telatin

#!/bin/bash

# A first example of 'for loop' to iterate a set of commands over a list of files

SamFilesCount=$(ls *.sam | wc -l);
if [[ $SamFilesCount -eq 0 ]]
then
      echo " Warning: there are no .sam files to process in this directory!"
      exit;
fi

telatin

#!/bin/bash
# A mock script, with at least a nice error

REFERENCE='/db/genome.fasta'

for INPUT in *.fastq;
do
         fastx_trimmer -i $INPUT -l 90 -Q 33 -o trimmed_${INPUT}
         bwa mem $REFERENCE trimmed_${INPUT} > ${IPUT}.sam
         samtools view -bS ${INPUT}.sam > ${INPUT}.bam

telatin

#!/bin/bash

# Make the script "exit" when a command fails, or a variable is mistyped
set -euo pipefail

# Make the scrip "exit" if the shell expansion (*.fastq) fails
shopt -s failglob

# Check if at least a parameter was passed
if [[ $# == 0 ]]

telatin

#!/bin/bash

echo "Total arguments:      $#";
echo "-----------------------------------";

echo "Your first argument:  $1";
echo "Your second argument: $2";
echo "Your third argument:  $3";

telatin

NC_000913       1       81
NC_000913       2       85
NC_000913       3       87
NC_000913       4       91
NC_000913       5       91
NC_000913       6       94
NC_000913       7       95
NC_000913       8       101
NC_000913       9       103
NC_000913       10      108

telatin

NC_000913       0       1       81
NC_000913       1       2       85
NC_000913       2       3       87
NC_000913       3       5       91
NC_000913       5       16      94
NC_000913       16      17      95
NC_000913       17      18      101
NC_000913       18      19      103
NC_000913       19      20      108
NC_000913       10      11      113

telatin

<person> 
  <name>Andrea</name> 
  <surname>Telatin</surname> 
  <hobbies>Hiking</hobbies> 
  <hobbies>Cooking</hobbies> 
  <hobbies>Graphic Design</hobbies> 
</person>

telatin

<person>
   <name>Andrea</name>
   <surname>Telatin</surname>
   <hobbies>
        <hobby>Hiking</hobby>
        <hobby>Cooking</hobby>
        <hobby>Graphic Design</hobby>
   </hobbies>
</person>

telatin

   <hobbies>
        <hobby order="1">Hiking</hobby>
        <hobby order="2">Cooking</hobby>
        <hobby order="3">Graphic Design</hobby>
   </hobbies>

telatin

<PubmedArticle>
    <MedlineCitation Status="In-Data-Review" Owner="NLM">
        <PMID Version="1">29079838</PMID>
        <DateCreated>
            <Year>2017</Year>
            <Month>10</Month>
            <Day>28</Day>
        </DateCreated>
       <Article PubModel="Electronic">
            <Journal>