced_ERCC_transcript.txt', 'w')
blast_file = open('blast.txt')
out_file = open ('out.txt', 'w')
blast_transcript = {}
blast_file.readline()
for line in blast_file:
blasttranscript = columns[0].strip()
blastsize = columns[1].strip()
blast_transcript[blasttranscript] = int(blastsize)
blastsize = blast_transcript[blasttranscript]
size = ercctranscript_size[transcript]
print size
if transcript not in blast_transcript:
unknown_transcript.write('{0}\n'.format(transcript))
else:
size = ercctranscript_size[transcript]
if blastsize >= 0.9*size:
print >> out_file, transcript, True
else:
print >> out_file, transcript, False
But I have a problem storing all size length to the value size as it is always
comes back with the last entry.
Could anyone explain to me what I am doing wrong and how I should set the
values for each dictionary? I am really new to python and this is my first
script
Thanks for your help everybody!
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