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It first calls ckFile to see if the file exists. Only if it does do the further statements get executed. The file size check is performed by piping the result of ls -l <file> to and an awk script that just echos the file size part of the line (field 5). This chained command is executed by putting it in backquotes back quotes and its result stored in the SZ variable, which is then checked to see if it was the string "0".
Other niceties
A good shell script should Of course a program could still produce a file with a non-0 size then error with a non-0 exit code. How might you address this possibility?
OK, enough of boring (but neccessary!) error checking. Onward to more interesting things!
Other niceties
Another time-honored program-writing convention is to provide your users with information on how to run the program The first thing our script does, after capturing its first 4 command line arguments in variables, is to check whether the last required argument (PAIRED, the 4th argument) is empty, and if so, prints detailed usage information. So when someone doesn't know or remember what arguments the script takes (perhaps you, 6 months from now), they can just invoke the script with no arguments to find out:
| Code Block |
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user$ ./align_bwa.sh
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Align fastq data with bwa, producing a sorted indexed BAM file.
align_bwa.sh in_file out_pfx assembly paired(0|1)
in_file For single-end alignments, path of the input fastq file.
For paired-end alignemtts, path to the the R1 fastq file
which must contain the string '_R1.' in its name. The
corresponding 'R2' must have the same path except for '_R1'
out_pfx Desired prefix of output files.
assembly One of: hg19 hg18 mm10 mm9 sacCer3 sacCer3 ecoli
paired 0 = single end alignment; 1 = paired end.
Example:
align_bwa.sh my.fastq mrna_b1_ln1 hg18 0
align_bwa.sh my_L001_R1.fastq swi6_b2_ln1 sacCer3 1
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A good shell script should also be relatively easy to call. That's why, for example, we have this script takes only a short name of the desired reference and uses it to select the correct path, and only requires the name of the R1 fastq for paired-end reads, using that path to determine the name of the R2 fastq file.
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