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"""Martel format for primersearch output files,
"""
import Martel
blank_line = Martel.AnyEol()
# Primer name D1S2660
primer_name = Martel.Group("primer_name",
Martel.ToEol())
primer_name_line = Martel.Str("Primer name ") + primer_name
# Amplimer 1
amplifier = Martel.Group("amplifier",
Martel.Re("[\d]+"))
amplimer_line = Martel.Str("Amplimer ") + amplifier + Martel.AnyEol()
# Sequence: AC074298 AC074298
# Telomere associated sequence for Arabidopsis thaliana TEL1N
# CCGGTTTCTCTGGTTGAAAA hits forward strand at 114 with 0 mismatches
# TCACATTCCCAAATGTAGATCG hits reverse strand at [114] with 0 mismatches
seq_indent = Martel.Str("\t")
sequence_id = Martel.Group("sequence_id",
Martel.ToEol())
sequence_descr = Martel.Group("sequence_descr",
Martel.ToEol())
sequence_info = sequence_id + sequence_descr
forward_strand_info = Martel.Group("forward_strand_info",
Martel.ToEol())
reverse_strand_info = Martel.Group("reverse_strand_info",
Martel.ToEol())
amplifier_sequence = Martel.Group("amplifier_sequence",
sequence_info +
forward_strand_info +
reverse_strand_info)
amplifier_sequence_lines = seq_indent + Martel.Str("Sequence: ") + \
amplifier_sequence
amplifier_length = Martel.Group("amplifier_length",
Martel.Re("[\d]+"))
amplifier_length_line = seq_indent + Martel.Str("Amplimer length: ") + \
amplifier_length + Martel.Str(" bp") + \
Martel.AnyEol()
record = Martel.Group("primersearch_record",
Martel.Rep1(blank_line + primer_name_line +
Martel.Rep(amplimer_line +
amplifier_sequence_lines +
amplifier_length_line)))
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