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jgi_scripts_removeasneeded
jgi_scripts_removeasneeded
 
 
oneoffs
oneoffs
 
 
rescripts
rescripts
 
 
AAI_BLASTnPARSE.py
AAI_BLASTnPARSE.py
 
 
AAI_calculate.py
AAI_calculate.py
 
 
BLASTcombinestatlists.py
BLASTcombinestatlists.py
 
 
README.md
README.md
 
 
SAGcontigeditnames.py
SAGcontigeditnames.py
 
 
SAGgeneseditnames.py
SAGgeneseditnames.py
 
 
Syn_nonsyn_sites_percodon.txt
Syn_nonsyn_sites_percodon.txt
 
 
allfasta2fastq.py
allfasta2fastq.py
 
 
analyzeBLAST.py
analyzeBLAST.py
 
 
analyzeBLAST2.py
analyzeBLAST2.py
 
 
analyze_sharedhits.py
analyze_sharedhits.py
 
 
annotateclusters.py
annotateclusters.py
 
 
batchalignandtree.py
batchalignandtree.py
 
 
bbh_fasta.py
bbh_fasta.py
 
 
blastCoverageCalc_2.py
blastCoverageCalc_2.py
 
 
blastSAGVMetas.py
blastSAGVMetas.py
 
 
blast_besthit.py
blast_besthit.py
 
 
calc_codonbias.py
calc_codonbias.py
 
 
calculateCovVals.py
calculateCovVals.py
 
 
catFASTA.py
catFASTA.py
 
 
clusterannotations.py
clusterannotations.py
 
 
clusters2fasta.py
clusters2fasta.py
 
 
combine_phylosiftout.py
combine_phylosiftout.py
 
 
compEst_makeIncompSetCluster.py
compEst_makeIncompSetCluster.py
 
 
compareSAGhits.py
compareSAGhits.py
 
 
concatGenes2geneome.py
concatGenes2geneome.py
 
 
concatenateFastaALN.py
concatenateFastaALN.py
 
 
concatfnacontigs.py
concatfnacontigs.py
 
 
contig_len.py
contig_len.py
 
 
countbasesFNA.py
countbasesFNA.py
 
 
countingSNPsbyloci.py
countingSNPsbyloci.py
 
 
countmetareads.py
countmetareads.py
 
 
countreads.py
countreads.py
 
 
coverageCalc_blast6.py
coverageCalc_blast6.py
 
 
fakeSAGcompleteness.py
fakeSAGcompleteness.py
 
 
fakenames16.py
fakenames16.py
 
 
filterGeneLenGeneGainLoss.py
filterGeneLenGeneGainLoss.py
 
 
filterallblasts.py
filterallblasts.py
 
 
filterbylen3.py
filterbylen3.py
 
 
filterbylen3_batch.py
filterbylen3_batch.py
 
 
find_svsns_sites.py
find_svsns_sites.py
 
 
findreplace_shortnames.py
findreplace_shortnames.py
 
 
findreplace_shortnames_rev.py
findreplace_shortnames_rev.py
 
 
fixBLASTwShortName.py
fixBLASTwShortName.py
 
 
fixfakenames2.py
fixfakenames2.py
 
 
gbk2faa.py
gbk2faa.py
 
 
gbk2faafna_unfinished?.py
gbk2faafna_unfinished?.py
 
 
gbk2fna.py
gbk2fna.py
 
 
gbk_extractGeneInfo.py
gbk_extractGeneInfo.py
 
 
gbk_extractGeneInfo2.py
gbk_extractGeneInfo2.py
 
 
gcContent.py
gcContent.py
 
 
gene_sweep_analysis.py
gene_sweep_analysis.py
 
 
gettincodonsinorder.py
gettincodonsinorder.py
 
 
hitcounts.py
hitcounts.py
 
 
lenfixsep_coverage.py
lenfixsep_coverage.py
 
 
linkContigs_coverage.py
linkContigs_coverage.py
 
 
makebed_fromIMG.py
makebed_fromIMG.py
 
 
mdireachSAG.py
mdireachSAG.py
 
 
menamesfix.py
menamesfix.py
 
 
norm_gene_cov_work.py
norm_gene_cov_work.py
 
 
norm_genecounts.py
norm_genecounts.py
 
 
orderSNPSandsites.py
orderSNPSandsites.py
 
 
parseALLvALLblastapart.py
parseALLvALLblastapart.py
 
 
parseBLASTSAGsvsMetaResults2.py
parseBLASTSAGsvsMetaResults2.py
 
 
parseBLASTSAGsvsMetaResults_acI.py
parseBLASTSAGsvsMetaResults_acI.py
 
 
parseBLASTSAGsvsMetaResults_acI2.py
parseBLASTSAGsvsMetaResults_acI2.py
 
 
parseMCLclusters.py
parseMCLclusters.py
 
 
parseProttest.py
parseProttest.py
 
 
parse_phylosift_sts.py
parse_phylosift_sts.py
 
 
poolBLASTS.py
poolBLASTS.py
 
 
recipbestblast_allset.py
recipbestblast_allset.py
 
 
regextesting.py
regextesting.py
 
 
removelinebreaks.py
removelinebreaks.py
 
 
rm_badMediancorrGFM.py
rm_badMediancorrGFM.py
 
 
rm_lowcorrcontigs.py
rm_lowcorrcontigs.py
 
 
rm_rRNAhits.py
rm_rRNAhits.py
 
 
splitcoveragfile.py
splitcoveragfile.py
 
 
tbnamesfix.py
tbnamesfix.py
 
 

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README

What is this repository for?

  • Compilation of all of Sarah Stevens' scripts

This repo is shockly poorly documented, as are some of the scripts in it
I'm working toward become more reproducible (one step at at time)
Newer scripts will have better documentation

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Unorganized mess of Sarah's Stevens scripts

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