Improve setup.

pomo-dev · Jul 26, 2016 · 30b18ed · 30b18ed
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diff --git a/.gitignore b/.gitignore
@@ -1 +1,2 @@
 build/
+cflib.egg-info/
diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
-# cflib
+# Counts file library
 
-`cflib` provides scripts to convert between fasta, VCF and counts
-files.  Counts files are used by
+This python library `cflib` provides scripts to convert between fasta,
+VCF and counts files.  Counts files are used by
 [PoMo](http://www.cibiv.at/software/iqtree/doc/Polymorphism-Aware-Models/),
 an implementation of a polymorphism-aware phylogenetic model.  We
 advice you to use PoMo implemented in
@@ -37,12 +37,18 @@ This will create a folder `cflib` which includes the library and the
 conversion scripts.  In the folder `cflib`, execute
 
 ```sh
-$ python setyp.py install --user
+$ easy_install --user .
 ```
 
 The `--user` flag is optional and tells Python to install `cflib` and
 the scripts only for this user but not system wide.
 
+If you want to uninstall `cflib`, you can `pip`
+
+```sh
+$ pip uninstall cflib
+```
+
 # Example
 
 Sample data can be found in [examples](./examples).  Assuming that
@@ -92,10 +98,10 @@ As requested, the sequence names in `example.fasta` are, e.g.,
 `example.fasta` into the counts file `example_from_fasta.cf`:
 
 ```sh
-$ ./FastaToCounts.py example.fasta example_from_fasta.cf
+$ FastaToCounts.py example.fasta example_from_fasta.cf
 ```
 
-# Conversion Scripts
+# Conversion scripts
 
 All conversion scripts can be found in the [scripts](./scripts)
 folder:
@@ -116,7 +122,10 @@ folder:
   sequence alignments with VCF files to counts format.
 
 Each script comes with its own documentation.  Please execute, e.g.,
-`./FastaToCounts.py --help`.
+
+```sh
+$ FastaToCounts.py --help
+```
 
 # Documentation
 

diff --git a/docs/_build/latex/Makefile b/docs/_build/latex/Makefile
@@ -0,0 +1,78 @@
+# Makefile for Sphinx LaTeX output
+
+ALLDOCS = $(basename $(wildcard *.tex))
+ALLPDF = $(addsuffix .pdf,$(ALLDOCS))
+ALLDVI = $(addsuffix .dvi,$(ALLDOCS))
+
+# Prefix for archive names
+ARCHIVEPRREFIX =
+# Additional LaTeX options
+LATEXOPTS =
+# format: pdf or dvi
+FMT = pdf
+
+LATEX = latex
+PDFLATEX = pdflatex
+MAKEINDEX = makeindex
+
+all: $(ALLPDF)
+all-pdf: $(ALLPDF)
+all-dvi: $(ALLDVI)
+all-ps: all-dvi
+	for f in *.dvi; do dvips $$f; done
+
+all-pdf-ja:
+	for f in *.pdf *.png *.gif *.jpg *.jpeg; do extractbb $$f; done
+	for f in *.tex; do platex -kanji=utf8 $(LATEXOPTS) $$f; done
+	for f in *.tex; do platex -kanji=utf8 $(LATEXOPTS) $$f; done
+	for f in *.tex; do platex -kanji=utf8 $(LATEXOPTS) $$f; done
+	-for f in *.idx; do mendex -U -f -d "`basename $$f .idx`.dic" -s python.ist $$f; done
+	for f in *.tex; do platex -kanji=utf8 $(LATEXOPTS) $$f; done
+	for f in *.tex; do platex -kanji=utf8 $(LATEXOPTS) $$f; done
+	for f in *.dvi; do dvipdfmx $$f; done
+
+zip: all-$(FMT)
+	mkdir $(ARCHIVEPREFIX)docs-$(FMT)
+	cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT)
+	zip -q -r -9 $(ARCHIVEPREFIX)docs-$(FMT).zip $(ARCHIVEPREFIX)docs-$(FMT)
+	rm -r $(ARCHIVEPREFIX)docs-$(FMT)
+
+tar: all-$(FMT)
+	mkdir $(ARCHIVEPREFIX)docs-$(FMT)
+	cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT)
+	tar cf $(ARCHIVEPREFIX)docs-$(FMT).tar $(ARCHIVEPREFIX)docs-$(FMT)
+	rm -r $(ARCHIVEPREFIX)docs-$(FMT)
+
+gz: tar
+	gzip -9 < $(ARCHIVEPREFIX)docs-$(FMT).tar > $(ARCHIVEPREFIX)docs-$(FMT).tar.gz
+
+bz2: tar
+	bzip2 -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar
+
+xz: tar
+	xz -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar
+
+# The number of LaTeX runs is quite conservative, but I don't expect it
+# to get run often, so the little extra time won't hurt.
+%.dvi: %.tex
+	$(LATEX) $(LATEXOPTS) '$<'
+	$(LATEX) $(LATEXOPTS) '$<'
+	$(LATEX) $(LATEXOPTS) '$<'
+	-$(MAKEINDEX) -s python.ist '$(basename $<).idx'
+	$(LATEX) $(LATEXOPTS) '$<'
+	$(LATEX) $(LATEXOPTS) '$<'
+
+%.pdf: %.tex
+	$(PDFLATEX) $(LATEXOPTS) '$<'
+	$(PDFLATEX) $(LATEXOPTS) '$<'
+	$(PDFLATEX) $(LATEXOPTS) '$<'
+	-$(MAKEINDEX) -s python.ist '$(basename $<).idx'
+	$(PDFLATEX) $(LATEXOPTS) '$<'
+	$(PDFLATEX) $(LATEXOPTS) '$<'
+
+clean:
+	rm -f *.log *.ind *.aux *.toc *.syn *.idx *.out *.ilg *.pla *.ps *.tar *.tar.gz *.tar.bz2 *.tar.xz $(ALLPDF) $(ALLDVI)
+
+.PHONY: all all-pdf all-dvi all-ps clean zip tar gz bz2 xz
+.PHONY: all-pdf-ja
+
diff --git a/docs/_build/latex/cflib.aux b/docs/_build/latex/cflib.aux
@@ -0,0 +1,184 @@
+\relax 
+\providecommand\hyper@newdestlabel[2]{}
+\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
+\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
+\global\let\oldcontentsline\contentsline
+\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
+\global\let\oldnewlabel\newlabel
+\gdef\newlabel#1#2{\newlabelxx{#1}#2}
+\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
+\AtEndDocument{\ifx\hyper@anchor\@undefined
+\let\contentsline\oldcontentsline
+\let\newlabel\oldnewlabel
+\fi}
+\fi}
+\global\let\hyper@last\relax 
+\gdef\HyperFirstAtBeginDocument#1{#1}
+\providecommand\HyField@AuxAddToFields[1]{}
+\providecommand\HyField@AuxAddToCoFields[2]{}
+\select@language{english}
+\@writefile{toc}{\select@language{english}}
+\@writefile{lof}{\select@language{english}}
+\@writefile{lot}{\select@language{english}}
+\newlabel{index::doc}{{}{1}{}{section*.2}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {1}cflib}{3}{chapter.1}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\@writefile{loliteral-block}{\addvspace {10\p@ }}
+\newlabel{index:welcome-to-the-documentation-of-cflib}{{1}{3}{cflib}{chapter.1}{}}
+\newlabel{index:cflib}{{1}{3}{cflib}{chapter.1}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {2}Contents}{5}{chapter.2}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\@writefile{loliteral-block}{\addvspace {10\p@ }}
+\newlabel{index:contents}{{2}{5}{Contents}{chapter.2}{}}
+\newlabel{main:module-libPoMo.main}{{2}{5}{Contents}{section*.3}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {2.1}libPoMo.main}{5}{section.2.1}}
+\newlabel{main:libpomo-main}{{2.1}{5}{libPoMo.main}{section.2.1}{}}
+\newlabel{main::doc}{{2.1}{5}{libPoMo.main}{section.2.1}{}}
+\newlabel{main:libPoMo.main.a}{{2.1}{5}{libPoMo.main}{section*.4}{}}
+\newlabel{main:libPoMo.main.binom}{{2.1}{5}{libPoMo.main}{section*.5}{}}
+\newlabel{main:libPoMo.main.dsRatio}{{2.1}{5}{libPoMo.main}{section*.6}{}}
+\newlabel{main:libPoMo.main.get_data_from_cf_line}{{2.1}{5}{libPoMo.main}{section*.7}{}}
+\newlabel{main:libPoMo.main.get_species_from_cf_headerline}{{2.1}{5}{libPoMo.main}{section*.8}{}}
+\newlabel{main:libPoMo.main.is_number}{{2.1}{5}{libPoMo.main}{section*.9}{}}
+\newlabel{main:libPoMo.main.mutModel}{{2.1}{5}{libPoMo.main}{section*.10}{}}
+\newlabel{main:libPoMo.main.probability_matrix}{{2.1}{5}{libPoMo.main}{section*.11}{}}
+\newlabel{main:libPoMo.main.read_data_write_HyPhy_input}{{2.1}{5}{libPoMo.main}{section*.12}{}}
+\newlabel{main:libPoMo.main.selModel}{{2.1}{6}{libPoMo.main}{section*.13}{}}
+\newlabel{main:libPoMo.main.setGM}{{2.1}{6}{libPoMo.main}{section*.14}{}}
+\newlabel{main:libPoMo.main.setGS}{{2.1}{6}{libPoMo.main}{section*.15}{}}
+\newlabel{main:libPoMo.main.timeStr}{{2.1}{6}{libPoMo.main}{section*.16}{}}
+\newlabel{seqbase:module-libPoMo.seqbase}{{2.1}{6}{libPoMo.main}{section*.17}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {2.2}libPoMo.seqbase}{6}{section.2.2}}
+\newlabel{seqbase::doc}{{2.2}{6}{libPoMo.seqbase}{section.2.2}{}}
+\newlabel{seqbase:libpomo-seqbase}{{2.2}{6}{libPoMo.seqbase}{section.2.2}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.1}Objects}{6}{subsection.2.2.1}}
+\newlabel{seqbase:objects}{{2.2.1}{6}{Objects}{subsection.2.2.1}{}}
+\newlabel{seqbase:libPoMo.seqbase.NotAValidRefBase}{{2.2.1}{7}{Objects}{section*.18}{}}
+\newlabel{seqbase:libPoMo.seqbase.Region}{{2.2.1}{7}{Objects}{section*.19}{}}
+\newlabel{seqbase:libPoMo.seqbase.Region.print_info}{{2.2.1}{7}{Objects}{section*.20}{}}
+\newlabel{seqbase:libPoMo.seqbase.Seq}{{2.2.1}{7}{Objects}{section*.21}{}}
+\newlabel{seqbase:libPoMo.seqbase.Seq.get_base}{{2.2.1}{7}{Objects}{section*.22}{}}
+\newlabel{seqbase:libPoMo.seqbase.Seq.get_exon_nr}{{2.2.1}{7}{Objects}{section*.23}{}}
+\newlabel{seqbase:libPoMo.seqbase.Seq.get_in_frame}{{2.2.1}{7}{Objects}{section*.24}{}}
+\newlabel{seqbase:libPoMo.seqbase.Seq.get_out_frame}{{2.2.1}{8}{Objects}{section*.25}{}}
+\newlabel{seqbase:libPoMo.seqbase.Seq.get_rc}{{2.2.1}{8}{Objects}{section*.26}{}}
+\newlabel{seqbase:libPoMo.seqbase.Seq.get_region}{{2.2.1}{8}{Objects}{section*.27}{}}
+\newlabel{seqbase:libPoMo.seqbase.Seq.get_region_no_description}{{2.2.1}{8}{Objects}{section*.28}{}}
+\newlabel{seqbase:libPoMo.seqbase.Seq.is_synonymous}{{2.2.1}{8}{Objects}{section*.29}{}}
+\newlabel{seqbase:libPoMo.seqbase.Seq.print_data}{{2.2.1}{9}{Objects}{section*.30}{}}
+\newlabel{seqbase:libPoMo.seqbase.Seq.print_fa_entry}{{2.2.1}{9}{Objects}{section*.31}{}}
+\newlabel{seqbase:libPoMo.seqbase.Seq.print_fa_header}{{2.2.1}{9}{Objects}{section*.32}{}}
+\newlabel{seqbase:libPoMo.seqbase.Seq.print_info}{{2.2.1}{9}{Objects}{section*.33}{}}
+\newlabel{seqbase:libPoMo.seqbase.Seq.purge}{{2.2.1}{9}{Objects}{section*.34}{}}
+\newlabel{seqbase:libPoMo.seqbase.Seq.rev_comp}{{2.2.1}{9}{Objects}{section*.35}{}}
+\newlabel{seqbase:libPoMo.seqbase.Seq.set_rc}{{2.2.1}{9}{Objects}{section*.36}{}}
+\newlabel{seqbase:libPoMo.seqbase.Seq.toggle_rc}{{2.2.1}{9}{Objects}{section*.37}{}}
+\newlabel{seqbase:libPoMo.seqbase.SequenceDataError}{{2.2.1}{9}{Objects}{section*.38}{}}
+\newlabel{seqbase:libPoMo.seqbase.gz_open}{{2.2.1}{9}{Objects}{section*.39}{}}
+\newlabel{seqbase:libPoMo.seqbase.stripFName}{{2.2.1}{9}{Objects}{section*.40}{}}
+\newlabel{fasta:module-libPoMo.fasta}{{2.2.1}{9}{Objects}{section*.41}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {2.3}libPoMo.fasta}{10}{section.2.3}}
+\newlabel{fasta::doc}{{2.3}{10}{libPoMo.fasta}{section.2.3}{}}
+\newlabel{fasta:libpomo-fasta}{{2.3}{10}{libPoMo.fasta}{section.2.3}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.1}Objects}{10}{subsection.2.3.1}}
+\newlabel{fasta:objects}{{2.3.1}{10}{Objects}{subsection.2.3.1}{}}
+\newlabel{fasta:libPoMo.fasta.FaSeq}{{2.3.1}{10}{Objects}{section*.42}{}}
+\newlabel{fasta:libPoMo.fasta.FaSeq.get_distance}{{2.3.1}{10}{Objects}{section*.43}{}}
+\newlabel{fasta:libPoMo.fasta.FaSeq.get_seq_base}{{2.3.1}{10}{Objects}{section*.44}{}}
+\newlabel{fasta:libPoMo.fasta.FaSeq.get_seq_by_id}{{2.3.1}{10}{Objects}{section*.45}{}}
+\newlabel{fasta:libPoMo.fasta.FaSeq.get_seq_names}{{2.3.1}{10}{Objects}{section*.46}{}}
+\newlabel{fasta:libPoMo.fasta.FaSeq.print_info}{{2.3.1}{10}{Objects}{section*.47}{}}
+\newlabel{fasta:libPoMo.fasta.FaStream}{{2.3.1}{10}{Objects}{section*.48}{}}
+\newlabel{fasta:libPoMo.fasta.FaStream.close}{{2.3.1}{11}{Objects}{section*.49}{}}
+\newlabel{fasta:libPoMo.fasta.FaStream.print_info}{{2.3.1}{11}{Objects}{section*.50}{}}
+\newlabel{fasta:libPoMo.fasta.FaStream.read_next_seq}{{2.3.1}{11}{Objects}{section*.51}{}}
+\newlabel{fasta:libPoMo.fasta.MFaStrFilterProps}{{2.3.1}{11}{Objects}{section*.52}{}}
+\newlabel{fasta:libPoMo.fasta.MFaStream}{{2.3.1}{12}{Objects}{section*.53}{}}
+\newlabel{fasta:libPoMo.fasta.MFaStream.close}{{2.3.1}{12}{Objects}{section*.54}{}}
+\newlabel{fasta:libPoMo.fasta.MFaStream.orient}{{2.3.1}{12}{Objects}{section*.55}{}}
+\newlabel{fasta:libPoMo.fasta.MFaStream.print_info}{{2.3.1}{12}{Objects}{section*.56}{}}
+\newlabel{fasta:libPoMo.fasta.MFaStream.print_msa}{{2.3.1}{12}{Objects}{section*.57}{}}
+\newlabel{fasta:libPoMo.fasta.MFaStream.read_next_align}{{2.3.1}{12}{Objects}{section*.58}{}}
+\newlabel{fasta:libPoMo.fasta.NotAFastaFileError}{{2.3.1}{13}{Objects}{section*.59}{}}
+\newlabel{fasta:libPoMo.fasta.filter_mfa_str}{{2.3.1}{13}{Objects}{section*.60}{}}
+\newlabel{fasta:libPoMo.fasta.init_seq}{{2.3.1}{13}{Objects}{section*.61}{}}
+\newlabel{fasta:libPoMo.fasta.open_seq}{{2.3.1}{13}{Objects}{section*.62}{}}
+\newlabel{fasta:libPoMo.fasta.read_align_from_fo}{{2.3.1}{13}{Objects}{section*.63}{}}
+\newlabel{fasta:libPoMo.fasta.read_seq_from_fo}{{2.3.1}{14}{Objects}{section*.64}{}}
+\newlabel{fasta:libPoMo.fasta.save_as_vcf}{{2.3.1}{14}{Objects}{section*.65}{}}
+\newlabel{vcf:module-libPoMo.vcf}{{2.3.1}{14}{Objects}{section*.66}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {2.4}libPoMo.vcf}{14}{section.2.4}}
+\newlabel{vcf::doc}{{2.4}{14}{libPoMo.vcf}{section.2.4}{}}
+\newlabel{vcf:libpomo-vcf}{{2.4}{14}{libPoMo.vcf}{section.2.4}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.4.1}Objects}{15}{subsection.2.4.1}}
+\newlabel{vcf:objects}{{2.4.1}{15}{Objects}{subsection.2.4.1}{}}
+\newlabel{vcf:libPoMo.vcf.NotANucBaseError}{{2.4.1}{15}{Objects}{section*.67}{}}
+\newlabel{vcf:libPoMo.vcf.NotAVariantCallFormatFileError}{{2.4.1}{15}{Objects}{section*.68}{}}
+\newlabel{vcf:libPoMo.vcf.NucBase}{{2.4.1}{15}{Objects}{section*.69}{}}
+\newlabel{vcf:libPoMo.vcf.NucBase.get_alt_base_list}{{2.4.1}{16}{Objects}{section*.70}{}}
+\newlabel{vcf:libPoMo.vcf.NucBase.get_base_ind}{{2.4.1}{16}{Objects}{section*.71}{}}
+\newlabel{vcf:libPoMo.vcf.NucBase.get_info}{{2.4.1}{16}{Objects}{section*.72}{}}
+\newlabel{vcf:libPoMo.vcf.NucBase.get_ref_base}{{2.4.1}{16}{Objects}{section*.73}{}}
+\newlabel{vcf:libPoMo.vcf.NucBase.get_speciesData}{{2.4.1}{16}{Objects}{section*.74}{}}
+\newlabel{vcf:libPoMo.vcf.NucBase.print_info}{{2.4.1}{16}{Objects}{section*.75}{}}
+\newlabel{vcf:libPoMo.vcf.NucBase.purge}{{2.4.1}{16}{Objects}{section*.76}{}}
+\newlabel{vcf:libPoMo.vcf.NucBase.set_ploidy}{{2.4.1}{16}{Objects}{section*.77}{}}
+\newlabel{vcf:libPoMo.vcf.VCFSeq}{{2.4.1}{16}{Objects}{section*.78}{}}
+\newlabel{vcf:libPoMo.vcf.VCFSeq.append_nuc_base}{{2.4.1}{16}{Objects}{section*.79}{}}
+\newlabel{vcf:libPoMo.vcf.VCFSeq.get_header_line_string}{{2.4.1}{16}{Objects}{section*.80}{}}
+\newlabel{vcf:libPoMo.vcf.VCFSeq.get_nuc_base}{{2.4.1}{17}{Objects}{section*.81}{}}
+\newlabel{vcf:libPoMo.vcf.VCFSeq.has_base}{{2.4.1}{17}{Objects}{section*.82}{}}
+\newlabel{vcf:libPoMo.vcf.VCFSeq.print_header_line}{{2.4.1}{17}{Objects}{section*.83}{}}
+\newlabel{vcf:libPoMo.vcf.VCFSeq.print_info}{{2.4.1}{17}{Objects}{section*.84}{}}
+\newlabel{vcf:libPoMo.vcf.VCFStream}{{2.4.1}{17}{Objects}{section*.85}{}}
+\newlabel{vcf:libPoMo.vcf.VCFStream.close}{{2.4.1}{17}{Objects}{section*.86}{}}
+\newlabel{vcf:libPoMo.vcf.VCFStream.print_info}{{2.4.1}{17}{Objects}{section*.87}{}}
+\newlabel{vcf:libPoMo.vcf.VCFStream.read_next_base}{{2.4.1}{17}{Objects}{section*.88}{}}
+\newlabel{vcf:libPoMo.vcf.check_fixed_field_header}{{2.4.1}{17}{Objects}{section*.89}{}}
+\newlabel{vcf:libPoMo.vcf.get_header_line_string}{{2.4.1}{18}{Objects}{section*.90}{}}
+\newlabel{vcf:libPoMo.vcf.get_indiv_from_field_header}{{2.4.1}{18}{Objects}{section*.91}{}}
+\newlabel{vcf:libPoMo.vcf.get_nuc_base_from_line}{{2.4.1}{18}{Objects}{section*.92}{}}
+\newlabel{vcf:libPoMo.vcf.init_seq}{{2.4.1}{18}{Objects}{section*.93}{}}
+\newlabel{vcf:libPoMo.vcf.open_seq}{{2.4.1}{18}{Objects}{section*.94}{}}
+\newlabel{vcf:libPoMo.vcf.update_base}{{2.4.1}{18}{Objects}{section*.95}{}}
+\newlabel{cf:module-libPoMo.cf}{{2.4.1}{18}{Objects}{section*.96}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {2.5}libPoMo.cf}{19}{section.2.5}}
+\newlabel{cf::doc}{{2.5}{19}{libPoMo.cf}{section.2.5}{}}
+\newlabel{cf:libpomo-cf}{{2.5}{19}{libPoMo.cf}{section.2.5}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.5.1}The Counts Format}{19}{subsection.2.5.1}}
+\newlabel{cf:the-counts-format}{{2.5.1}{19}{The Counts Format}{subsection.2.5.1}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.5.2}Convert to Counts Format}{19}{subsection.2.5.2}}
+\newlabel{cf:convert-to-counts-format}{{2.5.2}{19}{Convert to Counts Format}{subsection.2.5.2}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.5.3}Objects}{20}{subsection.2.5.3}}
+\newlabel{cf:objects}{{2.5.3}{20}{Objects}{subsection.2.5.3}{}}
+\newlabel{cf:libPoMo.cf.CFStream}{{2.5.3}{20}{Objects}{section*.97}{}}
+\newlabel{cf:libPoMo.cf.CFStream.read_next_pos}{{2.5.3}{20}{Objects}{section*.98}{}}
+\newlabel{cf:libPoMo.cf.CFWriter}{{2.5.3}{21}{Objects}{section*.99}{}}
+\newlabel{cf:libPoMo.cf.CFWriter.add_base_to_sequence}{{2.5.3}{22}{Objects}{section*.100}{}}
+\newlabel{cf:libPoMo.cf.CFWriter.close}{{2.5.3}{22}{Objects}{section*.101}{}}
+\newlabel{cf:libPoMo.cf.CFWriter.set_force}{{2.5.3}{22}{Objects}{section*.102}{}}
+\newlabel{cf:libPoMo.cf.CFWriter.set_offset}{{2.5.3}{22}{Objects}{section*.103}{}}
+\newlabel{cf:libPoMo.cf.CFWriter.set_ploidy}{{2.5.3}{23}{Objects}{section*.104}{}}
+\newlabel{cf:libPoMo.cf.CFWriter.set_seq}{{2.5.3}{23}{Objects}{section*.105}{}}
+\newlabel{cf:libPoMo.cf.CFWriter.write_HLn}{{2.5.3}{23}{Objects}{section*.106}{}}
+\newlabel{cf:libPoMo.cf.CFWriter.write_Ln}{{2.5.3}{23}{Objects}{section*.107}{}}
+\newlabel{cf:libPoMo.cf.CFWriter.write_Rn}{{2.5.3}{23}{Objects}{section*.108}{}}
+\newlabel{cf:libPoMo.cf.CountsFormatWriterError}{{2.5.3}{23}{Objects}{section*.109}{}}
+\newlabel{cf:libPoMo.cf.NoSynBase}{{2.5.3}{23}{Objects}{section*.110}{}}
+\newlabel{cf:libPoMo.cf.NotACountsFormatFileError}{{2.5.3}{23}{Objects}{section*.111}{}}
+\newlabel{cf:libPoMo.cf.cf_to_fasta}{{2.5.3}{23}{Objects}{section*.112}{}}
+\newlabel{cf:libPoMo.cf.faseq_append_base_of_cfS}{{2.5.3}{23}{Objects}{section*.113}{}}
+\newlabel{cf:libPoMo.cf.fasta_to_cf}{{2.5.3}{23}{Objects}{section*.114}{}}
+\newlabel{cf:libPoMo.cf.interpret_cf_line}{{2.5.3}{24}{Objects}{section*.115}{}}
+\newlabel{cf:libPoMo.cf.weighted_choice}{{2.5.3}{24}{Objects}{section*.116}{}}
+\newlabel{cf:libPoMo.cf.write_cf_from_MFaStream}{{2.5.3}{24}{Objects}{section*.117}{}}
+\newlabel{cf:libPoMo.cf.write_cf_from_gp_stream}{{2.5.3}{24}{Objects}{section*.118}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {3}Indices and tables}{25}{chapter.3}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\@writefile{loliteral-block}{\addvspace {10\p@ }}
+\newlabel{index:indices-and-tables}{{3}{25}{Indices and tables}{chapter.3}{}}
+\@writefile{toc}{\contentsline {chapter}{Python Module Index}{27}{section*.119}}
+\@writefile{toc}{\contentsline {chapter}{Index}{29}{section*.120}}