:>"^@sdZddlmZddlZddZddZdd Zd d Zdd d dZdddZ dddZ e dkre dS)z4Common utility functions for various Bio submodules.)print_functionNc CsRyt|SWn=tk rMx t|D]\}}|}q+W|dSYnXdS)a`Count the number of items in an iterable. If the argument supports len(items), and some iterators do, then this returns len(items). Otherwise it will scan over the entries in order to count them. Exhausts a generator, but doesn't require creating a full list. >>> iterlen("abcde") 5 >>> iterlen(iter("abcde")) 5 N)len TypeError enumerate)itemsixcountr //tmp/pip-build-ww9dw3qa/biopython/Bio/_utils.pyiterlens   r cCs4x-|j}| s(|r|jr|SqWdS)z?Read through whitespaces, return the first non-whitespace line.N)readlinestrip)handleliner r r read_forward's rcCsG|j|}|s!tdt||krCtd||S)aZRead the specified number of characters from the given handle. Raise a ValueError("Empty file.") if the length of data read is zero. The reason for having a separate function for the header is it enables raising an empty file error if the length of the data read is zero. This might not always be the case later in the file. z Empty file.z1Improper header, cannot read %d bytes from handle)read ValueErrorr)rlengthdatar r r _read_header1s  rcCs2t||kr.|d|t||S|S)z&Truncate the given string for display.N)r)stringmax_lenZ concat_charr r r trim_strAsr?cCsCt||r?|dk r,|t||Stt||S|S)zzReturn string of the given object's attribute. Defaults to the given fallback value if attribute is not present. N)hasattrgetattrstr)objattrfmtfallbackr r r getattr_strHs  r#cCs|s d}tjj|}xtjjtjj|drtjjtjj|drtjjtjj|dStjj|\}}||krP|}q!Wtdtjj|dS)aFind the absolute path of Biopython's Tests directory. Arguments: start_dir -- Initial directory to begin lookup (default to current dir) If the directory is not found up the filesystem's root directory, an exception will be raised. .ZBioZTestsz$Not within Biopython source tree: %rN)ospathabspathisdirjoinsplitr) start_dirtargetnewtmpr r r find_test_dirTs !!  r/c Osddl}d|ji}|j|tjjtj}tdz'tjt ||j ||Wdtj|XtddS)z%Run doctest for the importing module.rNZ optionflagszRunning doctests...Done) doctestELLIPSISupdater%r&r'curdirprintchdirr/testmod) target_dirargskwargsr1Zdefault_kwargsZcur_dirr r r run_doctestus   r;__main__) __doc__ __future__rr%r rrrr#r/r;__name__r r r r s     !