SYMBOL INDEX (43 symbols across 17 files)

FILE: scripts/TEstrainer/scripts/TEtrim.py
  function single_trim (line 34) | def single_trim(aln_in):
  function con_maker (line 43) | def con_maker(aln_in):

FILE: scripts/TEstrainer/scripts/initial_mafft_setup.py
  function file_check (line 26) | def file_check(file_name, debug):
  function size_check (line 53) | def size_check(var_name, size):
  function df_to_fasta (line 60) | def df_to_fasta(df, path, name, overwrite):
  function blast_to_bed (line 81) | def blast_to_bed(df):

FILE: scripts/TEstrainer/scripts/trf_parser.py
  function parse_args (line 5) | def parse_args():
  function main (line 17) | def main():

FILE: scripts/divergenceCalc/divergence_calc.py
  function file_check (line 36) | def file_check(repeat_library, in_gff, genome, out_gff, temp_dir):
  function splitter (line 50) | def splitter(in_seq, temp_dir):
  function parse_gff (line 58) | def parse_gff(in_gff):
  function file_name_generator (line 71) | def file_name_generator():
  function Kimura80 (line 77) | def Kimura80(qseq, sseq):
  function outer_func (line 108) | def outer_func(genome_path, temp_dir, timeoutSeconds, chunk_path):
  function tmp_out_parser (line 191) | def tmp_out_parser(file_list, simple_gff, other_gff):

FILE: scripts/extract_align.py
  function get_args (line 19) | def get_args():
  function CREATE_TE_OUTFILES (line 47) | def CREATE_TE_OUTFILES(LIBRARY):
  function EXTRACT_BLAST_HITS (line 56) | def EXTRACT_BLAST_HITS(GENOME, BLAST, LBUFFER, RBUFFER, HITNUM):
  function MUSCLE (line 88) | def MUSCLE(TOALIGN):
  function CONSENSUSGEN (line 94) | def CONSENSUSGEN(ALIGNED):
  function DIRS (line 106) | def DIRS(DIR):
  function main (line 112) | def main():

FILE: scripts/repeatCraft/helper/combineGFFoverlapm.py
  function combineGff (line 7) | def combineGff(ltrgff,column,outfile):

FILE: scripts/repeatCraft/helper/extraFuseTEm.py
  function truefusete (line 7) | def truefusete(gffp,gapsize,outfile):

FILE: scripts/repeatCraft/helper/extraTrueMergeTEm.py
  function extratruemergete (line 6) | def extratruemergete(gffp,outfile):

FILE: scripts/repeatCraft/helper/filtershortm.py
  function filtershortTE (line 3) | def filtershortTE(rmgff,m,tesize,mapfile,outfile):

FILE: scripts/repeatCraft/helper/fuseltr.py
  function fuseltr (line 7) | def fuseltr(rmgff,ltrgff_p,ltr_maxlength,ltr_flank,outfile):

FILE: scripts/repeatCraft/helper/fusetem.py
  function fusete (line 7) | def fusete(gffp,outfile,gapsize=150):

FILE: scripts/repeatCraft/helper/rcStatm.py
  function rcstat (line 4) | def rcstat(rclabelp,rmergep,outfile,ltrgroup=True):

FILE: scripts/repeatCraft/helper/reformatm.py
  function reformat (line 4) | def reformat(rmgff,rmout,outfile):

FILE: scripts/repeatCraft/helper/repeatcraftHelper.py
  function reformat (line 11) | def reformat(rmgff,rmout,outfile):
  function filtershortTE (line 49) | def filtershortTE(rmgff,m,tesize,mapfile,outfile):
  function fuseltr (line 119) | def fuseltr(rmgff,ltrgff_p,ltr_maxlength,ltr_flank,outfile):
  function fusete (line 198) | def fusete(gffp,outfile,gapsize=150):
  function combineGff (line 342) | def combineGff(ltrgff,column,outfile):
  function truefusete (line 383) | def truefusete(gffp,gapsize,outfile):
  function trumergeLTR (line 549) | def trumergeLTR(rmgff,outfile):
  function truemergete (line 661) | def truemergete(rmgff,outfile):
  function extratruemergete (line 793) | def extratruemergete(gffp,outfile):
  function rcstat (line 890) | def rcstat(rclabelp,rmergep,outfile,ltrgroup=True):

FILE: scripts/repeatCraft/helper/truemergeltrm.py
  function trumergeLTR (line 4) | def trumergeLTR(rmgff,outfile):

FILE: scripts/repeatCraft/helper/truemergeltrmErrorManagement.py
  function trumergeLTR (line 4) | def trumergeLTR(rmgff,outfile):

FILE: scripts/repeatCraft/helper/truemergetem.py
  function truemergete (line 4) | def truemergete(rmgff,outfile):