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1 #!/bin/bash
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2 set -e;
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3 email_address_of_user=$1;
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4 echo "email: " $email_address_of_user;
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5
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6 echo "Calculation of Y-linked genes started."
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7 ./scripts/prepare_statistics.sh;
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8 echo "Statistics done";
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9
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10 #filter contigs, which are candidate Y genes - very divergent from their X counterparts
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11 perl scripts/filter_diverged_Y_contigs.pl scripts/statistics/stat_mother scripts/statistics/stat_father scripts/statistics/stat_daughter scripts/statistics/stat_son >Y_results.txt;
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12 perl scripts/get_sequences_based_on_ids.pl references/reference_male.fasta Y_list >Y_results_sequences.txt;
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13
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14 if [[ -s Y_list ]] ; then
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15 get_results_in_bam_file ()
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16 {
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17 for ARG in "$@";
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18 do
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19 ./scripts/createBamFromResults.sh Y_list bam/aln_cleaned_sorted_deduplicated_${ARG}_male.bam bam/${ARG}_male.bam;
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20 samtools index bam/${ARG}_male.bam;
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21 done;
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22 }
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23
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24 get_results_in_bam_file mother father daughter son;
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25 wait;
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26 #send BAM files with corresponding contigs
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27 mutt -s "LINKYX: Results of computation for Y-linked genes" $email_address_of_user -a bam/mother_male.bam -a bam/mother_male.bam.bai -a bam/father_male.bam -a bam/father_male.bam.bai -a bam/daughter_male.bam -a bam/daughter_male.bam.bai -a bam/son_male.bam -a bam/son_male.bam.bai < messages_to_user/message_results_sentBamY;
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28 else
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29 #we found NO genes
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30 echo "No sequences found." >Y_results.txt;
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31 echo "No sequences found." >Y_results_sequences.txt;
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32 fi |
