英文:
Merge files with the same name but different code - UNIX
问题
我想要合并具有相同部分的文件：
XX_barcode2_XX.fastq
XX_barcode2_XX.fastq
XX_barcode3_XX.fastq
XX_barcode3_XX.fastq
XX_barcode4_XX.fastq
XX_barcode4_XX.fastq
所以，我想要一个用于barcode2的文件，一个用于barcode3等等...
我尝试了这个：
for i in {2 .. 96};
do
cat *_barcode$i*.fastq >> barcode$i.fastq;
done
但它不起作用。有什么想法？
英文:
I would like to merge files which have the same part of the same:
XX_barcode2_XX.fastq
XX_barcode2_XX.fastq
XX_barcode3_XX.fastq
XX_barcode3_XX.fastq
XX_barcode4_XX.fastq
XX_barcode4_XX.fastq
So, I would like a file for barcode2, a file for barcode3 etc...
I was trying this:
for i in {2 .. 96};
do
cat *_barcode$i*.fastq >> barcode$i.fastq;
done
but it does not work. Any ideas?
答案1
得分: 1
我会这样做：
#!/bin/bash
echo "file2 A" > XX_barcode2_XX.fastq
echo "file2 B" > XX_barcode2_YY.fastq
echo "file3 A" > XX_barcode3_XX.fastq
echo "file3 B" > XX_barcode3_YY.fastq
echo "file4 A" > XX_barcode4_XX.fastq
echo "file4 B" > XX_barcode4_YY.fastq
for i in {2..96}
do
echo "i=$i"
if find . -name "*_barcode$i*.fastq"
then
echo "in if"
cat "*_barcode$i*.fastq" >> "barcode$i.fastq"
fi
done
- 脚本顶部只是为我创建文件以供测试。
if find ...是为了仅处理存在的文件。否则，它会创建从5到96的空文件。如果不需要，可以删除它。- 如果不需要调试消息，可以删除
echo语句。 - 在
for循环中，您在{2 .. 96}周围放了空格，bash对于空格放错地方非常挑剔。 - 您可以在发布之前使用 https://www.shellcheck.net/ 验证您的语法。
- 并且不需要使用
;来结束行，这不是C语言
英文:
I would do it like that:
#!/bin/bash
echo "file2 A" > XX_barcode2_XX.fastq
echo "file2 B" > XX_barcode2_YY.fastq
echo "file3 A" > XX_barcode3_XX.fastq
echo "file3 B" > XX_barcode3_YY.fastq
echo "file4 A" > XX_barcode4_XX.fastq
echo "file4 B" > XX_barcode4_YY.fastq
for i in {2..96}
do
echo "i=$i"
if find . -name "*_barcode$i*.fastq"
then
echo "in if"
cat "*_barcode$i*.fastq" >> "barcode$i.fastq"
fi
done
- the top of the script it just to create files for me to test with.
- the
if find ...is to process only files that do exist. Otherwise, it creates empty files form 5 to 96. You can remove that if not required. - you can remove the
echostatements if you do not need debug messages. - in your
forloop, you had put spaces around the{2 .. 96}, bash is very particular about spaces in the wrong places. - you can validate your syntax using https://www.shellcheck.net/ before posting.
- and
;are not required to end lines, this is not C
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