def make_empty_library_ini(type, microhaplotypes=False):
ini = RawConfigParser(allow_no_value=True)
ini.optionxform = str
ini.add_comment = MethodType(ini_add_comment, ini)
# Create sections and add comments to explain how to use them.
ini.add_section("genome_position")
ini.add_comment(
"genome_position", #smart, str, non-str, full
"Specify the chromosome number and positions of the first and last reported nucleotide of "
"each marker (both inclusive, using human genome build GRCh38%s). This range should not "
"include the primer binding sites.%s" %
(" and rCRS for human mtDNA" if type != "str" else "",
" This section is required for automatic configuration of markers; it is optional "
"for markers that are explictily configured in this library file."
if type != "smart" else ""))
if type != "str":
ini.add_comment(
"genome_position",
"Specify 'M' as the chromosome name for markers on mitochondrial "
"DNA. Allele names generated for these markers will follow mtDNA "
"nomenclature guidelines (Parson et al., 2014). If one of your "
"mtDNA fragments starts near the end of the reference sequence "
"and continues at the beginning, you can obtain correct base "
"numbering by specifying the fragment's genome position as \"M, "
"(starting position), 16569, 1, (ending position)\". This tells "
"FDSTools that the marker is a concatenation of two fragments, "
"where the first fragment ends at position 16569 and the second "
"fragment starts at position 1. Similarly, for a fragment that "
"spans position 3107 in the rCRS (which is nonexistent), you may "
"specify \"M, (starting position), 3106, 3108, (ending "
"position)\".")
if microhaplotypes or type == "full":
ini.add_section("microhaplotype_positions")
ini.add_comment(
"microhaplotype_positions",
"For each microhaplotype marker, specify one or more positions of SNPs that should "
"be reported as part of the microhaplotype.%s" %
(" If the [genome_position] of the marker is given, positions must be within the "
"given range. Otherwise, the reference sequence must be explicitly provided in "
"the [no_repeat] section position 1 refers to the first base in the reference "
"sequence." if type in ("non-str", "full") else ""))
ini.add_section("flanks")
ini.add_comment(
"flanks",
"The TSSV tool will use a pair of short anchor sequences just outside the reported range "
"of each marker (e.g., primer sequences) to identify which input reads correspond to "
"which marker. %s The sequence may contain IUPAC codes for ambiguous positions to account "
"for degenerate bases in the primers or for bisulfite-converted targets in methylation-"
"based studies (e.g., Y matches either C or T)." %
("Specify two comma-separated values: left flank and right flank sequence, in the same "
"sequence orientation (strand)." if type in ("str", "non-str") else
("The default length of the anchor sequences used can be specified as an argument to "
"the TSSV tool. Individual alternative lengths can be specified here for each marker. "
"Specify two comma-separated values: one for the left and one for the right flank. "
"The value can be a number (the length of sequence to use) or an explicit anchor "
"sequence to use.%s" %
(" For markers configured explicitly in this library file, the anchor sequences "
"must be specified explicitly as well." if type == "full" else "")))
)
ini.add_section("max_expected_copies")
ini.add_comment(
"max_expected_copies",
"By default, the Allelefinder tool will report up to 2 alleles per marker, but only a "
"single allele for markers %son the Y chromosome. If this is incorrect, specify the "
"maximum expected number of copies (i.e., alleles) for each marker in a "
"single-contributor reference sample here." %
("on mitochondrial DNA or " if type != "str" else ""))
ini.add_section("expected_allele_length")
ini.add_comment(
"expected_allele_length",
"Specify one or two values for each marker. The first value gives the "
"expected minimum length (in nucleotides, %sexcluding flanks) of the "
"alleles and the second value (if given) specifies the maximum allele "
"length expected for that marker (both inclusive). The TSSV tool will filter "
"sequences that have a length outside this range." %
("including prefix and suffix, " if type in ("str", "full") else ""))
if type in ("str", "full"):
ini.add_section("prefix")
ini.add_comment(
"prefix",
"For explicitly-configured STR markers: Specify the prefix sequence of each STR "
"marker. The prefix is the sequence between the left flank and the repeat and is "
"omitted from allele names. The sequence is used as the reference sequence for that "
"marker when generating allele names. Deviations from the reference are expressed as "
"variants.")
ini.add_section("suffix")
ini.add_comment(
"suffix",
"For explicitly-configured STR markers: Specify the suffix sequence of each STR "
"marker. The suffix is the sequence between the repeat and the right flank. The "
"sequence is used as the reference sequence for that marker when generating allele "
"names.")
ini.add_section("repeat")
ini.add_comment(
"repeat",
"For explicitly-configured STR markers: Specify the repeat structure of each STR "
"marker in space-separated triples of sequence, minimum number of repeats, and "
"maximum number of repeats.")
ini.add_section("length_adjust")
ini.add_comment(
"length_adjust",
"For explicitly-configured STR markers: To prevent discrepancies between traditional "
"CE allele numbers and the CE number in FDSTools allele names, the CE allele number "
"as calculated by FDSTools is based on the length of the repeat sequence minus the "
"adjustment specified here.")
ini.add_section("block_length")
ini.add_comment(
"block_length",
"For explicitly-configured STR markers: Specify the repeat unit length of each STR "
"marker. By default, the length of the repeat unit of the longest repeat is used."
)
if type in ("non-str", "full"):
ini.add_section("no_repeat")
ini.add_comment(
"no_repeat",
"For explicitly-configured non-STR markers: Specify the reference sequence for each "
"non-STR marker.")
return ini
