93 lines
2.1 KiB
Python
93 lines
2.1 KiB
Python
#!/usr/bin/python
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import getopt
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import numpy
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import sys
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from laydi import dataset
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VERSION = "0.1.0"
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dataset_fn = "-"
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def print_help():
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print "illumina2ftsv %s" % VERSION
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print
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print "Usage: illumina2ftsv [options] <illumina_genome_studio_file>"
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print
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def parse_options():
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s_opts = "d:h"
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l_opts = ["dataset", "help"]
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options, params = getopt.getopt(sys.argv[1:], s_opts, l_opts)
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for opt, val in options:
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if opt in ["-d", "--dataset"]:
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global dataset_fn
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dataset_fn = val
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elif opt in ["-h", "--help"]:
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print_help()
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sys.exit(0)
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if len(params) != 1:
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print_help()
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sys.exit(1)
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return params
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def read_illumina_file(fn):
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fd = open(fn)
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line = fd.readline()
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if line.strip() != "Illumina Inc. GenomeStudio version 1.7.0":
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raise Exception("File cannot be recognized as Illumina textual data")
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headers = {}
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line= fd.readline()
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while line.strip() != "":
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key, val = line.split("=", 1)
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headers[key.strip()] = val.strip()
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line = fd.readline()
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col_headers = fd.readline().split('\t')
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values = []
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line = fd.readline()
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while line != "":
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values.append([x.strip() for x in line.split('\t')])
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line = fd.readline()
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probe_col = col_headers.index("ProbeID")
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print "probe id column:"
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header_cols = []
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samples = []
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for i, colname in enumerate(col_headers):
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if colname.startswith("AVG_Signal-"):
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header_cols.append(i)
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samples.append(colname.split("-", 1)[1])
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print header_cols
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print samples
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a = numpy.array(values)
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m = numpy.array(a[:,header_cols], dtype='d')
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print m
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probe_ids = list(a[:, probe_col])
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print "samples: ", len(samples)
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print "probe_ids: ", len(probe_ids)
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print "shape: ", m.shape
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ds = dataset.Dataset(m.transpose(), [('samples', samples), ('probe-ids', probe_ids)], name="Average Expr.")
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dataset.write_ftsv("test.ftsv", ds)
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if __name__ == '__main__':
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fn = parse_options()[0]
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read_illumina_file(fn)
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