GitHub - kdiverson/seqTools: Some simple python scripts to help you work with biological sequence data (DNA, proteins, etc) I'll add more as I create them (or find them on my hard drive)

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Some simple python scripts to help you work with biological sequence data (DNA, proteins, etc) I'll add more as I create them (or find them on my hard drive)

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Name		Name	Last commit message	Last commit date
Latest commit History 11 Commits
README		README
TESTcalcN50N90.py		TESTcalcN50N90.py
bam_coverage.pl		bam_coverage.pl
blastXMLparser.py		blastXMLparser.py
calcN50.py		calcN50.py
calcN50N90.pl		calcN50N90.pl
compareAssemblies.sh		compareAssemblies.sh
compareFasta.py		compareFasta.py
compareFastas.py		compareFastas.py
contigStats.py		contigStats.py
countHits.py		countHits.py
findEukGenes.py		findEukGenes.py
fq_all2std.pl		fq_all2std.pl
getBLASThitsbyquery.py		getBLASThitsbyquery.py
getBPerror.py		getBPerror.py
getCOGcat.py		getCOGcat.py
getFastaHeaders.py		getFastaHeaders.py
getGInumber.py		getGInumber.py
getGeneMappings.py		getGeneMappings.py
getGenes.py		getGenes.py
getKEGGgeneID.py		getKEGGgeneID.py
getMissingSeqs.py		getMissingSeqs.py
getNOGcatbytaxid.py		getNOGcatbytaxid.py
getNOGmapping.py		getNOGmapping.py
getReadCoverage.py		getReadCoverage.py
getSNPcountByPos.py		getSNPcountByPos.py
getSNPgenes.py		getSNPgenes.py
getSelfBLAST.py		getSelfBLAST.py
getSignificantMatches.py		getSignificantMatches.py
getSubjects.py		getSubjects.py
getTaxid.py		getTaxid.py
getTranslatedGenes.py		getTranslatedGenes.py
getcatcount.py		getcatcount.py
getcatcount2.py		getcatcount2.py
getcatcount2early.py		getcatcount2early.py
getcatcount2early2.py		getcatcount2early2.py
getcatcount2late.py		getcatcount2late.py
getcatcount2late2.py		getcatcount2late2.py
getcatcount3.py		getcatcount3.py
getcatcountsvariants.py		getcatcountsvariants.py
getcommonvarients.py		getcommonvarients.py
getcoregenes.py		getcoregenes.py
getdesccounts.py		getdesccounts.py
getdesccountsearly.py		getdesccountsearly.py
getdesccountslate.py		getdesccountslate.py
geteggNOGprotein.py		geteggNOGprotein.py
getfullgenefuncatEARLY.py		getfullgenefuncatEARLY.py
getfullgenefuncatLATE.py		getfullgenefuncatLATE.py
getfunccatbytaxidEARLY2.py		getfunccatbytaxidEARLY2.py
getfunccatbytaxidLATE2.py		getfunccatbytaxidLATE2.py
getgenesbypos.py		getgenesbypos.py
getnohits.py		getnohits.py
getqueryhit.py		getqueryhit.py
gettaxfromKEGGBLAST.py		gettaxfromKEGGBLAST.py
gettaxidandfuncat.py		gettaxidandfuncat.py
gettaxidandfuncatEARLY.py		gettaxidandfuncatEARLY.py
gettaxidandfuncatLATE.py		gettaxidandfuncatLATE.py
gettaxidfromeggNOGdb.py		gettaxidfromeggNOGdb.py
getvarientcounts.py		getvarientcounts.py
listFilesInDir.py		listFilesInDir.py
loadBLASTdata.py		loadBLASTdata.py
mapKEGGhits.py		mapKEGGhits.py
mapKEGGhitsFromDB.py		mapKEGGhitsFromDB.py
meanCoverageBAM.pl		meanCoverageBAM.pl
prinseq-lite.pl		prinseq-lite.pl
readmga.py		readmga.py
removeNseqs.py		removeNseqs.py
removeShortContigs.py		removeShortContigs.py
seqChopper2.py		seqChopper2.py
slideChopper.py		slideChopper.py
transposecountfile.py		transposecountfile.py
transposetsv.py		transposetsv.py
trimseq.py		trimseq.py

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Some simple tools I've created to do mundane things. Maybe you'll find them usefull.
You could probably use biopython to do many of the same things but I wanted sctipts that don't require any modules to be installed outside of good ol' python.

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Some simple python scripts to help you work with biological sequence data (DNA, proteins, etc) I'll add more as I create them (or find them on my hard drive)

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