bash string split and concatenate

Question

I have hundreds files need to loop through for an analysis using a bash script. One step I need to do is to split a long string and cat it as an output name. For example, suppose I have one string such like:

5018.a.Radiation_Induced_Lymphoma.Tumor__p53+_-.SL200300_SL200300.exome_1tier.mm10.kapa_re_cap_v6_3utr.final.bam

What I wanted is to rename it as two output file names such as:

5018.a.Radiation_Induced_Lymphoma.Tumor__p53+_-.SL200300_SL200300.exome_1tier.mm10.kapa_re_cap_v6_3utr.final_R1.fastq
5018.a.Radiation_Induced_Lymphoma.Tumor__p53+_-.SL200300_SL200300.exome_1tier.mm10.kapa_re_cap_v6_3utr.final_R2.fastq

The only changes are removing .bam from the original and cat _R1.fastq and _R2_fastq. Does somebody know how to realize it using bash commands?

score 1 · Accepted Answer · answered Mar 23 '17 at 13:27

1

somefile=blahblahblah.final.bam
foo "$somefile" "${somefile%.*}_R1.fastq" "${somefile%.*}_R2.fastq"

answered Mar 23 '17 at 13:27

Ignacio Vazquez-Abrams

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bash string split and concatenate

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