Mercurial > repos > erinija > dnp_binary_strings

annotate dnp-subset-dinuc-profile.sh @ 0:611156829647 draft default tip

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"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
author erinija
date Fri, 01 May 2020 12:07:46 +0000
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1 #!/bin/sh
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2 if test "$#" -ne 3; then
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3
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4 echo " CALL "
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5 echo " sh subset_dinuc_profile.sh input.fasta dinucleotides output"
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6 echo ""
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7 echo " INPUT"
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8 echo " input.fasta - a batch of nucleosome (or any DNA) DNA sequences "
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9 echo " dinucleotides - any subset of dinucleotides enclosed by quotes as 'AA AC AG AT CA CC' "
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10 echo ""
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11 echo " OUTPUT"
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12 echo " output - file name to write the output in tabular format, columns have names as AA.f AA.r ..."
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13 echo ""
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14 echo " DESCRIPTION"
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15 echo " Compute dinucleotide frequency profiles on forward and its complementary "
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16 echo " sequences from a batch of fasta sequences. Output columns are labelled by AA.f, AA.r ... "
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17 echo ""
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18 echo " Example of input fasta lines"
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19 echo " >chr9:42475963-42476182"
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20 echo " CCAGGCAGACCCCATATTCAAGCTGCTGCCCCAGGGTGGTGTACAGATCTGGGGAGAAGAAGGATGA"
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21 echo " >chr9:42476175-42476394"
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22 echo " TCTGCACTCCAGCATGCCTGAGGAGAGGAGGGAATGCAGGATCCTAGTGGAAAGAGTACCAAGCTGG"
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23 echo ""
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24 echo " Example of output table"
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25 echo " AA.f AA.r AC.f AC.r ..."
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26 echo " 0.076000 0.059000 0.065000 0.078000 ..."
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27 echo " 0.082000 0.060000 0.057000 0.076000 ..."
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28 echo " 0.067000 0.075000 0.049000 0.071000 ..."
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29 echo ""
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30 echo ""
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31 echo " REQUIREMENT"
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32 echo " dnp-diprofile installed"
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33 echo " conda install -c bioconda dnp-diprofile"
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34
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35 exit 0
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36 fi
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37
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38 name=$1
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39 diset=$2
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40 out=$3
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41
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42 call=dnp-diprofile
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43
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44 ## the dinucleotide profiles are computed for the subset of dinucleotides listed in $diset
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45 ## the profiles are outputs as columns of a table
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46
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47 # prepare fasta, we copy here because
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48 # in galaxy we don't have fa ending which is required by the dinuc
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49 cp ${name} ${name}.fa
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50
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51 # compute length of the fasta sequence
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52 seq=`head -n2 $name | tail -n1`
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53 len=${#seq}
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54 #echo "Sequence length = " $len
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55
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56
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57 # for each dinucleotide compute the forward
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58 # and complementary profile and save
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59 # in separate columns that will be merged in the end
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60 for di in ${diset}
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61 do
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62 #echo ${di}
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63 echo ${di}.f > ${di}.f
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64 ${call} ${name}.fa -di ${di} -sl ${len} >> ${di}.f
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65 echo ${di}.r > ${di}.r
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66 ${call} ${name}.fa -di ${di} -sl ${len} -c >> ${di}.r
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67 echo ${di}.f >> names
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68 echo ${di}.r >> names
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69 done;
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70 paste `cat names` > ${out}
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71 rm names
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72 rm ${name}.fa
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73 rm *.f *.r
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74 exit 0