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Write error to stderr 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3514 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
weisburd 2010-06-09 17:09:10 +00:00
parent 9b2fcc4711
commit a3ccf49f5b
1 changed files with 9 additions and 7 deletions
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16
python/genomicAnnotatorScripts/MergeTwoTables.py
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@ -3,7 +3,7 @@ import os
def print_help(): def print_help():
print("\n" + os.path.split(sys.argv[0])[1] + " [file1] [file2] \n" + \ sys.stderr.write("\n" + os.path.split(sys.argv[0])[1] + " [file1] [file2] \n" + \
" Takes two tab-delimited tables and merges them, so that the output is sorted by genomic position.\n" + \ " Takes two tab-delimited tables and merges them, so that the output is sorted by genomic position.\n" + \
" Both input files must be in AnnotatorInputTable format (http://www.broadinstitute.org/gsa/wiki/index.php/GenomicAnnotator#Data_Formats),\n" + \ " Both input files must be in AnnotatorInputTable format (http://www.broadinstitute.org/gsa/wiki/index.php/GenomicAnnotator#Data_Formats),\n" + \
" and must have identical headers.\n") " and must have identical headers.\n")
@ -27,21 +27,23 @@ try:
file1 = open(sys.argv[1]) file1 = open(sys.argv[1])
header1 = read_header(file1) header1 = read_header(file1)
except Exception, e: except Exception, e:
print("ERROR: While reading header from file \"" + sys.argv[1] + "\": " + str(e)) sys.stderr.write("ERROR: While reading header from file \"" + sys.argv[1] + "\": " + str(e) + "\n")
sys.exit(0) sys.exit(0)
try: try:
file2 = open(sys.argv[2]) file2 = open(sys.argv[2])
header2 = read_header(file2) header2 = read_header(file2)
except e: except e:
print("ERROR: While reading header from file \"" + sys.argv[1] + "\": " + str(e)) sys.stderr.write("ERROR: While reading header from file \"" + sys.argv[1] + "\": " + str(e) + "\n")
sys.exit(0) sys.exit(0)
if len(header1) != len(header2):
sys.stderr.write("ERROR: The two files' headers are of different lengths: \n" + str(header1) + "\n" + str(header2) + "\n")
sys.exit(0)
if header1 != header2: if header1 != header2:
print("ERROR: The two files have different headers: \n" + str(header1) + "\n" + str(header2)) sys.stderr.write("WARNING: The two files' headers are of different lengths: \nHeader1: " + str(header1) + "\nHeader2: " + str(header2) + "\nUsing header1.\n")
sys.exit(0)
print("\t".join(header1)) print("\t".join(header1))
@ -95,7 +97,7 @@ def read_line(file_obj):
except StopIteration: except StopIteration:
return (None, None) return (None, None)
except Exception, e: except Exception, e:
print("ERROR: While reading file \"" + sys.argv[1] + "\": " + str(e)) sys.stderr.write("ERROR: While reading file \"" + sys.argv[1] + "\": " + str(e) + "\n")
sys.exit(0) sys.exit(0)