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Asked: 2026-05-14T04:19:38+00:00

I have a data that looks like this 1:SRX000566 Submitter: WoldLab Study: RNASeq expression

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I have a data that looks like this

1:SRX000566
Submitter: WoldLab
Study: RNASeq expression profiling for ENCODE project(SRP000228)
Sample: Human cell line GM12878(SRS000567)
Instrument: Solexa 1G Genome Analyzer
Total: 4 runs, 62.7M spots, 2.1G bases
Run #1: SRR002055, 11373440 spots, 375323520 bases
Run #2: SRR002063, 22995209 spots, 758841897 bases
Run #3: SRR005091, 13934766 spots, 459847278 bases
Run #4: SRR005096, 14370900 spots, 474239700 bases

2:SRX000565
Submitter: WoldLab
Study: RNASeq expression profiling for ENCODE project(SRP000228)
Sample: Human cell line GM12878(SRS000567)
Instrument: Solexa 1G Genome Analyzer
Total: 3 runs, 51.2M spots, 1.7G bases
Run #1: SRR002052, 12607931 spots, 416061723 bases
Run #2: SRR002054, 12880281 spots, 425049273 bases
Run #3: SRR002060, 25740337 spots, 849431121 bases

3:SRX012407
Submitter: GEO
Study: GSE17153: Illumina sequencing of small RNAs from C. elegans embryos(SRP001363)
Sample: Caenorhabditis elegans(SRS006961)
Instrument: Illumina Genome Analyzer II
Total: 1 run, 3M spots, 106.8M bases
Run #1: SRR029428, 2965597 spots, 106761492 bases

Is there a compact way to convert them into tabular format (tab separated).
Hence 1 entry/row per chunk. In these case 3 rows.

I tried this but doesn’t seem to work.

perl -laF/\n/ `-000ne"print join chr(9),@F" myfile.txt`
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1 Answer

  1. Editorial Team

    if you don’t mind awk

    $ awk -vRS= -vFS="\n" '{$1=$1}1' OFS="\t" file
1:SRX000566     Submitter: WoldLab      Study: RNASeq expression profiling for ENCODE project(SRP000228)        Sample: Human cell line GM12878(SRS000567)  Instrument: Solexa 1G Genome Analyzer    Total: 4 runs, 62.7M spots, 2.1G bases  Run #1: SRR002055, 11373440 spots, 375323520 bases      Run #2: SRR002063, 22995209 spots, 758841897 bases   Run #3: SRR005091, 13934766 spots, 459847278 bases      Run #4: SRR005096, 14370900 spots, 474239700 bases
2:SRX000565     Submitter: WoldLab      Study: RNASeq expression profiling for ENCODE project(SRP000228)        Sample: Human cell line GM12878(SRS000567)  Instrument: Solexa 1G Genome Analyzer    Total: 3 runs, 51.2M spots, 1.7G bases  Run #1: SRR002052, 12607931 spots, 416061723 bases      Run #2: SRR002054, 12880281 spots, 425049273 bases   Run #3: SRR002060, 25740337 spots, 849431121 bases
3:SRX012407     Submitter: GEO  Study: GSE17153: Illumina sequencing of small RNAs from C. elegans embryos(SRP001363)   Sample: Caenorhabditis elegans(SRS006961)    Instrument: Illumina Genome Analyzer II Total: 1 run, 3M spots, 106.8M bases    Run #1: SRR029428, 2965597 spots, 106761492 bases

    otherwise an equivalent of the above awk statement

    #!/usr/bin/perl
$\ = "\n";
$/ = "\n\n";
while (<>) {
    chomp;
    @F = split(/\n/, $_);
    print join("\t",@F);
}
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