Renamed directory illumina2ftsv to illumina to gather all Illumina-relevant

scripts there. Added laydi-annot-illumina script that generates Laydi annotation files from Illumina text annotation files.
2011-01-04 11:43:24 +00:00
parent f001d12584
commit 5f1f4d0dc2
2 changed files with 96 additions and 2 deletions
@@ -0,0 +1,92 @@
+#!/usr/bin/python
+
+import getopt
+import numpy
+import sys
+
+from laydi import dataset
+
+VERSION = "0.1.0"
+
+dataset_fn = "-"
+
+def print_help():
+    print "illumina2ftsv %s" % VERSION
+    print 
+    print "Usage: illumina2ftsv [options] <illumina_genome_studio_file>"
+    print
+
+
+def parse_options():
+    s_opts = "d:h"
+    l_opts = ["dataset", "help"]
+
+    options, params = getopt.getopt(sys.argv[1:], s_opts, l_opts)
+
+    for opt, val in options:
+        if opt in ["-d", "--dataset"]:
+            global dataset_fn
+            dataset_fn = val
+        elif opt in ["-h", "--help"]:
+            print_help()
+            sys.exit(0)
+
+    if len(params) != 1:
+        print_help()
+        sys.exit(1)
+
+    return params
+
+def read_illumina_file(fn):
+    fd = open(fn)
+    line = fd.readline()
+    if line.strip() != "Illumina Inc. GenomeStudio version 1.7.0":
+        raise Exception("File cannot be recognized as Illumina textual data")
+
+    headers = {}
+    line= fd.readline()
+    while line.strip() != "":
+        key, val = line.split("=", 1)
+        headers[key.strip()] = val.strip()
+        line = fd.readline()
+    
+    col_headers = fd.readline().split('\t')
+    
+    values = []
+    line = fd.readline()
+    while line != "":
+        values.append([x.strip() for x in line.split('\t')])
+        line = fd.readline()
+
+    probe_col = col_headers.index("ProbeID")
+    print "probe id column:"   
+
+    header_cols = []
+    samples = []
+    for i, colname in enumerate(col_headers):
+        if colname.startswith("AVG_Signal-"):
+            header_cols.append(i)
+            samples.append(colname.split("-", 1)[1])
+
+    print header_cols
+    print samples
+
+    a = numpy.array(values)
+    m = numpy.array(a[:,header_cols], dtype='d')
+    print m
+    
+    probe_ids = list(a[:, probe_col])
+
+    print "samples: ", len(samples)
+    print "probe_ids: ", len(probe_ids)
+    print "shape: ", m.shape
+
+    ds = dataset.Dataset(m.transpose(), [('samples', samples), ('probe-ids', probe_ids)], name="Average Expr.")
+    dataset.write_ftsv("test.ftsv", ds)
+
+if __name__ == '__main__':
+    
+    fn = parse_options()[0]
+    read_illumina_file(fn)
+
+