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annotate orthologs/ucsb_hamster/ucsb_galaxy_hamster.sh @ 0:5b9a38ec4a39 draft default tip

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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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children
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/bin/sh
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2 # set -x
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 # Uncomment 'set -x' for debug information
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 #############################################
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 # UCSB HAMSTER - GALAXY HISTORY #
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7 # #
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 # Executed when user chooses Galaxy history #
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 #############################################
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10
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11 # Set your hamster script location here. The directory containing these scripts should be in
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12 #your path
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 script="hamstrsearch_local-hmmer3.pl"
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 # Set your unbuild.py script location here
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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15 unbuild="unbuild.py"
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 # Set your emap2fasta.pl script location here
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 emap2fasta="emap2fasta.pl"
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18
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19
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 # 1 - Sequence input file
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21 # 2 - Proteins results output file
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 # 3 - CDS results output file
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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23 # 4 - Screen log
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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24 # 5 - Species name
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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25 # 6 - whether to use EST flag D=DNA so use -est flag P=Protein so do not use -est flag in hmmstr call
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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26 # 7 - HMM Input from UCSB HMMBUILD
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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27 # 8 - MUSCLE data from UCSB MUSCLE
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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28 # 9 - Reference Species File
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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29 # 10 - Reference Species Name
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30
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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31 input=$1
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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32 proteins=$2
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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33 cdsfile=$3
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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34 screenlog=$4
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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35 speciesName=$5
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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36 datatype=$6
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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37 hmm_data=$7
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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38 muscle_data=$8
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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39 filepath=`pwd`
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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40 tail="_prot"
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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41 tail2="_temp"
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42
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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43 # set flag based on input
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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44 if [ $datatype = "P" ];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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45 then
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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46 estflag="-protein"
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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47 else
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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48 estflag="-est"
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49 fi
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50
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51 refspfile=${9}
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52 refsphist=${10}
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53
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54
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55
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56 echo "Protein or EST? : $estflag" >> $screenlog
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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57 echo "Reference genome file from galaxy history: $refspfile" >> $screenlog
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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58 echo "Reference species genome name: $refsphist" >> $screenlog
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59
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60 # unbuild.py here on $hmm_data
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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61 mkdir core
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62 mkdir core/hmm_dir
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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63 cp $hmm_data core/core.fa
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64
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65 $unbuild core/hmm_dir core/core.fa
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66 cp core/hmm_dir/hmmlist.txt core/hmmlist.txt
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67
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68 # use formatdb to generate new blastdb from this input file
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69 refsphistGALAXY=$refsphist
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70 mkdir $refsphistGALAXY
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71
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72 cp $muscle_data $refsphistGALAXY/$refsphist$tail2
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73 $emap2fasta $refsphistGALAXY/$refsphist$tail2 $refsphist
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74 cp full.fasta core/core.fa
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75
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76 cp $refspfile $refsphistGALAXY/$refsphist$tail
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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77 cd $refsphistGALAXY
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78 formatdb -t $refsphist -i $refsphist$tail -n $refsphist$tail
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79
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80 echo "*** Direcotry Structure of Ref. Genome ***" >> $screenlog
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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81 ls -l >> $screenlog
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82 echo >> $screenlog
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83
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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84 cd $filepath
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85
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86 # script execution
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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87 $script -sequence_file=$1 $estflag -taxon=$5 -hmmset=core -refspec=$refsphistGALAXY -galaxyout=$2 -2galaxyout=$cdsfile 2>log.txt >> $screenlog