{ "id": 402580, "title": "What is a FASTA File and How To Read It", "url": "/competitions/cafa-5-protein-function-prediction/discussion/402580", "author_name": "", "post_date": "2023-04-18T23:00:24.548886700Z", "votes": 24, "comment_count": 2, "views": 0, "content": "

What is a FASTA file?

\n

A FASTA file is a common file format used to store DNA or protein sequences along with their identifying information. The file consists of a header line starting with the > character, followed by one or more lines of sequence data.

\n

Here is an example:

\n
\nMNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNK\nRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWN\nYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGY\nHPAARDRQFEKDRSFEIINVLLELDNKVPINWAQGFIY\n
\n

If we parse the file we get:

\n
ID: P20536\nName: P20536\nDescription: P20536 sp|P20536|UNG_VACCC Uracil-DNA glycosylase OS=Vaccinia virus (strain Copenhagen) OX=10249 GN=UNG PE=1 SV=1\nNumber of features: 0\nSeq('MNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLK...FIY')\n
\n

How to read a FASTA file in Python

\n
 Bio  SeqIO\n\n\nfilename = \nfasta_sequences = SeqIO.parse((filename),)\n\n\n fasta  fasta_sequences:\n    (fasta)\n    (, fasta.)\n    (, (fasta))\n    \n
\n

Example

\n

", "messages": [ { "id": "2226436", "postDate": "04/18/2023 23:00:24", "content": "

What is a FASTA file?

\n

A FASTA file is a common file format used to store DNA or protein sequences along with their identifying information. The file consists of a header line starting with the > character, followed by one or more lines of sequence data.

\n

Here is an example:

\n
\nMNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNK\nRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWN\nYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGY\nHPAARDRQFEKDRSFEIINVLLELDNKVPINWAQGFIY\n
\n

If we parse the file we get:

\n
ID: P20536\nName: P20536\nDescription: P20536 sp|P20536|UNG_VACCC Uracil-DNA glycosylase OS=Vaccinia virus (strain Copenhagen) OX=10249 GN=UNG PE=1 SV=1\nNumber of features: 0\nSeq('MNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLK...FIY')\n
\n

How to read a FASTA file in Python

\n
 Bio  SeqIO\n\n\nfilename = \nfasta_sequences = SeqIO.parse((filename),)\n\n\n fasta  fasta_sequences:\n    (fasta)\n    (, fasta.)\n    (, (fasta))\n    \n
\n

Example

\n

", "rawMarkdown": "### What is a FASTA file?\n\nA FASTA file is a common file format used to store DNA or protein sequences along with their identifying information. The file consists of a header line starting with the `>` character, followed by one or more lines of sequence data.\n\nHere is an example:\n```shell\n>P20536 sp|P20536|UNG_VACCC Uracil-DNA glycosylase OS=Vaccinia virus (strain Copenhagen) OX=10249 GN=UNG PE=1 SV=1\nMNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNK\nRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWN\nYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGY\nHPAARDRQFEKDRSFEIINVLLELDNKVPINWAQGFIY\n```\n\nIf we parse the file we get:\n\n```shell\nID: P20536\nName: P20536\nDescription: P20536 sp|P20536|UNG_VACCC Uracil-DNA glycosylase OS=Vaccinia virus (strain Copenhagen) OX=10249 GN=UNG PE=1 SV=1\nNumber of features: 0\nSeq('MNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLK...FIY')\n```\n\n### How to read a FASTA file in Python\n\n```python\nfrom Bio import SeqIO\n\n# Open the FASTA file\nfilename = \"/kaggle/input/cafa-5-protein-function-prediction/Train/train_sequences.fasta\"\nfasta_sequences = SeqIO.parse(open(filename),'fasta')\n\n# Loop over each sequence and print its ID and length\nfor fasta in fasta_sequences:\n print(fasta)\n print(\"Sequence ID:\", fasta.id)\n print(\"Sequence length:\", len(fasta))\n break\n```\n\n### Example\n\n", "votes": null }, { "id": "2226484", "postDate": "04/19/2023 01:18:24", "content": "

Hi @alejopaullier

\n

Thanks for the code sample! That's helpful.

\n

Just to clarify: this not the standard FASTA format:

\n
ID: P20536\nName: P20536\nDescription: P20536 sp|P20536|UNG_VACCC Uracil-DNA glycosylase OS=Vaccinia virus (strain Copenhagen) OX=10249 GN=UNG PE=1 SV=1\nNumber of features: 0\nSeq('MNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLK...FIY')\n
\n

This is a standard FASTA record format that we are providing:

\n
>P20536 sp|P20536|UNG_VACCC Uracil-DNA glycosylase OS=Vaccinia virus (strain Copenhagen) OX=10249 GN=UNG PE=1 SV=1\nMNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNK\nRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWN\nYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGY\nHPAARDRQFEKDRSFEIINVLLELDNKVPINWAQGFIY\n
\n

As stated by @alejopaullier the line after the \">\" is the header, and the rest of the record is the amino acid sequence. For more information on the specific header format see File Descriptions in Data section,

\n

The above code provided by should work in reading the FASTA files, you would need to have biopython installed. Examples on sequence file IO are provided here.

", "rawMarkdown": "Hi @alejopaullier \n\nThanks for the code sample! That's helpful. \n\nJust to clarify: this not the standard FASTA format:\n\n```\nID: P20536\nName: P20536\nDescription: P20536 sp|P20536|UNG_VACCC Uracil-DNA glycosylase OS=Vaccinia virus (strain Copenhagen) OX=10249 GN=UNG PE=1 SV=1\nNumber of features: 0\nSeq('MNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLK...FIY')\n```\n\n**This** is a standard FASTA record format that we are providing:\n\n```\n>P20536 sp|P20536|UNG_VACCC Uracil-DNA glycosylase OS=Vaccinia virus (strain Copenhagen) OX=10249 GN=UNG PE=1 SV=1\nMNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNK\nRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWN\nYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGY\nHPAARDRQFEKDRSFEIINVLLELDNKVPINWAQGFIY\n```\nAs stated by @alejopaullier the line after the \">\" is the header, and the rest of the record is the amino acid sequence. For more information on the specific header format see File Descriptions in [Data](https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/data) section, \n\nThe above code provided by should work in reading the FASTA files, you would need to have [biopython](https://biopython.org) installed. Examples on sequence file IO are provided [here](https://biopython.org/wiki/SeqIO).", "votes": null }, { "id": "2226512", "postDate": "04/19/2023 02:06:43", "content": "

Thanks for the clarification @iddux1 I will edit the post!

", "rawMarkdown": "Thanks for the clarification @iddux1 I will edit the post!", "votes": null } ], "comments": [ { "id": 2226484, "author_name": "iddux1", "author_url": "", "post_date": "04/19/2023 01:18:24", "content": "

Hi @alejopaullier

\n

Thanks for the code sample! That's helpful.

\n

Just to clarify: this not the standard FASTA format:

\n
ID: P20536\nName: P20536\nDescription: P20536 sp|P20536|UNG_VACCC Uracil-DNA glycosylase OS=Vaccinia virus (strain Copenhagen) OX=10249 GN=UNG PE=1 SV=1\nNumber of features: 0\nSeq('MNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLK...FIY')\n
\n

This is a standard FASTA record format that we are providing:

\n
>P20536 sp|P20536|UNG_VACCC Uracil-DNA glycosylase OS=Vaccinia virus (strain Copenhagen) OX=10249 GN=UNG PE=1 SV=1\nMNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNK\nRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWN\nYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGY\nHPAARDRQFEKDRSFEIINVLLELDNKVPINWAQGFIY\n
\n

As stated by @alejopaullier the line after the \">\" is the header, and the rest of the record is the amino acid sequence. For more information on the specific header format see File Descriptions in Data section,

\n

The above code provided by should work in reading the FASTA files, you would need to have biopython installed. Examples on sequence file IO are provided here.

", "votes": null, "replies": [ { "id": 2226512, "author_name": "alejopaullier", "author_url": "", "post_date": "04/19/2023 02:06:43", "content": "

Thanks for the clarification @iddux1 I will edit the post!

", "votes": null, "replies": [] } ] } ], "raw_markdown_by_id": { "2226436": "### What is a FASTA file?\n\nA FASTA file is a common file format used to store DNA or protein sequences along with their identifying information. The file consists of a header line starting with the `>` character, followed by one or more lines of sequence data.\n\nHere is an example:\n```shell\n>P20536 sp|P20536|UNG_VACCC Uracil-DNA glycosylase OS=Vaccinia virus (strain Copenhagen) OX=10249 GN=UNG PE=1 SV=1\nMNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNK\nRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWN\nYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGY\nHPAARDRQFEKDRSFEIINVLLELDNKVPINWAQGFIY\n```\n\nIf we parse the file we get:\n\n```shell\nID: P20536\nName: P20536\nDescription: P20536 sp|P20536|UNG_VACCC Uracil-DNA glycosylase OS=Vaccinia virus (strain Copenhagen) OX=10249 GN=UNG PE=1 SV=1\nNumber of features: 0\nSeq('MNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLK...FIY')\n```\n\n### How to read a FASTA file in Python\n\n```python\nfrom Bio import SeqIO\n\n# Open the FASTA file\nfilename = \"/kaggle/input/cafa-5-protein-function-prediction/Train/train_sequences.fasta\"\nfasta_sequences = SeqIO.parse(open(filename),'fasta')\n\n# Loop over each sequence and print its ID and length\nfor fasta in fasta_sequences:\n print(fasta)\n print(\"Sequence ID:\", fasta.id)\n print(\"Sequence length:\", len(fasta))\n break\n```\n\n### Example\n\n", "2226484": "Hi @alejopaullier \n\nThanks for the code sample! That's helpful. \n\nJust to clarify: this not the standard FASTA format:\n\n```\nID: P20536\nName: P20536\nDescription: P20536 sp|P20536|UNG_VACCC Uracil-DNA glycosylase OS=Vaccinia virus (strain Copenhagen) OX=10249 GN=UNG PE=1 SV=1\nNumber of features: 0\nSeq('MNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLK...FIY')\n```\n\n**This** is a standard FASTA record format that we are providing:\n\n```\n>P20536 sp|P20536|UNG_VACCC Uracil-DNA glycosylase OS=Vaccinia virus (strain Copenhagen) OX=10249 GN=UNG PE=1 SV=1\nMNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNK\nRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWN\nYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGY\nHPAARDRQFEKDRSFEIINVLLELDNKVPINWAQGFIY\n```\nAs stated by @alejopaullier the line after the \">\" is the header, and the rest of the record is the amino acid sequence. For more information on the specific header format see File Descriptions in [Data](https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/data) section, \n\nThe above code provided by should work in reading the FASTA files, you would need to have [biopython](https://biopython.org) installed. Examples on sequence file IO are provided [here](https://biopython.org/wiki/SeqIO).", "2226512": "Thanks for the clarification @iddux1 I will edit the post!" }, "source": "meta" }