CSV format

The CSV sequence file format #

The CSV (Comma-Separated Values) files are formatted as plain text where each line represents a data record, and each field within that record is separated by a comma.

Converting FASTA file to CSV #

Use the obicsv command to convert a fasta file to CSV format, with the -i and -s options, to print the sequence identifier and the nucleotide sequence respectively, and the -k option to retain the desired attributes. Each record in the FASTA file corresponds to a line in the output file:

📄 two_sequences.fasta
>AB061527 {"count":1,"definition":"Sorex unguiculatus mitochondrial NA, complete genome.","family_name":"Soricidae","family_taxid":9376,"genus_name":"Sorex","genus_taxid":9379,"obicleandb_level":"family","obicleandb_trusted":2.2137847111025621e-13,"species_name":"Sorex unguiculatus","species_taxid":62275,"taxid":62275}
ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
agcttaaaactcaaaggacttggcggtgctttatatccct
>AL355887 {"count":2,"definition":"Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.","family_name":"Hominidae","family_taxid":9604,"genus_name":"Homo","genus_taxid":9605,"obicleandb_level":"genus","obicleandb_trusted":0,"species_name":"Homo sapiens","species_taxid":9606,"taxid":9606}
ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac
agcttaaaactcaaaggacctggcagttctttatatccct
obicsv -k count -k taxid -k family_taxid -k family_name \
       -i -s \
       two_sequences.fasta > two_sequences.csv

id,count,taxid,scientific_name,family_taxid,family_name,sequence
AB061527,1,62275,NA,9376,Soricidae,ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct
AL355887,2,9606,NA,9604,Hominidae,ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaacagcttaaaactcaaaggacctggcagttctttatatccct

The result of the obicsv can be reformatted with the csvlook command (the -I option disables the reformatting of values):

csvlook -I two_sequences.csv

| id       | count | taxid | family_taxid | family_name | sequence                                                                                             |
| -------- | ----- | ----- | ------------ | ----------- | ---------------------------------------------------------------------------------------------------- |
| AB061527 | 1     | 62275 | 9376         | Soricidae   | ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct |
| AL355887 | 2     | 9606  | 9604         | Hominidae   | ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaacagcttaaaactcaaaggacctggcagttctttatatccct |

Converting CSV file to FASTA format #

To convert a sequence file in CSV format to fasta format, you can use the obiconvert command:

obiconvert two_sequences.csv

>AB061527 {"count":1,"family_name":"Soricidae","family_taxid":"9376","taxid":"62275"}
ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
agcttaaaactcaaaggacttggcggtgctttatatccct
>AL355887 {"count":2,"family_name":"Hominidae","family_taxid":"9604","taxid":"9606"}
ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac
agcttaaaactcaaaggacctggcagttctttatatccct

Converting FASTQ file to CSV #

In the same way as for fasta files, use the obicsv command to convert a fastq file to CSV format (the -q option prints the quality of the sequence in the output):

📄 two_sequences.fastq
@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/1 {"ali_dir":"left","ali_length":62,"mode":"alignment","pairing_mismatches":{"(T:26)->(G:13)":62,"(T:34)->(G:18)":48},"score":484,"score_norm":0.968,"seq_a_single":46,"seq_ab_match":60,"seq_b_single":46} 
ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg
+
CCCCCCCBCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCCCCCCACCCCCACCCCCCCCCCCCCCCC
@HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/1 {"ali_dir":"left","ali_length":62,"mode":"alignment","pairing_mismatches":{"(A:02)->(G:30)":104,"(A:34)->(G:14)":64,"(C:02)->(A:30)":86,"(C:02)->(T:20)":108,"(C:27)->(G:32)":83,"(C:34)->(G:18)":57,"(T:02)->(G:26)":87,"(T:22)->(G:14)":66,"(T:29)->(G:11)":62,"(T:32)->(G:30)":48},"score":283,"score_norm":0.839,"seq_a_single":46,"seq_ab_match":52,"seq_b_single":46} 
ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaagagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg
+
CCCCCCCCCCCCCCCCCCCCCCCBBCCC?BCCCCCBC?CCCC@@;AVA`cWeb_TYC\UIN?IDP8QJMKRPVGLQAFPPc`AbAFB5A4>AAA56A><>8>>F@A><8??@BB+<?;?C@9CCCCCC<CC=CCCCCCCCCBC?CBCCCCC@CC
obicsv -i -s -q two_sequences.fastq > two_sequences.csv
csvlook -I two_sequences.csv

| id                                              | sequence                                                                                                                                                   | qualities                                                                                                                                                  |
| ----------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------- |
| HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/1  | ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg | CCCCCCCBCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCCCCCCACCCCCACCCCCCCCCCCCCCCC |
| HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/1 | ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaagagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg | CCCCCCCCCCCCCCCCCCCCCCCBBCCC?BCCCCCBC?CCCC@@;AVA`cWeb_TYC\UIN?IDP8QJMKRPVGLQAFPPc`AbAFB5A4>AAA56A><>8>>F@A><8??@BB+<?;?C@9CCCCCC<CC=CCCCCCCCCBC?CBCCCCC@CC |

Converting CSV file to FASTQ format #

obiconvert --fastq-output two_sequences.csv

@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/1 
ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg
+
CCCCCCCBCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCCCCCCACCCCCACCCCCCCCCCCCCCCC
@HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/1 
ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaagagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg
+
CCCCCCCCCCCCCCCCCCCCCCCBBCCC?BCCCCCBC?CCCC@@;AVA`cWeb_TYC\UIN?IDP8QJMKRPVGLQAFPPc`AbAFB5A4>AAA56A><>8>>F@A><8??@BB+<?;?C@9CCCCCC<CC=CCCCCCCCCBC?CBCCCCC@CC