本文整理汇总了Python中IOTools.getFirstLine方法的典型用法代码示例。如果您正苦于以下问题：Python IOTools.getFirstLine方法的具体用法？Python IOTools.getFirstLine怎么用？Python IOTools.getFirstLine使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类IOTools的用法示例。
在下文中一共展示了IOTools.getFirstLine方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: checkBlastRuns
# 需要导入模块: import IOTools [as 别名]
# 或者: from IOTools import getFirstLine [as 别名]
def checkBlastRuns( infiles, outfile ):
'''check if output files are complete.
'''
outf = IOTools.openFile( outfile, "w" )
outf.write( "chunkid\tquery_first\tquery_last\tfound_first\tfound_last\tfound_total\tfound_results\thas_finished\tattempts\t%s\n" %\
"\t".join(Logfile.RuntimeInformation._fields))
for infile in infiles:
E.debug( "processing %s" % infile)
chunkid = P.snip( os.path.basename( infile ), ".blast.gz" )
logfile = infile + ".log"
chunkfile = P.snip( infile, ".blast.gz" ) + ".fasta"
with IOTools.openFile( infile ) as inf:
l = inf.readline()
ids = set()
total_results = 0
for l in inf:
if l.startswith("#//"): continue
ids.add( int(l.split("\t")[0] ) )
total_results += 1
found_first = min(ids)
found_last = max(ids)
found_total = len(ids)
l = IOTools.getFirstLine( chunkfile )
query_first = l[1:-1]
l2 = IOTools.getLastLine( chunkfile, nlines = 2).split("\n")
query_last = l2[0][1:]
logresults = Logfile.parse( logfile )
outf.write( "\t".join( map(str, (\
chunkid, query_first, query_last,
found_first, found_last,
found_total, total_results,
logresults[-1].has_finished,
len(logresults),
"\t".join( map(str, logresults[-1]) ) ) ) ) + "\n" )
outf.close()