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Revert "updated code for lines 39,45,48"
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This reverts commit b832814.

Reverting master branch to previous commit# Please enter the commit message for your changes. Lines starting
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@aortiz24
aortiz24 committed Jul 22, 2017
1 parent b832814 commit 1f87c78
Showing 1 changed file with 7 additions and 7 deletions.
14 changes: 7 additions & 7 deletions mothur_prep.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -13,10 +13,10 @@ for x in `cat SRP018246.lst`
do
mothur "#fastq.info(fastq=SRP018246/$x.fastq)"
done
for x in `cat SRP018247.lst`
do
mothur "fastq.info(fastq=SRP018247/$x.fastq)"
done
#for x in `cat SRP018247.lst`
# do
# mothur "fastq.info(fastq=SRP018247/$x.fastq)"
#done

rm *.logfile

Expand All @@ -36,15 +36,15 @@ done

# create group file
# output mergegroups
mothur "#make.group(fasta=SRR655327.trim.fasta-SRR655328.trim.fasta-SRR655329.trim.fasta-SRR655330.trim.fasta-SRR655331.trim.fasta-SRR655332.trim.fasta-SRR655333.trim.fasta-SRR655334.trim.fasta-SRR655335.trim.fasta-SRR655336.trim.fasta-SRR655337.trim.fasta-SRR655338.trim.fasta-SRR655339.trim.fasta-SRR655340.trim.fasta-SRR655341.trim.fasta-SRR655342.trim.fasta-SRR655343.trim.fasta-SRR655344.trim.fasta-SRR655345.trim.fasta-SRR655346.trim.fasta-SRR655347.trim.fasta-SRR655348.trim.fasta-SRR655349.trim.fasta-SRR655350.trim.fasta-SRR655351.trim.fasta-SRR655352.trim.fasta-SRR655353.trim.fasta-SRR655354.trim.fasta-SRR655355.trim.fasta-SRR655356.trim.fasta-SRR655357.trim.fasta-SRR655358.trim.fasta-SRR655359.trim.fasta-SRR655360.trim.fasta-SRR655361.trim.fasta-SRR655362.trim.fasta-SRR655363.trim.fasta-SRR655364.trim.fastaSRR655990.trim.fasta-SRR655991.trim.fasta-SRR655992.trim.fasta-SRR655993.trim.fasta-SRR655994.trim.fasta-SRR655995.trim.fasta-SRR655996.trim.fasta-SRR655997.trim.fasta-SRR655998.trim.fasta-SRR655999.trim.fasta-SRR656000.trim.fasta-SRR656001.trim.fasta-SRR656002.trim.fasta-SRR656003.trim.fasta-SRR656004.trim.fasta-SRR656005.trim.fasta-SRR656006.trim.fasta-SRR656022.trim.fasta-SRR656023.trim.fasta-SRR656024.trim.fasta-SRR656025.trim.fasta-SRR656026.trim.fasta-SRR656027.trim.fasta-SRR656028.trim.fasta-SRR656029.trim.fasta-SRR656030.trim.fasta-SRR656031.trim.fasta-SRR656032.trim.fasta-SRR656033.trim.fasta, groups=field-field-field-field-lab-lab-lab-lab-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-lab-lab-lab-lab-field-field-field-field-field-field-field-field-field-field-field-field-field-lab-lab-lab-field-field-field-field-field-field-field-field-field-field-field-field-field-lab-field-field-field)"
mothur "#make.group(fasta=SRR655327.trim.fasta-SRR655328.trim.fasta-SRR655329.trim.fasta-SRR655330.trim.fasta-SRR655331.trim.fasta-SRR655332.trim.fasta-SRR655333.trim.fasta-SRR655334.trim.fasta-SRR655335.trim.fasta-SRR655336.trim.fasta-SRR655337.trim.fasta-SRR655338.trim.fasta-SRR655339.trim.fasta-SRR655340.trim.fasta-SRR655341.trim.fasta-SRR655342.trim.fasta-SRR655343.trim.fasta-SRR655344.trim.fasta-SRR655345.trim.fasta-SRR655346.trim.fasta-SRR655347.trim.fasta-SRR655348.trim.fasta-SRR655349.trim.fasta-SRR655350.trim.fasta-SRR655351.trim.fasta-SRR655352.trim.fasta-SRR655353.trim.fasta-SRR655354.trim.fasta-SRR655355.trim.fasta-SRR655356.trim.fasta-SRR655357.trim.fasta-SRR655358.trim.fasta-SRR655359.trim.fasta-SRR655360.trim.fasta-SRR655361.trim.fasta-SRR655362.trim.fasta-SRR655363.trim.fasta-SRR655364.trim.fasta, groups=field-field-field-field-lab-lab-lab-lab-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-field-lab-lab-lab-lab-field-field-field-field)"

# rename groups file
cp mergegroups analysis.groups

# make master fasta file (combines individual fasta files into a single file, analysis.fasta)
mothur "#merge.files(input=SRR655990.trim.fasta-SRR655991.trim.fasta-SRR655992.trim.fasta-SRR655993.trim.fasta-SRR655994.trim.fasta-SRR655995.trim.fasta-SRR655996.trim.fasta-SRR655997.trim.fasta-SRR655998.trim.fasta-SRR655999.trim.fasta-SRR656000.trim.fasta-SRR656001.trim.fasta-SRR656002.trim.fasta-SRR656003.trim.fasta-SRR656004.trim.fasta-SRR656005.trim.fasta-SRR656006.trim.fasta-SRR656022.trim.fasta-SRR656023.trim.fasta-SRR656024.trim.fasta-SRR656025.trim.fasta-SRR656026.trim.fasta-SRR656027.trim.fasta-SRR656028.trim.fasta-SRR656029.trim.fasta-SRR656030.trim.fasta-SRR656031.trim.fasta-SRR656032.trim.fasta-SRR656033.trim.fasta)"
mothur "#merge.files(input=SRR655327.trim.fasta-SRR655328.trim.fasta-SRR655329.trim.fasta-SRR655330.trim.fasta-SRR655331.trim.fasta-SRR655332.trim.fasta-SRR655333.trim.fasta-SRR655334.trim.fasta-SRR655335.trim.fasta-SRR655336.trim.fasta-SRR655337.trim.fasta-SRR655338.trim.fasta-SRR655339.trim.fasta-SRR655340.trim.fasta-SRR655341.trim.fasta-SRR655342.trim.fasta-SRR655343.trim.fasta-SRR655344.trim.fasta-SRR655345.trim.fasta-SRR655346.trim.fasta-SRR655347.trim.fasta-SRR655348.trim.fasta-SRR655349.trim.fasta-SRR655350.trim.fasta-SRR655351.trim.fasta-SRR655352.trim.fasta-SRR655353.trim.fasta-SRR655354.trim.fasta-SRR655355.trim.fasta-SRR655356.trim.fasta-SRR655357.trim.fasta-SRR655358.trim.fasta-SRR655359.trim.fasta-SRR655360.trim.fasta-SRR655361.trim.fasta-SRR655362.trim.fasta-SRR655363.trim.fasta-SRR655364.trim.fasta, output=analysis.trim.fasta)"

# make master qual file
mothur "#merge.files(input=SRR655990.trim.qual-SRR655991.trim.qual-SRR655992.trim.qual-SRR655993.trim.qual-SRR655994.trim.qual-SRR655995.trim.qual-SRR655996.trim.qual-SRR655997.trim.qual-SRR655998.trim.qual-SRR655999.trim.qual-SRR656000.trim.qual-SRR656001.trim.qual-SRR656002.trim.qual-SRR656003.trim.qual-SRR656004.trim.qual-SRR656005.trim.qual-SRR656006.trim.qual-SRR656022.trim.qual-SRR656023.trim.qual-SRR656024.trim.qual-SRR656025.trim.qual-SRR656026.trim.qual-SRR656027.trim.qual-SRR656028.trim.qual-SRR656029.trim.qual-SRR656030.trim.qual-SRR656031.trim.qual-SRR656032.trim.qual-SRR656033.trim.qual)"
mothur "#merge.files(input=SRR655327.trim.qual-SRR655328.trim.qual-SRR655329.trim.qual-SRR655330.trim.qual-SRR655331.trim.qual-SRR655332.trim.qual-SRR655333.trim.qual-SRR655334.trim.qual-SRR655335.trim.qual-SRR655336.trim.qual-SRR655337.trim.qual-SRR655338.trim.qual-SRR655339.trim.qual-SRR655340.trim.qual-SRR655341.trim.qual-SRR655342.trim.qual-SRR655343.trim.qual-SRR655344.trim.qual-SRR655345.trim.qual-SRR655346.trim.qual-SRR655347.trim.qual-SRR655348.trim.qual-SRR655349.trim.qual-SRR655350.trim.qual-SRR655351.trim.qual-SRR655352.trim.qual-SRR655353.trim.qual-SRR655354.trim.qual-SRR655355.trim.qual-SRR655356.trim.qual-SRR655357.trim.qual-SRR655358.trim.qual-SRR655359.trim.qual-SRR655360.trim.qual-SRR655361.trim.qual-SRR655362.trim.qual-SRR655363.trim.qual-SRR655364.trim.qual, output=analysis.trim.qual)"

rm *.logfile

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